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Database Name

Database URL

Accessibility

Year

Citation

Species

Tissue Or Brain Region

Sequencing Resolution

Read Technology

Classification Code

More Details

circBase

https://circrna.org/

Accessible

2014

1603

Human

Mouse

Drosophila melanogaster

Caenorhabditis elegans

brain

bulk

short

II_2

IV_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
circBase: a database for circular RNAs.	10.1261/rna.043687.113	unknown	unknown	unknown	circBase documentation provides identifier, gene, coordinate and sequence search plus table-browser retrieval of circRNAs keyed by head-to-tail splice junctions.

AceView

https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/

Accessible

2006

708

Human

Mouse

Rat

Caenorhabditis elegans

Arabidopsis thaliana

brain

hypothalamus

cerebellum

hippocampus

amygdala

substantia nigra

corpus callosum

fetal brain

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
AceView: a comprehensive cDNA-supported gene and transcripts annotation.	10.1186/gb-2006-7-s1-s12	Alzheimer disease brain neoplasms memory disorders glioblastoma	fetal brain	neuroblastoma	AceView provides gene-entry links and searchable transcript annotations reconstructed from aligned mRNAs and ESTs, including experimentally supported alternative variants.

VastDB

https://vastdb.crg.eu/wiki/Main_Page

Accessible

2017

391

Human

Mouse

Rat

Cow

Chicken

Zebrafish

Fruit fly

whole brain

cortex

heart

skeletal muscle

testis

bulk

short

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms.	10.1101/gr.220962.117	unknown	embryonic adult	neuron	VastDB searches by gene, splicing event or coordinates and serves PSI profiles for cassette exons, microexons, alternative splice sites and retained introns.

BrainSeq eQTL Phase 1

https://eqtl.brainseq.org/phase1/eqtl/

Not accessible

2018

337

Human

dorsolateral prefrontal cortex

bulk

short

II_2

III_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis.	10.1038/s41593-018-0197-y	schizophrenia	prenatal postnatal adult	unknown	BrainSeq's browser searches by gene, Ensembl ID or SNP and visualizes DLPFC eQTLs quantified at exon, junction and transcript feature levels.

SpliceAid 2

http://193.206.120.249/splicing_tissue.html

Accessible

2012

247

Human

brain

cerebellum

bulk

short

III_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
SpliceAid 2: a database of human splicing factors expression data and RNA target motifs.	10.1002/humu.21609	unknown	unknown	neuronal context	SpliceAid 2 exposes a sequence and protein-name query for experimentally supported splicing-factor RNA binding sites with tissue or cell-line filters.

CORTECON

https://cortecon.neuralsci.org/index.php?cort_mode=splicelist

Accessible

2014

199

Human

Mouse

cerebral cortex

bulk

short

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
CORTECON: a temporal transcriptome analysis of in vitro human cerebral cortex development from human embryonic stem cells.	10.1016/j.neuron.2014.05.013	unknown	embryonic stem cell day 0-day 77	human embryonic stem cells neural progenitor cells cortical neurons	CORTECON provides a gene search and a browsable list of the 100 most spliced genes, with links to records reporting changing exons during cortical development.

CattleGTEx

https://cattlegtex.kiz.ac.cn/

Accessible

2022

205

Cattle

hypothalamus

pituitary

spleen

immune system

bulk

short

I_2

II_1

II_2

III_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
A multi-tissue atlas of regulatory variants in cattle.	10.1038/s41588-022-01153-5	unknown	unknown	unknown	CattleGTEx states that all results are queryable and provides isoform and exon expression, alternative splicing, junction-level data and molecular QTL modules.

SPLICECODE DATABASE

https://scheiffele-splice.scicore.unibas.ch/

Accessible

2019

110

Mouse

neocortex

hippocampus

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Landscape of ribosome-engaged transcript isoforms reveals extensive neuronal-cell-class-specific alternative splicing programs.	10.1038/s41593-019-0465-5	unknown	adult	neurons	SPLICECODE provides gene-symbol search for alternative transcript-isoform analysis of ribosome-associated mRNAs from mouse neocortical and hippocampal cells.

TSVdb

http://www.tsvdb.com/

Accessible

2018

102

Human

brain tumor cohorts

bulk

short

I_2

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
TSVdb: a web-tool for TCGA splicing variants analysis.	10.1186/s12864-018-4775-x	glioblastoma multiforme brain lower grade glioma	unknown	unknown	TSVdb's official instructions document tumor and gene queries with exon/junction usage, alternative-splicing visualization and transcriptional isoform-expression plots.

SpliceVault

https://kidsneuro.shinyapps.io/splicevault/

Accessible

2023

Human

amygdala

anterior cingulate

caudate nucleus

cerebellar hemisphere

cerebellum

cortex

frontal cortex

hippocampus

hypothalamus

nucleus accumbens

putamen

spinal cord

substantia nigra

bulk

short

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
SpliceVault predicts the precise nature of variant-associated mis-splicing.	10.1038/s41588-022-01293-8	inherited disorders	unknown	unknown	The live SpliceVault application provides Variant and Gene/Transcript/Exon queries and controls for exon-skipping, cryptic-splice and other mis-splicing events.

CancerSplicingQTL

https://cancersplicingqtl-hust.org/#/

Accessible

2019

Human

brain

bulk

short

II_1

III_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
CancerSplicingQTL: a database for genome-wide identification of splicing QTLs in human cancer.	10.1093/nar/gky954	cancer	unknown	unknown	The current CancerSplicingQTL portal provides Single and Batch Search plus browse modules for cancer sQTLs, survival-sQTLs and GWAS-linked sQTLs.

NeuronSubtypeTranscriptomes

http://research-pub.gene.com/NeuronSubtypeTranscriptomes/

Accessible

2020

Mouse

cerebral cortex

bulk

short

I_2

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Genome-Wide Analysis of Differential Gene Expression and Splicing in Excitatory Neurons and Interneuron Subtypes.	10.1523/jneurosci.1615-19.2019	unknown	unknown	excitatory neurons PV interneurons SST interneurons VIP interneurons	The official portal supports Mouse-gene and study searches and opens cortical-neuron RNA-seq gene reports, including differential mRNA expression and splice-form usage.

circAtlas 3.0

https://ngdc.cncb.ac.cn/circatlas/

Accessible

2024

336

Vertebrata

unknown

bulk

long

short

I_1

I_2

II_2

IV_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
circAtlas 3.0: a gateway to 3 million curated vertebrate circular RNAs based on a standardized nomenclature scheme.	10.1186/s13059-020-02018-y 10.1093/nar/gkad770	unknown	unknown	unknown	circAtlas 3.0 supports browse and search by species, tissue, ID, host gene and position and displays full-length circRNA isoforms from long-read data.

SpliceNest

https://splicenest.molgen.mpg.de/

Accessible

2004

Human

brain

bulk

short

I_1

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Genome wide identification and classification of alternative splicing based on EST data.	10.1093/bioinformatics/bth288	unknown	unknown	unknown	SpliceNest provides organism-specific databases and cluster search for EST consensus models, with gene-structure and alternative-splicing visualization from genomic mappings.

ExonSkipDB

https://ccsm.uth.edu/ExonSkipDB/

Accessible

2020

Human

brain

bulk

short

I_1

I_2

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
ExonSkipDB: functional annotation of exon skipping event in human.	10.1093/nar/gkz917	cancer	unknown	unknown	ExonSkipDB is a navigable annotation database for human exon-skipping events across TCGA cancers and GTEx tissues, including skipped-transcript ORF and functional annotations.

TREGT

https://tregt.ibms.sinica.edu.tw/index.php

Accessible

2020

Human

brain

heart

liver

stomach

small intestine

colon

bulk

short

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Top-ranked expressed gene transcripts of human protein-coding genes investigated with GTEx dataset.	10.1038/s41598-020-73081-5	unknown	adult	unknown	TREGT provides gene search, advanced search and ranked transcript-expression views for alternatively spliced human protein-coding transcript isoforms across GTEx tissues.

Medaka mini Omics Data Portal

https://tulab.genetics.ac.cn/miniodp/species/medaka/

Accessible

2020

Medaka

embryo

ovary

testis

brain

heart

pituitary

bulk

single_cell

long

short

I_1

I_2

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis.	10.1101/gr.258871.119	unknown	embryo stages 6-41 larva adult	kidney lymphoid cells	The Medaka miniODP provides gene search and an interactive JBrowse 2 view with Ensembl and curated GFF3 annotation tracks for transcript and exon-intron models.

ASCancer Atlas

https://ngdc.cncb.ac.cn/ascancer/

Accessible

2023

Human

brain

bulk

short

I_1

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
ASCancer Atlas: a comprehensive knowledgebase of alternative splicing in human cancers.	10.1093/nar/gkac955	cancer	unknown	unknown	ASCancer Atlas provides gene and disease search plus Browse, Visualize and Toolkit modules for cancer-associated splicing events, PSI values and transcript structures.

RJunBase

http://www.rjunbase.org/

Accessible

2021

Human

brain

bulk

short

I_2

II_2

IV_1

IV_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
RJunBase: a database of RNA splice junctions in human normal and cancerous tissues.	10.1093/nar/gkaa1056	cancer	unknown	unknown	RJunBase provides Browse and gene search over linear, back-splice, fusion and tumor-specific junctions, with gene-level splicing patterns and junction-level expression profiles.

CSEminer

https://cseminer.stjude.org/

Accessible

2024

Human

brain

solid tumor tissues

bulk

short

I_1

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Discovery of immunotherapy targets for pediatric solid and brain tumors by exon-level expression.	10.1038/s41467-024-47649-y	pediatric solid tumors pediatric brain tumors	pediatric	unknown	CSE-Miner exposes Table, Gene and Heatmap views for cancer-specific alternative exons, with searchable exon IDs, genes, target diseases and expression summaries.

MAJIQlopedia

https://majiq.biociphers.org/majiqlopedia/

Accessible

2024

Human

brain

bulk

short

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
MAJIQlopedia: an encyclopedia of RNA splicing variations in human tissues and cancer.	10.1093/nar/gkad1043	cancer	unknown	unknown	MAJIQlopedia links searchable normal-tissue and cancer databases and summarizes annotated or unannotated splice junctions, complex variations and intron retention.

MeDAS

https://das.chenlulab.com/

Accessible

2021

Metazoa

forebrain

hindbrain

bulk

short

I_1

I_2

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
MeDAS: a Metazoan Developmental Alternative Splicing database.	10.1093/nar/gkaa886	unknown	embryonic postnatal adulthood	unknown	MeDAS provides Search and Statistics modules for developmental alternative-splicing events, exon inclusion and PSI estimates across embryonic and postnatal time courses.

FLIBase

http://www.flibase.org/

Accessible

2024

Human

brain

bulk

long

short

I_1

I_2

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
FLIBase: a comprehensive repository of full-length isoforms across human cancers and tissues.	10.1093/nar/gkad745	cancer	unknown	unknown	FLIBase provides gene search for full-length isoforms with complete sequences, splice-site annotations, expression, coding potential and long-read or short-read validation.

TAiC

http://www.shenglilabs.com/TAiC/

Accessible

2022

Human

brain tumor cohort

bulk

short

I_1

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Systematic characterization of cancer transcriptome at transcript resolution.	10.1038/s41467-022-34568-z	brain lower grade glioma	unknown	unknown	The TAiC publication describes a searchable and browsable portal for transcript-level expression, RNA sequences and transcript associations across more than 1,000 cancer cell lines.

IntroVerse

https://rytenlab.com/browser/app/introverse

Accessible

2023

Human

amygdala

anterior cingulate

caudate nucleus

cerebellar hemisphere

cerebellum

cortex

frontal cortex

hippocampus

hypothalamus

nucleus accumbens

putamen

spinal cord

substantia nigra

bulk

short

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
IntroVerse: a comprehensive database of introns across human tissues.	10.1093/nar/gkac1056	unknown	unknown	unknown	IntroVerse provides gene and genomic-position queries and displays annotated introns, novel splice junctions and alternative-splicing events across human tissues.

SRTdb

http://www.shenglilabs.com/SRTdb/

Accessible

2022

Human

unknown

bulk

short

I_1

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
SRTdb: an omnibus for human tissue and cancer-specific RNA transcripts.	10.1186/s40364-022-00377-1	cancer	unknown	cancer cell lines	The SRTdb publication describes searches by transcript, gene and locus with assembled transcript structures and transcript-level expression across tissues and cancers.

ValidSpliceMut

https://validsplicemut.cytognomix.com/

Accessible

2018

—

Human

brain

tumor tissue

bulk

short

II_1

II_2

III_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Pan-cancer repository of validated natural and cryptic mRNA splicing mutations.	10.12688/f1000research.17204.3	glioblastoma lower-grade glioma cancer	adult	unknown	ValidSpliceMut searches validated splicing mutations by mutation, gene or genomic coordinates and reports splice-site strength changes and observed mutant splicing events.

OncoSplicing 3.0

http://www.oncosplicing.com/

Accessible

2025

Human

brain

brain tumor cohorts

bulk

short

II_1

II_2

III_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
OncoSplicing 3.0: an updated database for identifying RBPs regulating alternative splicing events in cancers.	10.1093/nar/gkae1098	glioblastoma multiforme brain lower grade glioma	unknown	unknown	OncoSplicing 3.0 provides MapAS and other browse modules for alternative-splicing events from TCGA and GTEx, including PSI and regulatory evidence.

ExonSkipAD

https://ccsm.uth.edu/ExonSkipAD/

Accessible

2021

Human

brain

bulk

short

II_1

III_1

III_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
ExonSkipAD provides the functional genomic landscape of exon skipping events in Alzheimer's disease.	10.1093/bib/bbaa438	Alzheimer disease	unknown	unknown	ExonSkipAD searches genes and browses Alzheimer disease exon-skipping events by nine brain regions, with PSI and functional ORF annotations.

CanIsoNet

https://www.caniso.net/

Accessible

2023

—

Human

brain

bulk

short

I_1

I_2

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
CanIsoNet: a database to study the functional impact of isoform switching events in diseases.	10.1093/bioadv/vbad050	Alzheimer disease Parkinson disease opioid-induced hyperalgesia	unknown	neuronal context	CanIsoNet provides gene and isoform searches plus disease browsing for disease-specific isoform-switching events and isoform interaction networks.

ASpdb

https://biodataai.uth.edu/ASpdb/

Accessible

2025

Human

brain disease context

bulk

short

I_1

I_2

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
ASpdb: an integrative knowledgebase of human protein isoforms from experimental and AI-predicted structures.	10.1093/nar/gkae1018	Alzheimer disease Prader-Willi syndrome cocaine-use disorder	unknown	unknown	ASpdb searches human genes and browses canonical and alternative isoforms with alternative-splicing annotations, sequences and comparative protein structures.

Cortexa

https://cortexa-01.zdv.uni-mainz.de/

Accessible

2024

Mouse

cerebral cortex

hippocampus

bulk

short

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Cortexa: a comprehensive resource for studying gene expression and alternative splicing in the murine brain.	10.1186/s12859-024-05919-y	unknown	embryonic postnatal	neural progenitor cells neurons	Cortexa searches Ensembl IDs or gene symbols and serves gene-expression and alternative-splicing results for mouse cortex and hippocampus.

GESUR

http://gesur.cancer-pku.cn/

Accessible

2019

Human

brain tumor cohorts

bulk

short

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Identification of transcriptional isoforms associated with survival in cancer patient.	10.1016/j.jgg.2019.08.003	glioblastoma multiforme brain lower grade glioma	unknown	unknown	GESUR accepts gene or transcript identifiers and interactively returns TCGA transcript-expression survival analyses across cancer cohorts.

GTEx Portal

https://gtexportal.org/

Accessible

2020

8620

Human

unknown

bulk

single_cell

short

I_1

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
The GTEx Consortium atlas of genetic regulatory effects across human tissues.	10.1038/ng.2653 10.1126/science.aaz1776 10.1126/science.1262110 10.1038/ng.3969	unknown	adult	unknown	GTEx Portal searches gene or transcript expression and its Transcript Browser visualizes transcript abundance and isoform structures across human tissues.

GEPIA2

http://gepia2.cancer-pku.cn/

Accessible

2019

4227

Human

normal brain

brain tumor cohorts

bulk

short

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis.	10.1093/nar/gkz430	glioblastoma multiforme brain lower grade glioma	unknown	unknown	GEPIA2's live Expression Analysis accepts gene symbols or Ensembl transcript IDs and explicitly offers gene/isoform searches across TCGA and GTEx cancer cohorts.

Human Protein Atlas

https://www.proteinatlas.org/

Accessible

2014

1219

Human

Mouse

Pig

cerebral cortex

hippocampal formation

amygdala

basal ganglia

thalamus

hypothalamus

midbrain

cerebellum

pons

medulla oblongata

spinal cord

white matter

choroid plexus

bulk

single_cell

short

I_1

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics.	10.1074/mcp.m113.035600	unknown	child adult	neuron astrocyte oligodendrocyte microglia	The searchable Human Protein Atlas gene page reports eight transcripts and a Protein Browser with selectable splice variants and transcript-related exon, intron and UTR structures.

MiTranscriptome

http://www.mitranscriptome.org/

Not accessible

2015

2523

Human

unknown

bulk

short

I_1

I_2

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
The landscape of long noncoding RNAs in the human transcriptome.	10.1038/ng.3192	cancer	unknown	cell lines	The MiTranscriptome publication describes a companion portal for ab initio-assembled human transcript models and lineage- and cancer-associated transcript expression; the original site is unavailable.

GeneCards

https://www.genecards.org/

Accessible

2010

1910

Human

brain

other tissues

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
GeneCards Version 3: the human gene integrator.	10.1093/database/baq020	neurological disease cancer other diseases	unknown	unknown	GeneCards is searchable and its Transcripts section catalogs Ensembl/RefSeq splice variants with transcript IDs, exon counts, exon/CDS/UTR structures, filtering and export.

FANTOM2

https://fantoms.gsc.riken.jp/2/db/

Accessible

2002

262

Mouse

brain

hypothalamus

cerebellum

bulk

long

I_1

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.	10.1038/nature01266	unknown	adult	unknown	The current FANTOM2 Functional Annotation Database exposes Search, BLAST and SSAHA functions for the approximately 60,000 mouse full-length cDNA collection and transcript annotations.

MiOncoCirc

http://ec2-52-91-79-148.compute-1.amazonaws.com:3838/circRNA/

Accessible

2019

1366

Human

brain

spinal cord

brain metastasis

bulk

short

I_2

II_2

IV_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
The Landscape of Circular RNA in Cancer.	10.1016/j.cell.2018.12.021	glioblastoma multiforme neuroblastoma	unknown	clinical tumor samples	The official MiOncoCirc Query Data application provides circRNA searches and abundance queries for cancer samples; records represent circular isoforms derived from back-spliced reads.

dbEST

https://www.ncbi.nlm.nih.gov/genbank/dbest/

Accessible

1991

2281

All organisms

brain

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Complementary DNA sequencing: expressed sequence tags and human genome project.	10.1126/science.2047873	unknown	unknown	unknown	NCBI dbEST stores transcript-derived single-pass cDNA sequence records and links users to searchable GenBank records, BLAST and programmatic sequence retrieval.

Human Protein Atlas Brain

https://www.proteinatlas.org/humanproteome/brain

Accessible

2020

965

Human

Mouse

Pig

cerebral cortex

hippocampal formation

amygdala

basal ganglia

thalamus

hypothalamus

midbrain

cerebellum

pons

medulla oblongata

spinal cord

white matter

choroid plexus

bulk

single_cell

short

I_1

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
An atlas of the protein-coding genes in the human, pig, and mouse brain.	10.1126/science.aay5947	unknown	child adult	neuron astrocyte oligodendrocyte microglia	The official Human Protein Atlas download documentation supplies transcript-level RNA-seq data, while gene pages expose selectable splice variants and exon-intron structures.

FANTOM CAT

https://fantom.gsc.riken.jp/cat/

Accessible

2017

934

Human

unknown

bulk

short

I_1

I_2

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
An atlas of human long non-coding RNAs with accurate 5' ends.	10.1038/nature21374	unknown	fetal adult	unknown	The official FANTOM CAT Browser links to an interactive ZENBU application for browsing genes and genomic loci with transcript models, genomic context and expression annotations.

PsychENCODE

https://www.psychencode.org/resources

Accessible

2018

945

Human

prefrontal cortex

hippocampus

striatum

cerebellum

bulk

single_cell

long

short

I_1

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Comprehensive functional genomic resource and integrative model for the human brain.	10.1126/science.aat8464	autism spectrum disorder schizophrenia bipolar disorder	fetal adult	neuron astrocyte oligodendrocyte	PsychENCODE Resources links the Developing Human Brain Transcript Browser and IsoPropeller resources for transcript reconstruction, quantification and long-read isoform analysis.

FANTOM5 promoter level mammalian expression atlas

https://fantom.gsc.riken.jp/5/

Accessible

2015

816

Human

Mouse

Rat

Dog

Chicken

Rhesus macaque

brain

cerebellum

amygdala

thalamus

hippocampus

cortex

spinal cord

bulk

short

I_1

I_2

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Gateways to the FANTOM5 promoter level mammalian expression atlas.	10.1186/s13059-014-0560-6	unknown	embryonic newborn adult	neuron cerebellar granule cell	FANTOM5 provides data and views for mammalian promoters and lncRNAs, including CAGE-defined transcript initiation models and expression-linked genomic browsing resources.

Human Protein Atlas tissue abundance atlas

https://www.proteinatlas.org/humanproteome/tissue

Accessible

2019

659

Human

cerebral cortex

cerebellum

heart

kidney

liver

lung

testis

bulk

single_cell

short

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
A deep proteome and transcriptome abundance atlas of 29 healthy human tissues.	10.15252/msb.20188503	unknown	adult	neuron astrocyte oligodendrocyte microglia	The Human Protein Atlas offers searchable entries and downloadable transcript-level RNA-seq expression for 186 samples across 40 tissues, with tissue and brain resources.

Allen Brain Atlas

https://brain-map.org/our-research/gene-expression

Accessible

2013

776

Human

Mouse

Rhesus macaque

prefrontal cortex

hippocampus

cerebellum

thalamus

striatum

spinal cord

whole brain

bulk

single_cell

short

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system.	10.1093/nar/gks1042	Alzheimer's disease other neurological diseases	prenatal postnatal adult	neuron astrocyte oligodendrocyte microglia other brain cell types	BrainSpan provides web and API queries and downloads for RNA-seq RPKM summarized to individual exons across cortical and subcortical structures and development.

conquer

http://imlspenticton.uzh.ch:3838/conquer

Not accessible

2018

665

Human

Mouse

unknown

single_cell

short

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Bias, robustness and scalability in single-cell differential expression analysis.	10.1038/nmeth.4612	unknown	unknown	unknown	The publication describes conquer as a consistently processed single-cell RNA-seq repository providing abundance estimates for both genes and transcripts plus analysis reports.

Braineac

https://www.braineac.org/

Accessible

2014

683

Human

cerebellar cortex

frontal cortex

hippocampus

putamen

substantia nigra

temporal cortex

thalamus

white matter

bulk

short

III_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Genetic variability in the regulation of gene expression in ten regions of the human brain.	10.1038/nn.3801 10.1111/j.1471-4159.2011.07432.x	Parkinson's disease schizophrenia	adult	unknown	The Braineac publication reports brain eQTL and allele-specific-expression queries, including exon-specific regulatory signals that identify alternative-splicing regulation.

ARCHS4

https://archs4.org/

Accessible

2018

664

Human

Mouse

unknown

bulk

short

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Massive mining of publicly available RNA-seq data from human and mouse.	10.1038/s41467-018-03751-6	unknown	unknown	unknown	The live ARCHS4 portal provides metadata search, interactive exploration and programmatic access to uniformly processed RNA-seq gene and transcript count matrices.

ENCODE Portal

https://www.encodeproject.org/

Accessible

2016

521

Human

Mouse

Drosophila melanogaster

C. elegans

brain

heart

liver

cell line

bulk

single_cell

long

short

I_1

I_2

II_2

III_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
ENCODE data at the ENCODE portal.	10.1093/nar/gkv1160	unknown	fetal adult	neuron glia stem cell	ENCODE links Experiment search to released long-read RNA-seq records; its documentation covers full-length transcripts, splice junctions, isoforms and transcript quantification.

Ensembl

https://www.ensembl.org/index.html

Accessible

2017

1133

Vertebrata

unknown

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Ensembl 2017.	10.1093/database/bas014 10.1093/database/baw093 10.1093/nar/gkw1104 10.1101/gr.1858004	unknown	unknown	unknown	Ensembl documents searchable transcript tables with stable transcript IDs and gene diagrams displaying all splice variants, exons, introns, coding sequence and UTRs.

UCSC Genome Browser

https://genome.ucsc.edu/

Accessible

2021

10507

Vertebrates

Invertebrates

unknown

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
The UCSC Genome Browser database: 2021 update.	10.1101/gr.229102 10.1093/nar/gkj144 10.1093/nar/gkq963 10.1093/nar/gky1095 10.1093/nar/gkaa1070 10.1093/nar/gkn875 10.1093/nar/gkw1134 10.1093/nar/gkz1012 10.1002/0471250953.bi0104s28 10.1002/0471142905.hg1806s71 10.1093/bioinformatics/btp414	unknown	unknown	unknown	UCSC Genome Browser and Table Browser search loci and transcript tracks; gene tracks represent transcripts with identifiers, exon coordinates and alternative isoforms.

HASDB

http://www.bioinformatics.ucla.edu/HASDB

Not accessible

2001

706

Human

brain

retina

nerve

bulk

short

I_1

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Genome-wide detection of alternative splicing in expressed sequences of human genes.	10.1093/nar/29.13.2850	unknown	unknown	unknown	The HASDB publication documents web queries over human exon, intron, splice-site and alternative-splice structures; the former UCLA path is no longer usable.

UCSC Known Genes

https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=knownGene

Accessible

2006

—

Human

amygdala

anterior cingulate cortex

caudate

cerebellar hemisphere

cerebellum

cortex

frontal cortex

hippocampus

hypothalamus

nucleus accumbens

putamen

spinal cord

substantia nigra

tibial nerve

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
The UCSC Known Genes.	10.1093/bioinformatics/btl048	unknown	adult	unknown	UCSC gene tracks represent searchable transcript isoforms with identifiers, sequences and exon coordinates; Known Genes/GENCODE models are browsable through Genome and Table Browsers.

LNCipedia

https://www.lncipedia.org/

Accessible

2019

520

Human

brain

bulk

short

I_1

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
LNCipedia 5: towards a reference set of human long non-coding RNAs.	10.1093/nar/gks915 10.1093/nar/gky1031 10.1093/nar/gku1060	glioblastoma	unknown	unknown	LNCipedia's live search and transcript-record interface returns annotated human lncRNA transcripts with transcript IDs, sequences, exon structures, isoforms and genome-browser links.

ToxoDB

https://toxodb.org/toxo/app

Accessible

2008

489

Toxoplasma gondii

unknown

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
ToxoDB: an integrated Toxoplasma gondii database resource.	10.1093/nar/gkm981	toxoplasmosis encephalitis	tachyzoite bradyzoite oocyst	unknown	The live ToxoDB application provides structured gene/transcript searches and record/genome-browser pages that expose transcript-supported exon-intron gene models.

FlyAtlas 2

https://flyatlas.gla.ac.uk/FlyAtlas2/

Accessible

2018

370

Drosophila melanogaster

brain

eye

crop

midgut

hindgut

Malpighian tubule

fat body

heart

ovary

testis

bulk

short

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
FlyAtlas 2: a new version of the Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data.	10.1093/nar/gkx976	unknown	larval adult	unknown	FlyAtlas 2's live gene search accepts transcript IDs and its result page displays separate transcript IDs and transcript FPKM tables across adult and larval tissues.

FlyBase

https://flybase.org/

Accessible

2024

304

Drosophila

unknown

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
FlyBase: updates to the Drosophila genes and genomes database.	10.1534/g3.115.018929 10.1093/genetics/iyad211	unknown	embryonic larval pupal adult	unknown	FlyBase Transcript Reports provide searchable annotated transcripts with exon-junction evidence, genomic location, transcript sequence and links to other transcripts and JBrowse.

Tissue-Specific CircRNA Database (TSCD)

http://gb.whu.edu.cn/TSCD

Not accessible

2017

347

Human

Mouse

brain

heart

kidney

liver

lung

pancreas

skeletal muscle

skin

spleen

testis

uterus

bulk

short

I_2

II_2

IV_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Comprehensive characterization of tissue-specific circular RNAs in the human and mouse genomes.	10.1093/bib/bbw081	unknown	fetal adult	unknown	The TSCD publication describes tissue and coordinate queries returning back-splice coordinates, junction reads, circRNA arcs and reference-transcript exon-intron structures.

Human Alternative Splicing Database

—

Not accessible

2002

421

Human

brain

retina

muscle

skin

testis

bulk

short

I_1

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Genome-wide detection of tissue-specific alternative splicing in the human transcriptome.	10.1093/nar/gkf492	neurological disease	adult	unknown	The publication describes a searchable Human Alternative Splicing Database with 667 tissue-specific splice forms across 46 tissues, including brain-specific forms and isoform structures.

Rat BodyMap Database

http://pgx.fudan.edu.cn/ratbodymap/index.html

Not accessible

2014

339

Rat

adrenal gland

brain

heart

kidney

lung

liver

skeletal muscle

spleen

thymus

testis

uterus

bulk

short

I_1

I_2

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages.	10.1038/ncomms4230	unknown	juvenile young adult adult aged	unknown	The publication describes a web database of 65,167 rat transcripts and 31,909 alternatively spliced variants with searchable tissue, age and transcript-level profiles.

Sensoryomics RNA Isoforms in hDRG

https://sensoryomics.shinyapps.io/RNAIsoforms/

Accessible

2018

—

Human

Mouse

dorsal root ganglion

spinal cord

bulk

single_cell

long

short

I_1

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Comparative transcriptome profiling of the human and mouse dorsal root ganglia: an RNA-seq-based resource for pain and sensory neuroscience research.	10.1097/j.pain.0000000000001217	neuropathy chronic pain	adult	sensory neuron nociceptor glial cell	The live Sensoryomics hDRG application provides a searchable repository of long-read RNA isoforms and explains how alternative splicing contributes to neuropathy and chronic pain.

CSCD 2.0

https://gb.whu.edu.cn/CSCD2/

Not accessible

2018

346

Human

tumor tissue

bulk

short

I_1

I_2

II_1

II_2

IV_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
CSCD: a database for cancer-specific circular RNAs.	10.1093/nar/gkx863	cancer	unknown	cancer cell line	The live official CSCD2 tutorial documents circRNA searches by donor and acceptor junction coordinates, junction-read counts, full-length sequences, exon structures and transcript annotations.

TCGA SpliceSeq

https://bioinformatics.mdanderson.org/TCGASpliceSeq/

Accessible

2016

314

Human

brain

bulk

short

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
TCGASpliceSeq a compendium of alternative mRNA splicing in cancer.	10.1093/nar/gkv1288	cancer	unknown	unknown	The live TCGA SpliceSeq interface supports gene searches, splice graphs, interactive transcript-splicing visualizations and PSI measurements for alternative splice events across cancers.

DIANA-LncBase v3.0

https://diana.e-ce.uth.gr/lncbasev3

Accessible

2020

272

Human

Mouse

unknown

bulk

short

I_2

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
DIANA-LncBase v3: indexing experimentally supported miRNA targets on non-coding transcripts.	10.1093/nar/gkz1036	cancer	unknown	unknown	The live DIANA-LncBase v3 expression module accepts lncRNA gene or transcript identifiers and returns transcript-level TPM expression and localization profiles across tissues and cell types.

Tissue Alternative-Splicing Web Compendium

—

Not accessible

2008

Human

brain

cortex

skeletal muscle

testis

blood

bulk

short

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines.	10.1038/ng.264	neuromuscular disease relevance cancer	fetal adult	neuron muscle cell blood cell	The publication documents a web compendium and CGI database for 24,426 alternative-splicing events, exon-junction probes and expression profiles across 48 tissues and cell lines.

Evo-devo mammalian lncRNAs

https://apps.kaessmannlab.org/lncRNA_app/

Accessible

2019

272

Mammalia

brain

cerebellum

heart

kidney

liver

testis

bulk

short

I_1

I_2

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Developmental dynamics of lncRNAs across mammalian organs and species.	10.1038/s41586-019-1341-x	unknown	prenatal postnatal	unknown	The live application lets users select mammalian lncRNAs and inspect gene models, genome-browser structure and transcript abundance across organs, developmental stages and species.

IRFinder; IRBase

https://irbase.igh.cnrs.fr/

Accessible

2017

267

Human

Mouse

unknown

bulk

short

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
IRFinder: assessing the impact of intron retention on mammalian gene expression.	10.1186/s13059-017-1184-4	unknown	unknown	unknown	The official IRBase portal provides dynamic sample and retained-intron queries, intron-retention ratios, event details and cross-sample comparisons.

NFINgb

https://nfingb.leibniz-fli.de/

Accessible

2015

286

Nothobranchius furzeri

unknown

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Insights into Sex Chromosome Evolution and Aging from the Genome of a Short-Lived Fish.	10.1016/j.cell.2015.10.071	aging	unknown	unknown	NFINgb provides a genome browser with searchable annotation tracks and protein-coding transcript and gene models distributed in GFF/GTF files.

NONCODE

https://v7.noncode.org/

Accessible

2021

408

Metazoa

Viridiplantae

unknown

bulk

single_cell

short

I_1

I_2

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants.	10.1093/nar/gkr1175 10.1093/nar/gkaa1046	cancer hematological disease	unknown	unknown	NONCODE v7 supports gene or transcript search and browse, with transcript location, sequence, expression, single-cell profiles, RNA structure and genome links.

A transcriptomic atlas of mouse neocortical layers

http://genserv.anat.ox.ac.uk/layers

Not accessible

2011

255

Mouse

somatosensory cortex

neocortical layers 1-6b

bulk

short

I_2

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
A transcriptomic atlas of mouse neocortical layers.	10.1016/j.neuron.2011.06.039	neurological disorders	P56	neuron glia	The online neocortical atlas provided transcript and gene expression views and highlighted candidate alternatively spliced transcripts with isoform switching across cortical layers.

recount3

https://rna.recount.bio/

Accessible

2021

231

Human

Mouse

unknown

bulk

short

I_2

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
recount3: summaries and queries for large-scale RNA-seq expression and splicing.	10.1186/s13059-021-02533-6	unknown	unknown	unknown	The official recount3 portal provides study exploration and uniformly processed RNA-seq gene, exon and exon-exon junction counts with regional and junction-level access.

HRT Atlas v1.0

https://housekeeping.unicamp.br/?about

Accessible

2021

169

Human

Mouse

brain

heart

liver

lung

kidney

blood

skeletal muscle

skin

bulk

short

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
HRT Atlas v1.0 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets.	10.1093/nar/gkaa609	unknown	unknown	unknown	The official HRT Atlas searches candidate reference transcripts by tissue or cell type and returns Ensembl transcript identifiers with quantitative stability and abundance rankings.

Microglia Genomic Atlas (MiGA)

https://xqtl.niagads.org/

Accessible

2022

196

Human

medial frontal gyrus

superior temporal gyrus

thalamus

subventricular zone

bulk

short

III_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Genetic analysis of the human microglial transcriptome across brain regions, aging and disease pathologies.	10.1038/s41588-021-00976-y	Alzheimer's disease Parkinson's disease multiple sclerosis schizophrenia	adult aged	microglia	The NIAGADS xQTL portal searches harmonized brain QTL results by gene, variant or region and explicitly includes bulk-RNA splicing QTLs, including the Microglia Genomic Atlas resource.

DeCoN

http://decon.fas.harvard.edu/

Not accessible

2015

235

Mouse

neocortex

bulk

short

I_1

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
DeCoN: genome-wide analysis of in vivo transcriptional dynamics during pyramidal neuron fate selection in neocortex.	10.1016/j.neuron.2014.12.024	unknown	E15 E16 E18 P1	callosal projection neuron corticothalamic projection neuron subcerebral projection neuron	DeCoN's interactive web platform searches genes and gene sets, displays individual transcript isoform identities and abundance across developing neuron classes, and links processed reads for exon-level inspection.

CIRCpedia v3

https://bits.fudan.edu.cn/circpediav3/

Accessible

2018

881

Eukaryota

unknown

bulk

long

short

I_1

I_2

II_1

II_2

IV_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
CIRCpedia v2: An Updated Database for Comprehensive Circular RNA Annotation and Expression Comparison.	10.1101/gr.202895.115 10.1016/j.gpb.2018.08.001	cancer	unknown	unknown	The live official CIRCpedia v3 offers Search, Browse and Analyze interfaces for circRNAs, back-splice junctions, alternative events and circular-versus-linear isoform expression.

aberrant splicing database

https://www.hgc.jp/~knakai/asdb.html

Accessible

1994

315

Mammalia

central nervous system

bulk

short

II_1

II_2

III_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Construction of a novel database containing aberrant splicing mutations of mammalian genes.	10.1016/0378-1119(94)90567-3	genetic disease	unknown	unknown	The Aberrant Splicing Database browses mammalian disease mutations affecting authentic or cryptic splice sites and records aberrant outcomes such as exon skipping, together with flanking splice-site sequences.

Zebrafish Information Network

https://zfin.org/

Accessible

2022

181

Danio rerio

whole organism

bulk

single_cell

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Zebrafish information network, the knowledgebase for Danio rerio research.	10.1093/genetics/iyac016	unknown	embryonic larval juvenile adult	unknown	ZFIN's expert-curated interface searches genes and transcripts; linked transcript records provide transcript identifiers, status, sequence and known transcript variants, including retained-intron annotations.

Broad Improved Canine Annotation v1

https://genome.ucsc.edu/cgi-bin/hgHubConnect

Accessible

2014

247

Dog

unknown

bulk

short

I_1

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts.	10.1371/journal.pone.0091172	unknown	unknown	unknown	The live UCSC Track Hub interface provides access to the Broad improved canine annotation hub containing coding, antisense and intergenic multi-exon transcript models.

FANTOM Web Resource

https://fantom.gsc.riken.jp/

Accessible

2019

221

Human

Mouse

Rat

Macaca mulatta

Gallus gallus

Canis lupus familiaris

brain

hippocampus

cerebellum

substantia nigra

spinal cord

blood

skin

bulk

short

I_1

I_2

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Update of the FANTOM web resource: expansion to provide additional transcriptome atlases.	10.1093/nar/gky1099	Down syndrome glioma	fetal adult	astrocyte brain vascular smooth muscle cell immune cell fibroblast	The live FANTOM web resource provides searchable and browsable full-length cDNA, transcript-cluster and FANTOM CAT transcript models with genomic and expression views.

NRED; Noncoding RNA Expression Database

http://jsm-research.imb.uq.edu.au/NRED

Not accessible

2009

260

Human

Mouse

brain

cerebellum

bulk

short

I_2

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
NRED: a database of long noncoding RNA expression.	10.1093/nar/gkn617	unknown	unknown	unknown	NRED supported gene- and platform-centric searches and returned expression measurements for individual long ncRNA transcripts, with filters for spliced targets.

TumorFusions

http://www.tumorfusions.org/

Not accessible

2018

225

Human

tumor tissue

bulk

short

I_1

I_2

II_2

IV_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
TumorFusions: an integrative resource for cancer-associated transcript fusions.	10.1093/nar/gkx1018	cancer	unknown	unknown	TumorFusions was a searchable portal cataloguing fusion transcripts and breakpoints, with exon- and transcript-level expression for fusion partner genes.

POSTAR3

http://111.198.139.65/

Accessible

2022

161

Human

Mouse

Zebrafish

Drosophila melanogaster

Caenorhabditis elegans

Arabidopsis thaliana

Saccharomyces cerevisiae

unknown

bulk

short

II_2

III_1

III_2

IV_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
POSTAR3: an updated platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins.	10.1093/nar/gkab702	cancer	unknown	unknown	The live POSTAR3 interface, the successor of CLIPdb and POSTAR, searches RBP-binding sites and includes alternative-splicing and circRNA-junction regulatory records.

LncBook

https://ngdc.cncb.ac.cn/lncbook/home

Accessible

2019

244

Human

unknown

bulk

short

I_1

I_2

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
LncBook: a curated knowledgebase of human long non-coding RNAs.	10.1093/nar/gky960	cancer	unknown	unknown	LncBook's browse and search interface opened transcript-specific pages containing genomic context, exon number, sequence, and expression profiles.

Ghost Database

https://ghost.zool.kyoto-u.ac.jp/default_ht.html

Accessible

2008

207

Ciona robusta

unknown

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations.	10.1186/gb-2008-9-10-r152	unknown	unknown	unknown	Ghost provides Search, Genome Browser, and BLAST access alongside Ciona genomic and cDNA resources and downloadable KH gene-model annotations.

FarmGTEx;PigGTEx

https://piggtex.farmgtex.org/

Accessible

2024

189

Pig

adipose

brain

heart

liver

lung

skeletal muscle

bulk

short

II_1

II_2

III_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
A compendium of genetic regulatory effects across pig tissues.	10.1038/s41588-023-01585-7	unknown	unknown	unknown	The PigGTEx portal exposes tissue-associated regulatory results; its publication reports LeafCutter-derived splice junctions, PSI values and cis-sQTLs across 34 tissues.

VEuPathDB

https://veupathdb.org/veupathdb/app

Accessible

2017

409

Eukaryotic pathogens

mouse brain

lung

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
EuPathDB: the eukaryotic pathogen genomics database resource.	10.1371/journal.pntd.0001455 10.1093/nar/gkw1105 10.1093/nar/gks1113	malaria toxoplasmosis cryptosporidiosis leishmaniasis Chagas disease African trypanosomiasis cryptococcosis	parasite life-cycle stages	unknown	VEuPathDB's live application and official service documentation expose gene/transcript searches, transcript attributes and gene-record/genome-browser views of transcript models.

PlanMine 3.0

https://planmine.mpinat.mpg.de/planmine/begin.do

Accessible

2019

150

Platyhelminthes

whole organism

bulk

single_cell

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
PlanMine 3.0-improvements to a mineable resource of flatworm biology and biodiversity.	10.1093/nar/gky1070	unknown	regeneration stages	neoblast neuron	PlanMine 3.0 provides template and keyword queries; searchable gene pages link to transcript pages and genome views containing predicted transcripts and overlapping transcriptome contigs.

deepBase v2.0

https://rna.sysu.edu.cn/deepbase3/index.html

Accessible

2016

203

Human

Mouse

Caenorhabditis elegans

Drosophila melanogaster

Danio rerio

brain

heart

liver

testis

bulk

short

I_1

I_2

II_2

IV_1

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
deepBase v2.0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data.	10.1093/nar/gkv1273	unknown	unknown	unknown	deepBase v2.0's Browse pages expose lncRNA transcript records and circRNA annotations; the exact v2 pipeline identifies circRNAs from back-splice sites and profiles ncRNA expression.

GREIN

https://www.ilincs.org/apps/grein/

Accessible

2019

184

Human

Mouse

Rat

brain

blood

lung

liver

tumor tissue

bulk

short

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data.	10.1038/s41598-019-43935-8	neurological disease cancer	embryonic adult aging	neuron glial cell immune cell epithelial cell	GREIN lets users search GEO RNA-seq studies and interactively explore raw and normalized transcript-level read counts and transcript-per-million abundances produced by Salmon, rather than only gene-level summaries.

UCSC Toil RNA-seq Recompute Compendium

https://xenabrowser.net/datapages/?hub=https%3A%2F%2Ftoil.xenahubs.net%3A443

Accessible

2018

194

Human

brain

heart

liver

lung

skeletal muscle

blood

bulk

short

I_1

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Unifying cancer and normal RNA sequencing data from different sources.	10.1038/sdata.2018.61	cancer	adult	unknown	The live UCSC Xena Toil data page exposes raw gene- and transcript-level expression datasets, and Xena interactively queries and visualizes transcript/exon expression across cohorts.

MacaM

https://genome.ucsc.edu/cgi-bin/hgGateway?db=rheMac8

Accessible

2014

Macaca mulatta

amygdala

caudate nucleus

cerebellum

globus pallidus

hippocampus

locus coeruleus

cerebral cortex

medulla oblongata

spinal cord

substantia nigra

thalamus

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
A new rhesus macaque assembly and annotation for next-generation sequencing analyses.	10.1186/1745-6150-9-20	unknown	adult	unknown	The live UCSC rheMac8 gateway exposes the MacaM rhesus assembly and searchable transcript gene-model tracks with annotated exon boundaries.

brainSCOPE

https://brainscope.psychencode.org/

Accessible

2024

Human

dorsolateral prefrontal cortex

single_cell

short

I_2

III_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Single-cell genomics and regulatory networks for 388 human brains.	10.1126/science.adi5199	schizophrenia bipolar disorder autism Alzheimer's disease	adult aging	astrocyte microglia oligodendrocyte excitatory neuron inhibitory neuron	brainSCOPE browses and visualizes single-cell QTL resources and provides cell-type-specific isoform-usage QTL records for 22 DLPFC cell types, linking isoSNPs to regulated isoGenes.

Xenbase

https://www.xenbase.org/xenbase/

Accessible

2018

177

Xenopus laevis

Xenopus tropicalis

unknown

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Xenbase: a genomic, epigenomic and transcriptomic model organism database.	10.1093/nar/gkx936	unknown	embryo larva adult	unknown	The live Xenbase portal searches Xenopus genes and transcripts and exposes mRNA records, exon-intron gene models, JBrowse views and transcript sequence resources.

Functional lncRNA Database

https://www.valadkhanlab.org/database

Not accessible

2012

175

Homo sapiens

Mus musculus

Rattus norvegicus

unknown

bulk

short

I_1

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Computational analysis of functional long noncoding RNAs reveals lack of peptide-coding capacity and parallels with 3' UTRs.	10.1261/rna.029520.111	unknown	unknown	unknown	The publication describes a curated functional-lncRNA database that includes lncRNA transcript and splicing variants; the former official database page is no longer available.

CircRiC

https://hanlaboratory.com/cRic

Accessible

2019

155

Human

tumor tissue

bulk

short

I_2

II_1

II_2

IV_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Comprehensive characterization of circular RNAs in ~ 1000 human cancer cell lines.	10.1186/s13073-019-0663-5	cancer	unknown	cancer cell lines	CircRiC provides interactive expression and biogenesis analyses for circRNAs generated by back-splicing across 935 cancer cell lines.

C. elegans Splice Browser

http://splicebrowse.ccbr.utoronto.ca/

Not accessible

2011

170

Caenorhabditis elegans

whole organism

bulk

short

I_1

I_2

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Genome-wide analysis of alternative splicing in Caenorhabditis elegans.	10.1101/gr.114645.110	unknown	embryonic larval adult	neuron muscle cell germ cell	The publication documents a gene-queryable C. elegans Splice Browser with known and novel junctions, alternative events, splice sites and relative isoform levels.

Msex_1.0

https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000262585.1/

Accessible

2016

153

Manduca sexta

brain

head

muscle

ovary

testis

midgut

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta.	10.1016/j.ibmb.2016.07.005	unknown	embryonic larval adult	insect cell	NCBI's official Manduca annotation report links searchable RefSeq records and summarizes annotated transcripts, exons and transcript variants for assembly Msex_1.0.

LIBD Stem Cell Browser

https://stemcell.libd.org/

Accessible

2020

134

Human

cerebral cortex

bulk

short

I_1

I_2

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs.	10.1038/s41467-019-14266-z	schizophrenia neuropsychiatric disease	neuronal differentiation maturation	induced pluripotent stem cell neural progenitor cell neuron	The LIBD Stem Cell Browser searches genes and subfeatures and provides separate exon and junction datasets across neuronal differentiation.

The Transcriptome of Xenopus tropicalis

https://jason.chuang.ca/research/xenopus

Accessible

2013

144

Xenopus tropicalis

whole embryo

whole organism

bulk

short

I_1

I_2

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development.	10.1101/gr.141424.112	unknown	two-cell embryo gastrula neurula tailbud tadpole	unknown	The official Xenopus portal lets users explore RefSeq and Ensembl developmental transcriptome datasets with interactive transcript and isoform visualizations.

RNA Atlas; R2 web portal

https://r2platform.com/rna_atlas/

Accessible

2021

140

Human

brain

blood

heart

kidney

liver

lung

testis

bulk

short

I_1

I_2

IV_1

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
The RNA Atlas expands the catalog of human non-coding RNAs.	10.1038/s41587-021-00936-1	unknown	fetal adult	primary cells cell lines	The official RNA Atlas page provides a Transcript Explorer for mRNA, lncRNA, circRNA and other transcripts, base-pair profiles, and downloadable transcript models in GTF format.

SpliceAid-F

http://www.caspur.it/SpliceAidF

Not accessible

2013

140

Human

brain

blood

muscle

other tissues

bulk

short

III_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
SpliceAid-F: a database of human splicing factors and their RNA-binding sites.	10.1093/nar/gks997	cancer genetic disease neurological disease	unknown	cell lines primary cells	The database publication describes curated, experimentally assessed splicing-factor binding sites and their functional effects; the former SpliceAid-F portal is no longer safely reachable.

Expression and Polyadenylation Database; xPAD

http://johnlab.org/xpad

Accessible

2012

144

Human

breast

colon

kidney

liver

prostate

tumor tissue

normal tissue

bulk

short

I_1

I_2

IV_5

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
An in-depth map of polyadenylation sites in cancer.	10.1093/nar/gks637	cancer	adult	HeLa-S3 HepG2 K562 MCF7	The xPAD publication documents alternative polyadenylation isoform structures and tissue-specific usage, while the former portal now redirects to unrelated and unsafe-looking commercial content.

LNCat

http://biocc.hrbmu.edu.cn/LNCat

Accessible

2017

143

Human

brain

blood

heart

liver

other tissues

bulk

short

I_1

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
A comprehensive overview of lncRNA annotation resources.	10.1093/bib/bbw015	unknown	unknown	unknown	The official LNCat endpoint remains online but returns an access-forbidden page from this environment, so its transcript-annotation interface could not be entered during this review.

FR-AgENCODE

https://www.fragencode.org/results.html

Accessible

2019

120

Cattle

Goat

Chicken

Pig

liver

T cells

adipose

brain

heart

muscle

other tissues

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Multi-species annotation of transcriptome and chromatin structure in domesticated animals.	10.1186/s12915-019-0726-5	unknown	adult	T cell	The official FR-AgENCODE results page provides RNA-seq annotations, downloadable results and UCSC Genome Browser track hubs for inspecting transcript structures across domesticated-animal species.

lncRNAfunc 2.0

https://lncrnafunc.xu-bioinfo.com/

Accessible

2022

Human

tumor tissue

matched normal tissue

bulk

short

I_2

II_1

III_1

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
lncRNAfunc: a knowledgebase of lncRNA function in human cancer.	10.1093/nar/gkab1035	cancer	adult	unknown	The official lncRNAfunc 2.0 portal is a searchable cancer lncRNA knowledgebase linking dysregulation to transcript remodeling and provides browsable lncRNA function pages with multi-layer evidence.

Vega

https://vega.archive.ensembl.org/index.html

Accessible

2005

394

Human

Mouse

Zebrafish

other vertebrates

brain

other tissues

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
The Vertebrate Genome Annotation (Vega) database.	10.1093/nar/gki135	genetic disease	embryonic adult	unknown	The official archived Vega Genome Browser remains searchable and browsable, describing a repository of high-quality manually annotated vertebrate gene models with species and region views.

RNAdb

http://research.imb.uq.edu.au/RNAdb

Not accessible

2007

169

Human

Mouse

other mammals

brain

blood

heart

liver

other tissues

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
RNAdb 2.0--an expanded database of mammalian non-coding RNAs.	10.1093/nar/gkl926	cancer genetic disease neurological disease	embryonic adult	unknown	The RNAdb 2.0 publication documents searchable mammalian ncRNA records with transcript length, chromosomal position and splicing status; the former official host no longer resolves in DNS.

Alternative Exon Database (AEDB)

http://www.ebi.ac.uk/asd/aedb/index.html

Not accessible

2000

173

Human

Mouse

Rat

other eukaryotes

brain

blood

muscle

other tissues

bulk

short

II_1

II_2

III_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
An alternative-exon database and its statistical analysis.	10.1089/104454900750058107	cancer genetic disease neurological disease	embryonic adult	unknown	The AEDB publication describes curated alternative exons, splice-site properties, tissue specificity, developmental regulation and disease associations; the former EMBL-EBI ASD/AEDB page now returns 404.

lncRNome

http://genome.igib.res.in/lncRNome

Not accessible

2013

147

Homo sapiens

unknown

bulk

short

I_1

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
lncRNome: a comprehensive knowledgebase of human long noncoding RNAs.	10.1093/database/bat034	cancer neurological disease	unknown	unknown	The publication describes lncRNome as a searchable knowledgebase with stable lncRNA gene and alternate-transcript identifiers, record pages and a genome browser.

QTLbase

http://www.mulinlab.org/qtlbase

Accessible

2020

113

Homo sapiens

whole blood

brain

bulk

short

III_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
QTLbase: an integrative resource for quantitative trait loci across multiple human molecular phenotypes.	10.1093/nar/gkz888	cardiovascular disease neurological disease	unknown	immune cell	QTLbase provides retrieval and visualization across molecular QTL types, including splicing QTL associations, tissues, phenotypes and variants.

Platynereis transcriptome BLAST database

https://jekelylab.ex.ac.uk/blastdbs/index.html

Accessible

2013

Platynereis dumerilii

whole animal

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
The neuropeptide complement of the marine annelid Platynereis dumerilii.	10.1186/1471-2164-14-906	unknown	larva adult	neuron	The official Jékely Lab page provides BLAST search over Platynereis transcriptome assemblies containing 351,625 and 611,345 annotated transcript sequences.

ASAP

http://www.bioinformatics.ucla.edu/ASAP

Not accessible

2003

165

Homo sapiens

brain

nerve

bulk

short

I_1

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
ASAP: the Alternative Splicing Annotation Project.	10.1093/nar/gkg029	unknown	unknown	unknown	The publication describes ASAP searches by gene, event and tissue, with exon-intron structures, observed alternative-splicing patterns and inferred full-length isoforms.

EASANA/FAST DB

http://www.fast-db.com/cgi-bin/easana/index.pl

Not accessible

2010

142

Homo sapiens

cerebellum

testis

spleen

muscle

heart

liver

thyroid

prostate

pancreas

breast

kidney

bulk

short

I_2

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Splicing factor and exon profiling across human tissues.	10.1093/nar/gkq008	unknown	adult	unknown	The publication documents EASANA/FAST DB views of alternative transcripts, tissue-specific splicing variants and differential exon inclusion.

SpliceAPP Branch Point Query

https://bc.imb.sinica.edu.tw/SpliceAPP/query.php

Accessible

2017

107

Homo sapiens

Mus musculus

Drosophila melanogaster

Caenorhabditis elegans

unknown

bulk

short

II_2

III_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Large-scale analysis of branchpoint usage across species and cell lines.	10.1101/gr.202820.115	inherited disease	unknown	unknown	The live SpliceAPP database supports gene/coordinate branchpoint queries and browses 3'/5' splice-site variant records with introns, branchpoints, disruption scores and predicted splicing effects.

Brain mRNA isoform atlas

https://isoformatlas.com/

Accessible

2024

178

Human

Mouse

human cortex

mouse hippocampus

mouse prefrontal cortex

mouse cerebellum

single_cell

long

I_1

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Single-cell long-read sequencing-based mapping reveals specialized splicing patterns in developing and adult mouse and human brain.	10.1038/s41467-020-20343-5 10.1038/s41593-024-01616-4	unknown	P1 P7 adult	neurons astrocytes oligodendrocytes microglia	The Brain mRNA isoform atlas Access data menu links human cortex and mouse hippocampus, prefrontal cortex, cerebellum and BICCN isoform viewers.

ASP

https://www.bioinformatics.ucla.edu/ASP

Not accessible

2004

150

Human

brain

other tissues

bulk

short

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Assessing the impact of alternative splicing on domain interactions in the human proteome.	10.1021/pr034064v	unknown	unknown	unknown	The paper describes ASP as a gene-searchable database of alternatively spliced protein isoforms with exon-defined splice forms, sequences and domain-architecture comparisons; the site is unavailable.

RefLnc

https://reflnc.gao-lab.org/

Accessible

2019

Human

brain

blood

heart

kidney

liver

lung

tumor tissue

bulk

short

I_1

I_2

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
An expanded landscape of human long noncoding RNA.	10.1093/nar/gkz621	cancer	adult	cancer cell lines primary cells	The live RefLnc portal searches a human lncRNA catalog and exposes merged reference/novel transcript models, gene-model structures and transcript expression across GTEx and TCGA samples.

MeT-DB V2.0

http://compgenomics.utsa.edu/MeTDB

Not accessible

2018

113

Human

Mouse

brain

heart

kidney

liver

testis

tumor tissue

bulk

short

I_2

IV_6

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
MeT-DB V2.0: elucidating context-specific functions of N6-methyl-adenosine methyltranscriptome.	10.1093/nar/gkx1080 10.1093/nar/gku1024	cancer metabolic disease	embryonic adult	stem cell cell lines primary cells	The MeT-DB V2.0 paper documents transcript-name filtering and downloadable gene/isoform FPKM and read-count values; the original UTSA database endpoint is no longer available.

ce11 staged dRNAseq track hub

https://genome.ucsc.edu/cgi-bin/hgTracks?db=ce11&hubUrl=https://bx.bio.jhu.edu/track-hubs/dRNAseq/hub.txt

Accessible

2020

Caenorhabditis elegans

whole organism

bulk

long

I_1

I_2

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
The full-length transcriptome of <i>C. elegans</i> using direct RNA sequencing.	10.1101/gr.251314.119	unknown	larval young adult adult	neuron muscle cell germ cell other cells	The live UCSC hub loads ce11 staged Nanopore direct-RNA tracks for full-length reads and isoform models across C. elegans development, supporting junction and transcript-structure browsing.

ConjoinG

http://metasystems.riken.jp/conjoing

Not accessible

2010

104

Human

brain

heart

kidney

liver

lung

pancreas

muscle

testis

uterus

bulk

short

I_1

II_1

II_2

IV_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Expression of conjoined genes: another mechanism for gene regulation in eukaryotes.	10.1371/journal.pone.0013284	cancer genetic disease	fetal adult	unknown	The ConjoinG paper documents searchable human conjoined transcripts formed by intergenic splicing, including junction exons, splice combinations and mRNA/EST validation; the site is unavailable.

GTEx

https://gtexportal.org/home/transcriptPage

Accessible

2015

Human

brain

heart

kidney

liver

lung

skeletal muscle

blood

other tissues

bulk

short

I_1

I_2

III_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
The Genotype-Tissue Expression (GTEx) Project: Linking Clinical Data with Molecular Analysis to Advance Personalized Medicine.	10.3390/jpm5010022	unknown	adult	unknown	The live GTEx Transcript Browser displays exon-resolved transcript structures and tissue transcript expression, while the portal also exposes tissue-specific splicing-QTL results.

Cancer RNA-Seq Nexus

http://syslab4.nchu.edu.tw/CRN

Not accessible

2016

102

Human

brain

breast

colon

kidney

liver

lung

prostate

tumor tissue

bulk

short

I_2

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells.	10.1093/nar/gkv1282	cancer	adult	cancer cells	The Cancer RNA-Seq Nexus paper documents GENCODE transcript-isoform FPKM/TPM queries and phenotype-specific transcript expression across cancers; the original server is unavailable.

intropolis (queried through Snaptron)

https://snaptron.cs.jhu.edu/

Accessible

2016

104

Human

brain

blood

cell lines

other tissues

bulk

short

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive.	10.1186/s13059-016-1118-6	neurological disease cancer relevance	fetal adult	tissue cells cell lines	The live Snaptron interface and web services query intropolis exon–exon junctions across tens of thousands of RNA-seq samples by genomic region, junction fields and sample metadata.

ChimerDB 4.0

https://kobic.re.kr/chimerdb/

Accessible

2020

Homo sapiens

tumor

bulk

short

I_1

IV_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
ChimerDB 4.0: an updated and expanded database of fusion genes.	10.1093/nar/gkz1013 10.1093/nar/gkp982	cancer	unknown	unknown	The official ChimerDB 4.0 portal searches curated, literature-mined and sequencing-derived fusion genes and provides fusion-structure views with transcript breakpoints and junction context.

ASCOT

http://ascot.cs.jhu.edu/

Accessible

2021

—

Homo sapiens

Mus musculus

brain

retina

liver

lung

bulk

single_cell

short

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
ASCOT identifies key regulators of neuronal subtype-specific splicing.	10.1038/s41588-021-00820-5 10.1101/501882	neurological disease retinal disease	postnatal development adult	neuron photoreceptor	The official ASCOT portal lets users select datasets and genes, explore alternative-splicing summaries, filter PSI and NAUC ranges, view UCSC tracks, and download underlying tables.

APADB

https://tools.genxpro.net/apadb

Accessible

2016

Homo sapiens

Mus musculus

Gallus gallus

unknown

bulk

short

I_1

IV_5

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
APADB: a database for alternative polyadenylation and microRNA regulation events.	10.1093/database/baw105	cancer	unknown	unknown	The official APADB route remains active and redirects to a credential gate for the APADB application; its alternative-polyadenylation database interface is currently restricted to authenticated users.

ASAP II

http://bioinfo.mbi.ucla.edu/ASAP2

Not accessible

2007

120

Metazoa

unknown

bulk

short

I_1

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species.	10.1093/nar/gkl884	cancer	unknown	unknown	The ASAP II publication documents searchable alternative-splicing events, tissue-specific isoforms and exon structures; the former UCLA database host now times out without loading a page.

Ocular Tissue Database

https://genome.uiowa.edu/otdb

Not accessible

2013

107

Homo sapiens

retina

optic nerve

optic nerve head

ciliary body

trabecular meshwork

sclera

lens

cornea

choroid

iris

bulk

short

I_2

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Exon-level expression profiling of ocular tissues.	10.1016/j.exer.2013.03.004	retinal disease glaucoma	adult	unknown	The Ocular Tissue Database publication describes searchable ocular RNA-seq expression and alternative transcript records; the former University of Iowa database URL now returns an official page-not-found response.

Ensembl zebrafish genome annotation

https://www.ensembl.org/Danio_rerio/Info/Index

Accessible

2012

119

Danio rerio

brain

heart

liver

other tissues

bulk

short

I_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Incorporating RNA-seq data into the zebrafish Ensembl genebuild.	10.1101/gr.137901.112	unknown	embryonic larval adult	unknown	Ensembl zebrafish provides searchable transcript models, exon structures and genome-browser evidence for alternative transcripts and RNA-seq-supported splice sites.

ASTD

http://www.ebi.ac.uk/astd

Not accessible

2009

110

Human

Mouse

Rat

brain

heart

kidney

liver

lung

other tissues

bulk

short

I_1

I_2

II_1

IV_5

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
ASTD: The Alternative Splicing and Transcript Diversity database.	10.1016/j.ygeno.2008.11.003	cancer genetic disease neurological disease	adult	cell lines primary cells	The ASTD publication documents searchable alternative initiation, polyadenylation and splicing variants, transcript structures and tissue-associated isoform states.

miRIAD

https://www.miriad-database.org/

Accessible

2014

Human

Rhesus macaque

Mouse

Opossum

Chicken

brain

cerebellum

heart

kidney

liver

testis

bulk

short

I_1

I_2

IV_5

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
miRIAD-integrating microRNA inter- and intragenic data.	10.1093/database/bau099	unknown	adult	unknown	miRIAD gene records visualize RefSeq transcript structures, alternative polyadenylation or UTR isoforms and tissue expression for intragenic-miRNA host genes.

SiT; isomics

https://www.isomics.eu/

Accessible

2023

Mouse

brain

olfactory bulb

hippocampus

bulk

long

short

I_1

I_2

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
The spatial landscape of gene expression isoforms in tissue sections.	10.1093/nar/gkad169	unknown	adult	neuron glial cell other brain cells	The isomics SiTx application exposes spatial full-length transcript isoforms, isoform switching, expression and alternative-splicing patterns in mouse tissue sections.

ALDB (Domestic-Animal Long Noncoding RNA Database)

http://res.xaut.edu.cn/aldb/index.jsp

Not accessible

2015

Sus scrofa

Gallus gallus

Bos taurus

brain

frontal cortex

occipital cortex

cerebellum

hypothalamus

bulk

short

I_1

I_2

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
ALDB: a domestic-animal long noncoding RNA database.	10.1371/journal.pone.0124003	unknown	unknown	unknown	The ALDB paper documents searchable pig, chicken and cow lincRNA transcripts, GBrowse exon models, GTF/GFF downloads and tissue expression; the original database is unavailable.

CATs / MAJIQ-CAT

https://tools.biociphers.org/majiq-cat/

Accessible

2020

Human

brain

heart

blood

skin

muscle

other tissues

bulk

short

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Mapping RNA splicing variations in clinically accessible and nonaccessible tissues to facilitate Mendelian disease diagnosis using RNA-seq.	10.1038/s41436-020-0780-y	Mendelian disease genetic disease	fetal adult	unknown	The live CATs/MAJIQ-CAT gene view exposes tissue expression and splicegraph local-splicing-variation data, enabling gene- and tissue-specific splicing-event comparison.

DirectRMDB

https://www.rnamd.org/directRMDB/

Accessible

2023

Homo sapiens

Mus musculus

Arabidopsis thaliana

unknown

bulk

long

I_1

I_2

IV_6

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology.	10.1093/nar/gkac1061	unknown	unknown	unknown	The live DirectRMDB detail page lists transcripts involved in each modification site together with transcript IDs, secondary structures, estimated counts and transcript TPM values.

Brain Cell lncRNA RNAseq Browser

http://jiaqianwulab.org/braincell/lncRNA.html

Accessible

2015

Mus musculus

cerebral cortex

bulk

short

I_1

I_2

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination.	10.1371/journal.pgen.1005669	neurological disease experimental autoimmune encephalomyelitis	oligodendrocyte development	astrocyte neuron oligodendrocyte precursor cell oligodendrocyte microglia endothelial cell pericyte neural stem cell	The live brain-cell lncRNA browser provides purified mouse neural-cell expression profiles and interactive genomic views of annotated lncRNA transcript models.

APASdb

http://ac.agrogene.ac.cn/utr

Not accessible

2015

Homo sapiens

Mus musculus

Danio rerio

unknown

bulk

short

I_1

I_2

IV_5

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals.	10.1093/nar/gku1076	cancer	unknown	unknown	The APASdb paper documents alternative-polyadenylation isoform maps, heterogeneous cleavage sites and quantified usage for distinct APA isoforms; the original database is unavailable.

LncExpDB

https://ngdc.cncb.ac.cn/lncexpdb

Accessible

2021

Homo sapiens

brain

heart

liver

lung

kidney

bulk

short

I_1

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
LncExpDB: an expression database of human long non-coding RNAs.	10.1093/nar/gkaa850	cancer neurological disease	organ development	unknown	LncExpDB 2.0 searches transcript identifiers from multiple reference catalogs and documents downloadable reference gene models plus transcript/exon annotation statistics alongside expression profiles.

HCSAS

http://202.114.72.39/database/human.html

Not accessible

2009

Homo sapiens

brain

lung

breast

colon

prostate

bulk

short

I_1

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
A global view of cancer-specific transcript variants by subtractive transcriptome-wide analysis.	10.1371/journal.pone.0004732	cancer	unknown	unknown	The HCSAS paper documents a web database of 15,093 cancer-specific alternatively spliced transcripts and matched normal-tissue variants; the original IP endpoint is unavailable.

uORFdb

https://www.bioinformatics.uni-muenster.de/tools/uorfdb

Accessible

2014

Eukaryota

unknown

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
uORFdb--a comprehensive literature database on eukaryotic uORF biology.	10.1093/nar/gkt952	cancer neurological disease	development	unknown	uORFdb searches NCBI transcript IDs and displays a per-transcript model with TLS, CDS, uORFs and optionally introns, plus downloadable transcript records.

FusionGDB

https://compbio.uth.edu/FusionGDB2

Accessible

2019

Homo sapiens

tumor

bulk

short

I_1

IV_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
FusionGDB: fusion gene annotation DataBase.	10.1093/nar/gky1067	cancer	unknown	unknown	FusionGDB provides breakpoint-specific fusion transcripts, partner-gene isoform structures, exon contexts, ORF analyses and full-length fusion transcript sequences.

retina.tigem.it

https://retina.tigem.it/

Accessible

2016

Homo sapiens

retina

bulk

short

I_1

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
An atlas of gene expression and gene co-regulation in the human retina.	10.1093/nar/gkw486	retinal disease	adult	unknown	RETINA searches 94,521 retinal transcripts and reports transcript IDs, genomic positions, relative transcript contribution and median TPM for disease genes.

CSCD2

https://geneyun.net/CSCD2/

Accessible

2022

Homo sapiens

tumor

bulk

short

I_1

II_2

IV_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
CSCD2: an integrated interactional database of cancer-specific circular RNAs.	10.1093/nar/gkab830	cancer	unknown	unknown	CSCD2 records expose circRNA back-splice junction read counts, parent-gene and mRNA annotation, genomic context and reconstructed full-length circRNA sequences.

AURA 2

http://aura.science.unitn.it/

Accessible

2014

Homo sapiens

Mus musculus

unknown

bulk

short

I_1

IV_5

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
AURA 2: Empowering discovery of post-transcriptional networks.	10.4161/trla.27738	cancer	unknown	unknown	AURA 2 searches transcript-specific 5-prime and 3-prime UTR models, displays spliced UTR structures and includes alternative-polyadenylation profiles and UTR annotations.

LncBook 2.0

https://ngdc.cncb.ac.cn/lncbook

Accessible

2023

Homo sapiens

brain

heart

liver

lung

kidney

bulk

short

I_1

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
LncBook 2.0: integrating human long non-coding RNAs with multi-omics annotations.	10.1093/nar/gkac999	cancer neurological disease	development	unknown	LncBook 2.0 searches hundreds of thousands of curated lncRNA transcripts and exposes transcript integration, gene structures, genomic locations and multi-omics annotations.

TyKiVa

http://tykiva.bii.a-star.edu.sg/SOGdb/cgi-bin/sogweb.pl

Not accessible

2007

Human

brain

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Genetic alterations in the tyrosine kinase transcriptome of human cancer cell lines.	10.1158/0008-5472.can-07-2703	astrocytoma glioblastoma neuroblastoma cancer	unknown	astrocytoma cell line glioblastoma cell line neuroblastoma cell line	The TyKiVa publication describes retrievable tyrosine-kinase transcript variants, including alternative-splicing and sequence-altering events across cancer cell lines.

cBARBEL; catfish EST resource

http://www.catfishgenome.org/cbarbel

Accessible

2010

Channel catfish

Blue catfish

brain

olfactory tissue

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies.	10.1186/gb-2010-11-1-r8	unknown	unknown	unknown	cBARBEL provides searches over catfish EST contigs and full-length cDNAs, an EST contig viewer and links to alternative-splicing resources.

ENCODE Project at UCSC

https://genome.ucsc.edu/ENCODE/

Accessible

2007

—

Human

Mouse

brain

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
The ENCODE Project at UC Santa Cruz.	10.1093/nar/gkl1017	brain tumor	unknown	neuroectodermal cell	The official ENCODE-at-UCSC archive provides experiment search, genome-browser tracks and RNA-seq track searches, including RNA-level annotations and full-length transcript start/end evidence.

CircNet 2.0

https://awi.cuhk.edu.cn/~CircNet/php/index.php

Not accessible

2022

304

Human

unknown

bulk

short

I_1

I_2

II_2

IV_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
CircNet 2.0: an updated database for exploring circular RNA regulatory networks in cancers.	10.1093/nar/gkv940 10.1093/nar/gkab1036	cancer	unknown	unknown	The live CircNet 2.0 database provides searchable circular-RNA records, back-splice and full-length isoform information, expression profiles and regulatory-network exploration across cancers.

Human brain circRNA catalog (ZENBU browser)

https://fantom.gsc.riken.jp/zenbu/gLyphs/#config=zIlof6KgK9gvAcJ-pYn0k;loc=hg19::chr8:104323868..105455214+

Accessible

2020

—

Human

cerebral cortex

cerebellum

bulk

short

I_2

II_2

IV_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
The Landscape of Circular RNA Expression in the Human Brain.	10.1016/j.biopsych.2019.07.029	autism spectrum disorder	unknown	unknown	The official linked ZENBU configuration opens a browsable genome view of the human-brain circRNA expression catalog, whose records are back-splice-junction-defined circular transcripts.

TranspoGene; microTranspoGene

http://transpogene.tau.ac.il/

Not accessible

2008

—

unknown

cerebellum

bulk

short

I_1

II_1

IV_6

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates.	10.1093/nar/gkm949	unknown	unknown	unknown	The TranspoGene publication documents searchable exonized and intronic transposable elements with transcript context; the former Tel Aviv University server now resets connections.

Exon Ontology

https://fasterdb.ens-lyon.fr/ExonOntology/

Accessible

2017

Human

Mouse

brain

choroid plexus

retina

bulk

short

I_1

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Identification of protein features encoded by alternative exons using Exon Ontology.	10.1101/gr.212696.116	cancer	unknown	brain microvascular endothelial cells choroid plexus epithelial cells retinal pigment epithelial cells epithelial cells mesenchymal cells	The official Exon Ontology interface analyzes exon coordinates against built-in first, constitutive, alternatively spliced and last coding exon categories and supports alternative-exon enrichment.

LincSNP 3.0

https://bio-bigdata.hrbmu.edu.cn/lincsnp/index.jsp

Accessible

2017

Human

brain

blood

tumor tissue

other tissues

bulk

short

I_1

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
LincSNP 2.0: an updated database for linking disease-associated SNPs to human long non-coding RNAs and their TFBSs.	10.1093/nar/gkw945	cancer cardiovascular disease neurological disease other diseases	unknown	cell lines primary cells	LincSNP 3.0 RNA-centric records include transcript IDs, transcript names and positions, while its genome browser exposes transcript structures and linked variants.

FasterDB

https://fasterdb.ens-lyon.fr/

Accessible

2014

Human

Mouse

brain

endothelium

epithelium

connective tissue

other tissues

bulk

short

I_1

I_2

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Endothelial, epithelial, and fibroblast cells exhibit specific splicing programs independently of their tissue of origin.	10.1101/gr.162933.113	cancer other diseases	adult	endothelial cell epithelial cell fibroblast cancer cell lines	FasterDB displays each gene's transcript splicing patterns, clickable exons and introns, alternative first and last exons and cell-specific splice-variant expression.

Nonhuman Primate Reference Transcriptome Resource (NHPRTR)

https://nhprtr.org/

Accessible

2015

non-human primates

unknown

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR).	10.1093/nar/gks1268 10.1093/nar/gku1110	unknown	unknown	unknown	The official NHPRTR portal provides tissue-specific primate RNA-seq, updated genome annotations, PacBio Iso-Seq full-length transcripts and processed alternative-isoform data across multiple tissues.

ANISEED

https://www.aniseed.cnrs.fr/

Accessible

2020

Tunicates

whole embryo

nervous system

heart

muscle

other tissues

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates.	10.1093/nar/gkz955	unknown	embryonic larval adult regeneration	embryonic cells neural cells muscle cells other cells	ANISEED searches tunicate genes and transcripts and exposes functionally annotated transcript models, genomic structures and developmental evidence.

Cross-ancestry atlas of gene, isoform, and splicing regulation

https://devbrainhub.gandallab.org/

Accessible

2024

Human

developing brain

cerebral cortex

bulk

short

I_2

II_1

III_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain.	10.1126/science.adh0829	autism schizophrenia bipolar disorder other neuropsychiatric disease	fetal first trimester second trimester	neural progenitor excitatory neuron interneuron glial cell	Developing Brain Hub provides gene, isoform and splicing QTL maps, isoform-level regulation and co-expression networks across developing human brain samples.

fast DB

http://www.fast-db.com/

Not accessible

2007

Human

Mouse

brain

heart

kidney

liver

lung

other tissues

bulk

short

I_1

I_2

II_1

II_2

III_1

IV_4

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
A new advance in alternative splicing databases: from catalogue to detailed analysis of regulation of expression and function of human alternative splicing variants.	10.1186/1471-2105-8-180	cancer genetic disease neurological disease	adult	cell lines primary cells	FAST DB provides gene-centered alternative transcripts, exon-intron structures, splice-event analyses and tissue-regulated alternative-splicing information.

biosino alternative splicing database (BASD)

http://humgene.biosino.cn/BASD.html

Not accessible

2004

Human

liver

lung

tumor tissue

matched normal tissue

bulk

short

I_1

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Identification of alternatively spliced mRNA variants related to cancers by genome-wide ESTs alignment.	10.1038/sj.onc.1207362	liver cancer lung cancer other cancers	adult	cancer cells primary cells	The BASD paper documents cancer-related alternatively spliced mRNA variants predicted from EST alignments and displayed as graphical and textual transcript structures; the site is unavailable.

Hollywood

http://hollywood.mit.edu/

Not accessible

2006

Human

Mouse

brain

heart

kidney

liver

lung

other tissues

bulk

short

I_1

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
HOLLYWOOD: a comparative relational database of alternative splicing.	10.1093/nar/gkj048	cancer genetic disease neurological disease	fetal adult	cell lines primary cells	The Hollywood paper documents alternative exons, splice sites, classified event types and graphical transcript-splicing patterns for human and mouse; the original database is unavailable.

X:Map

http://xmap.picr.man.ac.uk/

Not accessible

2008

Human

breast

tumor tissue

other tissues

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis.	10.1093/nar/gkm779 10.1186/gb-2007-8-5-r79	cancer other diseases	adult	MCF7 MCF10A other cell lines	The X:Map update paper documents transcript/exon identifier search and a hierarchical gene-transcript-exon-probeset browser with exon-expression overlays; the database is unavailable.

FusionCancer

http://donglab.ecnu.edu.cn/databases/FusionCancer

Not accessible

2015

Homo sapiens

tumor tissue

matched normal tissue

bulk

short

I_1

IV_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
FusionCancer: a database of cancer fusion genes derived from RNA-seq data.	10.1186/s13000-015-0310-4	bladder cancer breast cancer colorectal cancer glioblastoma lung cancer other cancers	unknown	cancer cell lines primary tumor cells	The FusionCancer paper documents searchable RNA-seq fusion records with breakpoints, chimeric transcript sequences and exon-level expression for fusion partners; the original site is unavailable.

Alternative Splicing Gallery

http://statgen.ncsu.edu/asg

Not accessible

2004

Homo sapiens

brain

other tissues

bulk

short

I_1

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome.	10.1093/nar/gkh731	unknown	unknown	cell lines primary tissues	The Alternative Splicing Gallery paper documents splicing graphs, interactive transcript assembly and exon-skipping, competing-splice-site and intron-retention events; the site is unavailable.

ALDH web database

https://www.aldh.org/

Accessible

2009

Homo sapiens

unknown

bulk

short

I_1

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Human aldehyde dehydrogenase genes: alternatively spliced transcriptional variants and their suggested nomenclature.	10.1097/fpc.0b013e3283329023	Alzheimer disease Sjögren-Larsson syndrome pyridoxine-dependent seizures type II hyperprolinemia cancer	unknown	unknown	The official ALDH database endpoint is access-restricted; its database organizes ALDH alternatively spliced transcript variants with exon counts, accession sequences and graphical structures.

Human Gene Mutation Database (HGMD)

https://www.hgmd.cf.ac.uk/ac/

Accessible

2006

Human

unknown

bulk

short

III_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
The Human Gene Mutation Database (HGMD) and its exploitation in the study of mutational mechanisms.	10.1002/0471250953.bi0113s12	human inherited disease neurological disease	unknown	unknown	HGMD supports gene and phenotype searches and offers a Splice mutation category, cataloguing disease variants that affect mRNA splicing.

NFINtb

https://nfintb.leibniz-fli.de/nfintb/

Accessible

2013

Nothobranchius furzeri

whole body

brain

skin

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
The transcript catalogue of the short-lived fish Nothobranchius furzeri provides insights into age-dependent changes of mRNA levels.	10.1186/1471-2164-14-185	unknown	embryo juvenile adult ageing	unknown	NFINtb is a searchable database of annotated cDNA contig assemblies; quick search, complex queries and BLAST retrieve transcript sequences and records.

DBASS3/DBASS5

https://www.dbass.org.uk/

Accessible

2011

182

Human

brain

blood

other tissues

bulk

short

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
DBASS3 and DBASS5: databases of aberrant 3'- and 5'-splice sites.	10.1093/nar/gkl535 10.1093/nar/gkq887	genetic disease cancer neurological disease	unknown	patient-derived cells	DBASS3 and DBASS5 are searchable databases of pathogenic aberrant 3-prime and 5-prime splice sites with mutation, phenotype, sequence and exon-intron context.

ratSCI

http://jiaqianwulab.org/ratSCI/ratSCI.html

Accessible

2017

Rat

spinal cord

bulk

short

I_1

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
The systematic analysis of coding and long non-coding RNAs in the sub-chronic and chronic stages of spinal cord injury.	10.1038/srep41008	spinal cord injury	adult sub-chronic injury chronic injury	neuron glial cell immune cell	The ratSCI browser supports gene-symbol navigation across genomic coordinates and displays refGene, lncRNA and RNA-seq transcript tracks for spinal-cord-injury samples.

eQTL Catalogue

https://www.ebi.ac.uk/eqtl/

Accessible

2023

317

Human

amygdala

anterior cingulate cortex

caudate

cerebellum

cerebral cortex

frontal cortex

hippocampus

hypothalamus

nucleus accumbens

putamen

substantia nigra

tibial nerve

bulk

short

I_2

II_1

II_2

III_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
eQTL Catalogue 2023: New datasets, X chromosome QTLs, and improved detection and visualisation of transcript-level QTLs.	10.1038/s41588-021-00924-w 10.1371/journal.pgen.1010932	unknown	unknown	microglia	The eQTL Catalogue provides REST queries and displayed human splicing QTL results linking variants to specific splicing events on nearby splice junctions.

MouSDB3

http://genomes.rockefeller.edu/MouSDB

Not accessible

2004

Mouse

brain

heart

kidney

liver

lung

other tissues

bulk

short

I_1

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Alternative splicing of mouse transcription factors affects their DNA-binding domain architecture and is tissue specific.	10.1186/gb-2004-5-10-r75	cancer neurological disease other diseases	embryonic adult	unknown	MouSDB3 maps mouse mRNA and EST evidence to the genome, establishes exon splice sites and transcript clusters, and records cassette exons, other splice variants and tissue distributions for transcription-factor isoforms.

EctoMap

https://monsoro-lab-ectomap.shinyapps.io/EctoMAP/

Accessible

2017

Xenopus laevis

neural plate

neural plate border

neural crest

epidermis

placode

ectoderm

bulk

short

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
A molecular atlas of the developing ectoderm defines neural, neural crest, placode, and nonneural progenitor identity in vertebrates.	10.1371/journal.pbio.2004045	congenital disease cancer	neurula stage embryonic	neural progenitor neural crest progenitor placodal progenitor epidermal progenitor	EctoMap lite accepts a transcript name and displays transcript RPKM across dissected neural and non-neural ectoderm regions and developmental stages.

PhenoGen

https://phenogen.org/gene.jsp

Accessible

2015

Rat

Mouse

whole brain

heart

liver

brown adipose tissue

bulk

short

I_1

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
The sequenced rat brain transcriptome--its use in identifying networks predisposing alcohol consumption.	10.1111/febs.13358	alcohol consumption alcohol use disorder genomic disorder	adult	unknown	PhenoGen's Genome/Transcriptome Browser supports gene or region queries, predefined transcriptome views and brain, liver, heart and kidney RNA-seq tracks for rat and mouse.

APAatlas

https://hanlaboratory.com/apa

Accessible

2020

Human

brain

heart

kidney

liver

lung

testis

blood

other tissues

bulk

short

I_1

I_2

IV_5

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
APAatlas: decoding alternative polyadenylation across human tissues.	10.1093/nar/gkz876	cancer other diseases	adult	mixed tissue cells	APAatlas Landscape queries APA events by gene, Ensembl gene or RefSeq mRNA ID and reports tissue-specific usage of alternative 3-prime-UTR transcript isoforms.

Ensembl Green Anole

https://www.ensembl.org/Anolis_carolinensis/Info/Annotation

Accessible

2013

Anolis carolinensis

brain

adrenal gland

dewlap skin

heart

liver

lung

ovary

skeletal muscle

regenerating tail

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Genome reannotation of the lizard Anolis carolinensis based on 14 adult and embryonic deep transcriptomes.	10.1186/1471-2164-14-49	unknown	embryonic adult regenerating	unknown	The live Ensembl Green Anole portal searches genes and transcripts and exposes RNA-supported transcript models, stable transcript identifiers and exon-intron structures in gene and genome views.

SpliceDisease

http://cmbi.bjmu.edu.cn/sdisease

Not accessible

2012

Human

other species

brain

blood

muscle

other tissues

bulk

short

II_1

III_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
SpliceDisease database: linking RNA splicing and disease.	10.1093/nar/gkr1171	genetic disease cancer neurological disease other diseases	unknown	patient-derived cells	SpliceDisease manually curates 2,337 experimentally supported mutation-splicing-disease entries with affected exon or intron sequence, mutation position and descriptions of the resulting splicing defect.

Exon-Intron Database (EID)

https://bpg.utoledo.edu/~afedorov/lab/eid.html

Not accessible

2006

Human

Mouse

Rat

Dog

Chicken

Danio rerio

Drosophila

Caenorhabditis elegans

Arabidopsis

brain

other tissues

bulk

short

I_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Advances in the Exon-Intron Database (EID).	10.1093/bib/bbl003	unknown	unknown	unknown	The EID update publication documents searchable exon, intron, mRNA and genomic representations with explicit boundaries and alternatively spliced isoforms; the former database host now resets connections.

miRNEST 2.0

http://rhesus.amu.edu.pl/mirnest/copy/

Accessible

2014

Plants

Animals

Viruses

root

leaf

flower

seed

brain

other tissues

bulk

short

I_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
miRNEST 2.0: a database of plant and animal microRNAs.	10.1093/nar/gkt1156	unknown	plant development animal development	plant cells animal cells	The official miRNEST endpoint is currently network-reachable but browser-restricted; miRNEST provides searchable pri-miRNA gene structures with experimentally supported splice sites.

CCDS

https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi

Accessible

2012

Human

Mouse

all tissues

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Tracking and coordinating an international curation effort for the CCDS Project.	10.1093/database/bas008	genetic disease cancer neurological disease	unknown	unknown	The NCBI CCDS interface searches CCDS, gene, nucleotide or protein identifiers in human and mouse releases and returns curated coding-exon transcript records.

ReproGenomics Viewer (RGV)

https://rgv2.genouest.org/

Accessible

2014

Rat

brain

cerebellum

cortex

testis

bulk

short

I_1

I_2

II_1

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
High-resolution profiling of novel transcribed regions during rat spermatogenesis.	10.1095/biolreprod.114.118166	infertility reproductive disorders	adult spermatogenesis	spermatocyte spermatid Sertoli cell	RGV provides a searchable study table with transcriptome filters, record pages and associated JBrowse tracks, including alternative-splicing and transcript-model studies.

SNP2APA

https://gong_lab.hzau.edu.cn/SNP2APA/

Accessible

2020

Human

brain

breast

kidney

lung

tumor tissue

other tissues

bulk

short

I_1

I_2

IV_5

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
SNP2APA: a database for evaluating effects of genetic variants on alternative polyadenylation in human cancers.	10.1093/nar/gkz793	cancer	adult	primary tumor cells normal tissue cells	SNP2APA supports quick search and browsing of cis-, trans-, survival- and GWAS-apaQTLs, with PDUI-quantified APA events that generate different 3-prime-UTR transcript isoforms.

GWAS-CaptureSeq

http://gwas-captureseq.dingerlab.org/

Not accessible

2017

Human

brain

blood

skin

testis

other tissues

bulk

short

I_1

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Intergenic disease-associated regions are abundant in novel transcripts.	10.1186/s13059-017-1363-3	genetic traits cancer neurological disease other diseases	adult	primary tissue cells melanoma cells	GWAS-CaptureSeq identifies and exposes 1,775 multi-exonic transcripts from disease-associated intronic and intergenic haploblocks, with assembled exon structures and tissue-specific expression across 21 human tissues.

CASGP database

http://globalisland.bii.a-star.edu.sg/~jiangtao/sas/index3.php?link=about

Not accessible

2010

Human

brain

testis

tumor tissue

other tissues

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns.	10.1093/nar/gkp954	cancer neurological disease genetic disease	adult spermatogenesis	primary tissue cells cell lines	The CASGP/USAGP database integrates 23,782 sense-antisense transcript pairs and provides genomic transcript arrangements with detailed exon-exon and exon-intron overlap structures, accessions and expression-sequence support.

circMine

http://www.biomedical-web.com/circmine_v2/

Accessible

2022

Human

brain

heart

blood

tumor tissue

other tissues

bulk

short

I_2

II_2

IV_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
circMine: a comprehensive database to integrate, analyze and visualize human disease-related circRNA transcriptome.	10.1093/nar/gkab809	cancer infection cardiovascular disease neurological disease other diseases	adult	cell lines primary tissue cells	circMine provides Search and Browse modules for 136,871 circRNAs and 1,821,448 disease-transcriptome entries, with circRNA expression and analysis functions.

ISOexpresso

http://wiki.tgilab.org/ISOexpresso

Not accessible

2016

Human

brain

breast

colon

lung

prostate

tumor tissue

other tissues

bulk

short

I_1

I_2

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
ISOexpresso: a web-based platform for isoform-level expression analysis in human cancer.	10.1186/s12864-016-2852-6	cancer	adult	primary tumor cells normal tissue cells	ISOexpresso exposes known transcript isoforms, exon structures and per-isoform TPM across TCGA cancers and normal tissues, supporting differential isoform expression, major-isoform switching and tumor-specific isoform analysis.

DBTSS

https://dbtss.hgc.jp/

Accessible

2015

242

Human

Mouse

brain

heart

kidney

liver

thymus

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data.	10.1093/nar/30.1.328 10.1093/nar/gkm901 10.1093/nar/gkp1017 10.1093/nar/gku1080 10.1093/nar/gkr1005 10.3233/isb-00146	lung adenocarcinoma small-cell lung cancer	fetal adult	lung adenocarcinoma cell small-cell lung cancer cell	DBTSS's live help documents gene-keyword searches and TSS/Genome Viewers that display full-length-cDNA/RefSeq-linked transcript gene models and exon-intron context.

isoform.io

https://www.isoform.io/

Accessible

2022

Homo sapiens

brain

heart

liver

lung

other tissues

bulk

short

I_1

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Structure-guided isoform identification for the human transcriptome.	10.7554/elife.82556	cancer neurological disease	adult	unknown	isoform.io provides Isoform Search and open access to predicted structures for isoforms of 237,275 human transcripts, with transcript-level RefSeq and GENCODE matching.

Expression Atlas

https://www.ebi.ac.uk/gxa/home

Accessible

2024

Eukaryota

brain

lung

leaf

bulk

single_cell

short

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Expression Atlas update: insights from sequencing data at both bulk and single cell level.	10.1093/nar/gkad1021	cancer	unknown	neuron glial cell	Expression Atlas provides experiment browse and search and official help for transcript views with kallisto-derived per-transcript abundance in supported bulk studies.

PALS db

http://palsdb.ym.edu.tw/

Not accessible

2002

Homo sapiens

Mus musculus

unknown

bulk

short

I_1

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
PALS db: Putative Alternative Splicing database.	10.1093/nar/30.1.186	cancer genetic disease	unknown	unknown	PALS db searches human and mouse genes for predicted alternative-splicing sites, displays exon skipping and alternative donor or acceptor events, and links each event to supporting mRNA or EST alignments.

CircInteractome

https://circinteractome.irp.nia.nih.gov/

Accessible

2018

Homo sapiens

unknown

bulk

short

II_2

IV_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Analysis of Circular RNAs Using the Web Tool CircInteractome.	10.1007/978-1-4939-7562-4_4	cancer neurological disease	unknown	unknown	CircInteractome searches circRNAs and retrieves genomic and mature sequences, best-matching transcripts and RBP sites at circRNA junctions, with junction-specific primer tools.

lncSLdb

http://bioinformatics.xidian.edu.cn/lncSLdb

Not accessible

2018

Homo sapiens

Mus musculus

Drosophila melanogaster

unknown

bulk

short

I_2

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
lncSLdb: a resource for long non-coding RNA subcellular localization.	10.1093/database/bay085	cancer neurological disease	unknown	unknown	lncSLdb provides searchable individual lncRNA transcript IDs and genomic coordinates together with experimentally supported nucleus-to-cytoplasm relative expression ratios or localization images.

EASED

http://eased.bioinf.mdc-berlin.de/

Not accessible

2004

Human

Mouse

Rat

Cow

Arabidopsis thaliana

Caenorhabditis elegans

Drosophila melanogaster

Danio rerio

Xenopus laevis

brain

bulk

short

I_1

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
EASED: Extended Alternatively Spliced EST Database.	10.1093/nar/gkh136	cancer	adult embryo newborn juvenile	unknown	EASED provides searchable alternative splice forms, splice-site profiles and exon-boundary events, with transcript, tissue, developmental and disease filters.

RhesusBase2; NGS-oriented Molecular Evolution Gateway

https://rhesusbase.com/

Not accessible

2014

Rhesus macaque

Human

brain

cerebellum

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Evolutionary interrogation of human biology in well-annotated genomic framework of rhesus macaque.	10.1093/molbev/msu084	unknown	unknown	unknown	RhesusBase searches by RhesusBase Transcript ID and provides gene pages and a genome browser for refined macaque gene structures and transcript annotations.

ASPicDB

https://www.cineca.it/ASPicDB/

Accessible

2011

Human

brain

central nervous system

peripheral nervous system

eye

breast

colon

lung

bulk

short

I_1

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing.	10.1093/nar/gkq1073 10.1186/1471-2105-6-244	cancer	adult	normal cell tumor cell	The ASPicDB update describes web queries and graphical views of annotated alternative-splicing transcripts, splice sites and protein isoforms.

ECgene

http://genome.ewha.ac.kr/ECgene

Not accessible

2007

Human

Mouse

Rat

Caenorhabditis elegans

Drosophila melanogaster

Zebrafish

Dog

Chicken

Rhesus macaque

brain

bulk

short

I_1

I_2

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
ECgene: an alternative splicing database update.	10.1093/nar/gkl992	cancer	unknown	unknown	The ECgene update describes searchable alternative-splicing gene models, isoforms, ASviewer graphics and tissue-specific transcript expression across species.

TreeshrewDB

http://www.treeshrewdb.org/

Accessible

2014

Tupaia belangeri

brain

bulk

long

short

I_1

I_2

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Tree shrew database (TreeshrewDB): a genomic knowledge base for the Chinese tree shrew.	10.1038/srep07145	depression myopia hepatitis	adult	unknown	TreeshrewDB 3.0 offers gene/lncRNA searches and GBrowse for a long-read isoform-supported genome annotation, plus tissue and cell expression profiles.

iDog

https://ngdc.cncb.ac.cn/idog/

Accessible

2019

Canis lupus familiaris

Canis lupus

Cuon alpinus

hippocampus

bulk

single_cell

short

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
iDog: an integrated resource for domestic dogs and wild canids.	10.1093/nar/gky1041	mucopolysaccharidosis Wilson disease	adult	unknown	iDog documentation states that Kallisto quantifies transcripts and that transcript and gene TPM profiles are integrated and visualized through searchable expression modules.

FarmGTEx

https://www.farmgtex.org/

Accessible

2025

Cattle

Pig

Chicken

frontal cortex

cerebellum

hypothalamus

bulk

short

III_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
The Farm Animal Genotype-Tissue Expression (FarmGTEx) Project.	10.1038/s41588-025-02121-5	unknown	adult	unknown	FarmGTEx links browsable CattleGTEx and PigGTEx atlases containing cis- and trans-sQTLs across farm-animal tissues, plus additional transcriptomic regulatory variants.

Genexpress IMAGE Knowledge Base

http://idefix.upr420.vjf.cnrs.fr/EXPR++

Not accessible

1999

Human

brain

bulk

short

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
The Genexpress IMAGE knowledge base of the human brain transcriptome: a prototype integrated resource for functional and computational genomics.	10.1101/gr.9.12.1313	unknown	infant fetal adult	unknown	The dedicated knowledge-base site browsed cDNA clone clusters with sequence/map data and transcript-level expression profiles from brain and other tissues.

ChiTaRS 8.0

http://biosrv.org/chitars/

Accessible

2020

Human

Mouse

Drosophila melanogaster

Rattus norvegicus

Bos taurus

Saccharomyces cerevisiae

Sus scrofa

Danio rerio

unknown

bulk

short

I_1

I_2

II_2

IV_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
ChiTaRS 5.0: the comprehensive database of chimeric transcripts matched with druggable fusions and 3D chromatin maps.	10.1093/nar/gkz1025	cancer Alzheimer's disease schizophrenia dyslexia rheumatoid arthritis systemic lupus erythematosus	unknown	HCC1263 VCaP MDA-MB-361	The official ChiTaRS 8.0 database provides searchable gene-fusion and fusion records, breakpoint data, RNA-seq collections and downloadable chimeric-transcript data.

Echinobase

https://www.echinobase.org/echinobase

Accessible

2024

Strongylocentrotus purpuratus

Lytechinus variegatus

Patiria miniata

Acanthaster planci

Anneissia japonica

Asterias rubens

Lytechinus pictus

nervous system

neural tissue

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Echinobase: a resource to support the echinoderm research community.	10.1093/genetics/iyae002	unknown	neural development regeneration	unknown	Echinobase provides mRNA and CDS BLAST, gene search, gene-page reports and genome resources with browsable mRNA records and gene models.

Transcript View of H-InvDB;VarySysDB

http://h-invitational.jp/varygene/home.htm

Not accessible

2008

Human

brain

bulk

short

I_1

IV_4

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Distribution and effects of nonsense polymorphisms in human genes.	10.1371/journal.pone.0003393	unknown	unknown	unknown	The study maps polymorphisms onto 36,712 H-InvDB representative transcripts and makes the records browsable through Transcript View and VarySysDB.

ezQTL

https://analysistools.cancer.gov/ezqtl/

Accessible

2022

Human

brain

blood

lung

liver

heart

skeletal muscle

skin

adipose tissue

bulk

short

III_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
ezQTL: A Web Platform for Interactive Visualization and Colocalization of QTLs and GWAS Loci.	10.1016/j.gpb.2022.05.004	complex traits cancer	adult	mixed tissue cells	ezQTL hosts searchable public QTL sources including GTEx eQTLs and sQTLs and provides locus tables, visualizations and GWAS colocalization analyses.

H-Invitational Database; H-InvDB

http://www.h-invitational.jp/

Not accessible

2010

Human

brain

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
H-InvDB in 2009: extended database and data mining resources for human genes and transcripts.	10.1093/nar/gkp1020	unknown	unknown	unknown	H-InvDB supplied Navigation Search and APIs over 219,765 annotated human transcripts, including cDNA-derived gene models and transcript records.

QFbase

http://genebank.nibio.go.jp/qfbase

Not accessible

2008

Macaca fascicularis

cerebrum

cerebellum

testis

liver

bulk

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta.	10.1186/1471-2164-9-90	unknown	unknown	unknown	QFbase searches full-length macaque cDNA clones and maps them graphically onto the rhesus macaque genome in a UCSC Genome Browser, exposing transcript structures.

variant.imb.uq.edu.au

http://variant.imb.uq.edu.au/

Not accessible

2006

Mouse

unknown

bulk

short

I_1

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases.	10.1186/gb-2006-7-1-r5	unknown	unknown	unknown	The web database visualized each mouse kinase or phosphatase locus in genomic context, annotated transcript models, and counted alternative splice-junction support.

ChiTaRS 2.1

https://chitars.bioinfo.cnio.es/

Accessible

2015

Human

Mouse

Drosophila

Danio rerio

Bos taurus

Rattus norvegicus

Sus scrofa

Saccharomyces cerevisiae

brain

breast

prostate

blood

tumor tissue

other tissues

bulk

short

I_1

II_2

IV_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
ChiTaRS 2.1--an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts.	10.1093/nar/gks1041 10.1093/nar/gku1199	cancer genetic disease	adult	MCF7 LNCaP VCaP other cell lines	The official ChiTaRS 2.1 database provides Full collection & Search, Breakpoints and Junction Search for chimeric transcripts with RNA-seq-supported fusion junctions.

TREND-DB

https://shiny.imbei.uni-mainz.de/trend-db

Accessible

2021

Human

neuroblastoma

bulk

short

I_1

IV_5

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
TREND-DB-a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation.	10.1093/nar/gkaa722	neuroblastoma	neuronal differentiation	BE(2)-C neuroblastoma cells neuronally differentiated cells	The official TREND-DB repository documents interactive queries of APA regulators and genes plus internal and UCSC visualization of APA-affected target RNAs.

GExplore

https://genome.science.sfu.ca/gexplore/home.html

Accessible

2019

Caenorhabditis elegans

Caenorhabditis briggsae

nervous system

embryonic tissue

bulk

single_cell

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
The <i>C. elegans</i> embryonic transcriptome with tissue, time, and alternative splicing resolution.	10.1101/gr.243394.118	Parkinson's disease association	embryo larva adult	ciliated neuron non-ciliated neuron glial cell	Current GExplore documentation states that its gene database contains all splice variants and provides searchable gene/protein identifiers, including variant-specific entries.

TDP43-LOF-db

https://mcao051.github.io/uoa-scotter/

Accessible

2022

Human

Mouse

brain

bulk

short

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Transcriptional targets of amyotrophic lateral sclerosis/frontotemporal dementia protein TDP-43 - meta-analysis and interactive graphical database.	10.1242/dmm.049418	amyotrophic lateral sclerosis frontotemporal dementia	adult	neuron	The official Scotter Lab page embeds the TDP43 loss-of-function application for interactive differential exon-usage and splicing analysis in ALS/FTD datasets.

TDP43 LOF DB v2

https://mcao051.github.io/TDP_LOF_v2/

Accessible

2023

Human

brain

bulk

short

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
A panel of TDP-43-regulated splicing events verifies loss of TDP-43 function in amyotrophic lateral sclerosis brain tissue.	10.1016/j.nbd.2023.106245	amyotrophic lateral sclerosis	adult	neuron	The official Scotter Lab v2 page embeds the updated TDP-43 loss-of-function application for interactive exon-usage and splicing signatures in ALS brain data.

SpliceVarDB

https://splicevardb.org/

Accessible

2024

Human

clinical tissue

bulk

short

II_1

II_2

III_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
SpliceVarDB: A comprehensive database of experimentally validated human splicing variants.	10.1016/j.ajhg.2024.08.002	rare disease cancer	unknown	unknown	The live SpliceVarDB interface filters experimentally tested variants by gene, validation method and splice classification and displays genomic and transcript consequences.

SilkBase

https://silkbase.ab.a.u-tokyo.ac.jp/

Accessible

2022

Bombyx mori

Bombyx mandarina

Trilocha varians

Ernolatia moorei

Samia ricini

brain

fat body

midgut

silk gland

testis

ovary

bulk

short

I_1

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
SilkBase: an integrated transcriptomic and genomic database for Bombyx mori and related species.	10.1093/database/baac040	unknown	egg larva pupa adult	unknown	The live SilkBase portal provides keyword search, genome browser, downloadable gene models and transcriptomic/genomic resources for Bombyx and related species.

FL-circAS

https://cosbi.ee.ncku.edu.tw/FL-circAS

Accessible

2024

Human

Mouse

brain

cortex

bulk

long

I_1

I_2

II_1

II_2

III_1

IV_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
FL-circAS: an integrative resource and analysis for full-length sequences and alternative splicing of circular RNAs with nanopore sequencing.	10.1093/nar/gkad829	neuroblastoma	unknown	SH-SY5Y neuroblastoma cell	FL-circAS supports search and browse of 884,636 human and 115,173 mouse BSJs, full-length circRNA isoforms, isoform expression, and alternative-splicing entropy.

Express

http://www.iupui.edu/~sysbio/express

Accessible

2018

Mouse

lens

retina

bulk

short

I_1

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Express: A database of transcriptome profiles encompassing known and novel transcripts across multiple development stages in eye tissues.	10.1016/j.exer.2018.01.009	unknown	embryonic postnatal	lens epithelial cell lens fiber cell rod photoreceptor	Express lets users query transcript-level TPM and navigate known and novel mouse eye isoforms across developmental stages, with downloadable isoform values and browser views.

LncRBase V.2;ClinicLSNP

https://dibresources.jcbose.ac.in/zhumur/lncrbase2

Accessible

2021

Human

Mouse

Rat

Drosophila melanogaster

Danio rerio

Gallus gallus

Bos taurus

Caenorhabditis elegans

breast

ovary

cervix

bulk

short

I_2

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
LncRBase V.2: an updated resource for multispecies lncRNAs and ClinicLSNP hosting genetic variants in lncRNAs for cancer patients.	10.1080/15476286.2020.1833529	breast cancer ovarian cancer cervical cancer	unknown	cancer cell line	LncRBase V.2 searches individual transcript IDs; each transcript detail page reports tissue-wise expression values, establishing searchable transcript-level abundance rather than gene-only expression.

LncAS2Cancer

https://lncrna2as.cd120.com/

Not accessible

2021

Human

tumor

cancer cell line

bulk

single_cell

short

I_1

II_1

II_2

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
LncAS2Cancer: a comprehensive database for alternative splicing of lncRNAs across human cancers.	10.1093/bib/bbaa179	cancer	unknown	unknown	LncAS2Cancer supports search, browse, visualization, and download of 50,859 lncRNA alternative-splicing events across eight event types and over 30 cancers.

FLJ Human cDNA Database

https://flj.lifesciencedb.jp/top/

Accessible

2009

Human

cerebral cortex

bulk

short

I_1

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Identification and functional analyses of 11,769 full-length human cDNAs focused on alternative splicing.	10.1093/dnares/dsp022	Alzheimer disease	adult	unknown	The live FLJ Human cDNA Database provides versioned full-length cDNA accessions, downloads and database links for mapped human cDNA and alternative-transcript resources.

KTCNlncDB

http://rhesus.amu.edu.pl/KTCNlncDB

Accessible

2017

Human

cornea

bulk

short

I_2

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
KTCNlncDB-a first platform to investigate lncRNAs expressed in human keratoconus and non-keratoconus corneas.	10.1093/database/baw168	keratoconus	unknown	unknown	The live KTCNlncDB browses 16,331 corneal lncRNA transcripts, interaction searches, BLAST and downloads, with transcript-level expression from keratoconus and controls.

CanSplice

http://portal.dukecancerinstitute.org/cansplice

Not accessible

2021

Human

tumor

bulk

short

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Differential alternative RNA splicing and transcription events between tumors from African American and White patients in The Cancer Genome Atlas.	10.1016/j.ygeno.2021.02.020	cancer	adult	unknown	CanSplice interactively queries TCGA alternative RNA-splicing events by cancer, race, gene, and exon and visualizes percent-spliced-in differences and clinical associations.

MIsoMine

http://guanlab.ccmb.med.umich.edu/misomine

Not accessible

2015

Mouse

brain

heart

kidney

liver

lung

bulk

short

I_1

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
MIsoMine: a genome-scale high-resolution data portal of expression, function and networks at the splice isoform level in the mouse.	10.1093/database/bav045	unknown	unknown	unknown	MIsoMine provided a searchable mouse portal with splice-isoform expression profiles, functional annotations, and isoform-level coexpression networks.

CeNGEN splicing data portal

https://www.cengen.org/cengen-splicing-data-portal/

Accessible

2025

Caenorhabditis elegans

nervous system

bulk

short

I_2

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Alternative splicing across the C. elegans nervous system.	10.1016/j.cell.2021.06.023 10.1038/s41467-025-58293-5 10.1101/2024.05.16.594567	unknown	L4	neuron	CeNGEN links differential-splicing gene and neuron queries, transcript quantification, a raw-data genome browser and detailed alternative-splicing documentation.

GRCg7b chicken lncRNA-enriched gene atlas

https://gega.sigenae.org/

Accessible

2024

Gallus gallus

unknown

bulk

short

I_1

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues.	10.1038/s41598-024-56705-y	unknown	embryonic juvenile adult	unknown	The live GEGA atlas searches 78,323 chicken genes and exposes interactive gene-model characteristics, annotations and expression across 47 tissues.

Cats-I; Anicom American Shorthair 1.0

https://cat.annotation.jp/

Accessible

2025

Felis catus

cerebrum

cerebellum

bulk

long

short

I_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Chromosome-scale assembly with improved annotation provides insights into breed-wide genomic structure and diversity in domestic cats.	10.1016/j.jare.2024.10.023	unknown	adult	unknown	Cats-I provides Gene Fetcher, BLAST, and JBrowse access to the cat assembly and its Iso-Seq-supported gene and transcript annotations, including newly identified splice variants.

SFMetaDB

http://sfmetadb.ece.tamu.edu/

Not accessible

2017

Mus musculus

brain

heart

skeletal muscle

cell culture

bulk

short

III_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
SFMetaDB: a comprehensive annotation of mouse RNA splicing factor RNA-Seq datasets.	10.1093/database/bax071	unknown	unknown	C2C12 myoblast	SFMetaDB lets users query mouse splicing factors to retrieve curated knockdown, knockout or overexpression RNA-seq datasets for downstream differential-splicing analysis.

LSAT

https://www.bork.embl.de/LSAT/

Not accessible

2006

Eukaryota

nervous system

bulk

short

I_1

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
LSAT: learning about alternative transcripts in MEDLINE.	10.1371/journal.pcbi.0010010 10.1093/bioinformatics/btk044	unknown	unknown	unknown	The LSAT publication describes a public MEDLINE-mined knowledge base with gene searches, alternative-transcript mechanisms, isoform counts and tissue-specific splicing evidence.

ALE-HSA21

https://bioinfo.na.iac.cnr.it/ALE-HSA21

Accessible

2014

Human

brain

heart

placenta

bulk

short

I_1

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
AnaLysis of Expression on human chromosome 21, ALE-HSA21: a pilot integrated web resource.	10.1093/database/bau009	Down syndrome	fetal adult	unknown	ALE-HSA21 supported Transcript ID searches and organized roughly 500 splice variants with exon-intron structures and three-dimensional alternative-transcript models.

ADAS-viewer

http://genomics.chpc.utah.edu/AD

Not accessible

2021

Human

cerebellum

temporal cortex

dorsolateral prefrontal cortex

frontal pole

inferior frontal gyrus

parahippocampal gyrus

superior temporal gyrus

bulk

short

I_2

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
ADAS-viewer: web-based application for integrative analysis of multi-omics data in Alzheimer's disease.	10.1038/s41540-021-00177-7	Alzheimer's disease	adult	unknown	ADAS-viewer offered interactive transcript- and exon-level Alzheimer multi-omics views, including alternative-splicing PSI and differential exon or transcript expression.

DBATE

http://bioinformatica.uniroma2.it/DBATE

Accessible

2013

Human

brain

heart

kidney

liver

lung

bulk

short

I_1

I_2

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
DBATE: database of alternative transcripts expression.	10.1093/database/bat050	unknown	adult	unknown	DBATE allowed searches of alternative transcripts and displayed each splice variant's exon composition and individual FPKM expression across tissues and cell lines.

READ DB

http://darwin.soic.iupui.edu/

Not accessible

2015

Human

brain

heart

kidney

liver

lung

bulk

short

I_2

III_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Database of RNA binding protein expression and disease dynamics (READ DB).	10.1093/database/bav072	unknown	adult	unknown	READ DB was an accessible RBP resource whose gene pages reported expression for each protein-coding transcript across 16 Human Body Map tissues.

MiasDB

http://47.88.84.236/Miasdb

Not accessible

2016

Human

unknown

bulk

short

II_1

III_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
MiasDB: A Database of Molecular Interactions Associated with Alternative Splicing of Human Pre-mRNAs.	10.1371/journal.pone.0155443	cancer neurological disease	unknown	unknown	MiasDB let users search 938 molecular interactions regulating 173 human alternative-splicing events, with event type, tissue or disease context, and regulatory networks.

AS-CMC

https://www.pmrc.re.kr/ASCMC

Not accessible

2022

Human

unknown

bulk

short

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
AS-CMC: a pan-cancer database of alternative splicing for molecular classification of cancer.	10.1038/s41598-022-25584-6	cancer	adult	unknown	The AS-CMC publication documents a web database for subtype-specific alternative-splicing events, PSI distributions, phenotype associations and pan-cancer comparisons.

MetazExp

https://bioinfo.njau.edu.cn/metazExp

Accessible

2022

Metazoa

unknown

bulk

short

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
MetazExp: a database for gene expression and alternative splicing profiles and their analyses based on 53 615 public RNA-seq samples in 72 metazoan species.	10.1093/nar/gkab933	unknown	unknown	unknown	The official MetazExp endpoint is live but campus-VPN restricted during maintenance; MetazExp provides searchable rMATS alternative-splicing profiles with PSI values across 72 metazoans.

PolyASite Atlas

https://polyasite.unibas.ch/

Accessible

2025

642

Human

Mouse

Rat

Chicken

Zebrafish

Caenorhabditis elegans

brain

brain cortex

cerebellum

eye

bulk

single_cell

short

I_1

I_2

IV_5

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
PolyASite v3.0: a multi-species atlas of polyadenylation sites inferred from single-cell RNA-sequencing data.	10.1101/gr.132563.111 10.1093/nar/gkz918 10.1101/gr.202432.115 10.1093/nar/gkae1043	unknown	unknown	cerebellar granule cells Purkinje cells cerebellar granule cell progenitors	The live PolyASite search accepts gene symbols, Ensembl IDs or genomic regions and returns poly(A)-site usage with exonic, intronic, terminal-exon and alternative-splicing classifications.

The Lair

https://pachterlab.github.io/lair

Accessible

2016

Human

Mouse

unknown

bulk

short

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
The Lair: a resource for exploratory analysis of published RNA-Seq data.	10.1186/s12859-016-1357-2	spinal muscular atrophy breast cancer	unknown	motor neuron MCF-7 cell	The Lair browses published RNA-seq analyses and provides interactive kallisto/sleuth transcript-level abundance reanalyses across multiple transcriptomes.

CAS-viewer

http://genomics.chpc.utah.edu/cas

Not accessible

2018

Human

tumor

bulk

short

I_1

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
CAS-viewer: web-based tool for splicing-guided integrative analysis of multi-omics cancer data.	10.1186/s12920-018-0348-8	cancer	adult	unknown	CAS-viewer lets users browse AS transcript isoforms, select exon-skipping, intron-retention, and alternative-splice-site events, and inspect PSI with TCGA multi-omics data.

ISOdb

http://isodb.xieslab.org/

Not accessible

2018

Human

Mouse

Chicken

Atlantic cod

Arabidopsis thaliana

Gossypium barbadense

Triticum aestivum

Amborella trichopoda

infratentorial brain tissue

bulk

long

I_1

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
ISOdb: A Comprehensive Database of Full-Length Isoforms Generated by Iso-Seq.	10.1155/2018/9207637	ependymoma	unknown	unknown	ISOdb let users search genes for full-length Iso-Seq splice isoforms, novel AS events, exon-intron diagrams, and JBrowse transcript alignments.

RTTPG

https://rttpg.ibms.sinica.edu.tw/

Accessible

2022

Human

brain

heart

kidney

liver

lung

bulk

short

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Dominant transcript expression profiles of human protein-coding genes interrogated with GTEx dataset.	10.1038/s41598-022-10619-9	unknown	adult	unknown	The live RTTPG database searches human gene IDs or symbols and visualizes top-ranked transcript expression across more than fifty GTEx tissue types.

scTEA-db

https://www.sctea-db.org/

Accessible

2024

Human

central nervous system

blood

bone marrow

heart

liver

pancreas

skin

single_cell

short

I_1

I_2

II_1

IV_5

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
scTEA-db: a comprehensive database of novel terminal exon isoforms identified from human single cell transcriptomes.	10.1093/nar/gkad878	unknown	fetal	unknown	scTEA-db filters novel terminal exons by gene, tissue, cell type, dataset, and sample, then displays associated transcript isoforms and single-cell evidence.

circExp

https://bioinfo-minzhao.org/soft/circexp

Accessible

2021

Human

brain

bulk

short

I_2

II_2

IV_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
circExp database: an online transcriptome platform for human circRNA expressions in cancers.	10.1093/database/baab045	cancer glioblastoma multiforme	adult	glioblastoma cell	The live circExp portal searches circBase IDs, cytobands, experiments and parental genes and reports cancer circRNA back-splice endpoints and expression comparisons.

NeuroCirc

https://voineagulab.github.io/NeuroCirc

Accessible

2021

Human

brain

dorsolateral prefrontal cortex

bulk

short

I_2

II_2

IV_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
NeuroCirc: an integrative resource of circular RNA expression in the human brain.	10.1093/bioinformatics/btab230	unknown	adult	neuron	The live NeuroCirc site provides About and Search modules for interactive exploration of circRNA expression, circQTLs and back-splice coordinates across human brain datasets.

PmDscam database

http://pmdscam.dbbs.ncku.edu.tw/

Not accessible

2019

Penaeus monodon

hemocyte

pleopod

stomach

bulk

long

short

I_1

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
The gene structure and hypervariability of the complete Penaeus monodon Dscam gene.	10.1038/s41598-019-52656-x 10.21203/rs.2.9774/v1	unknown	immune system development	immune cell nerve cell	The publication documents a PmDscam BLAST database covering 175 exons and mutually exclusive exon variants that generate more than 21 million predicted isoform combinations.

CASA

http://www.splicedb.net/casa

Accessible

2022

Human

blood

lung

colon

bulk

short

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
CASA: a comprehensive database resource for the COVID-19 Alternative Splicing Atlas.	10.1186/s12967-022-03699-8	COVID-19 viral infection	unknown	unknown	CASA lets users search and browse five alternative-splicing event types, exon-inclusion ratios, and differential exons across 2,163 human RNA-seq samples and 59 datasets.

Cancer DEIso

http://cosbi4.ee.ncku.edu.tw/DEIso

Accessible

2021

Human

tumor

bulk

short

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Cancer DEIso: An integrative analysis platform for investigating differentially expressed gene-level and isoform-level human cancer markers.	10.1016/j.csbj.2021.09.005	cancer	adult	unknown	Cancer DEIso searches cancer-associated gene and isoform markers, isoform-level expression, stage comparisons and survival analyses across 21 cancer types.

LivestockExp

https://bioinfo.njau.edu.cn/livestockExp

Accessible

2022

Cattle

Sheep

Pig

Horse

Chicken

brain

skeletal muscle

heart

liver

testis

bulk

short

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
A web-based database server using 43,710 public RNA-seq samples for the analysis of gene expression and alternative splicing in livestock animals.	10.1186/s12864-022-08881-2 10.1101/769273	unknown	animal development	unknown	The current official LivestockExp endpoint is online but campus-VPN restricted during maintenance; the database provides gene-level alternative-splicing event searches, junction counts and PSI profiles.

LeukemiaDB

http://bioinfo.life.hust.edu.cn/LeukemiaDB

Not accessible

2023

Human

blood

bone marrow

bulk

short

I_2

II_1

IV_1

IV_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
A comprehensive landscape of transcription profiles and data resources for human leukemia.	10.1182/bloodadvances.2022008410	leukemia	unknown	leukemia cell line	LeukemiaDB includes a dedicated module in which users search and browse alternative-splicing events and their expression and molecular information across leukemia samples and cell lines.

TransTEx database

https://bmi.cewit.stonybrook.edu/transtexdb

Accessible

2024

Human

brain

testis

liver

pituitary

skeletal muscle

bulk

short

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
TransTEx: novel tissue-specificity scoring method for grouping human transcriptome into different expression groups.	10.1093/bioinformatics/btae475	unknown	adult	unknown	TransTEx provides searchable tissue-specific profiles for 199,166 human transcripts and reports transcript-isoform TPM abundance derived from GTEx samples.

DMBAS

http://173.234.48.5/DMBAS

Not accessible

2013

Mouse

brain

bulk

short

I_1

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Global detection and identification of developmental stage specific transcripts in mouse brain using subtractive cross-screening algorithm.	10.1016/j.ygeno.2013.05.001	unknown	embryonic postnatal adult	unknown	DMBAS gives each alternatively spliced mouse brain transcript an individual page with gene structure and splicing-site information across developmental stages.

ExoPLOT

http://retrogenomics3.uni-muenster.de:3838/exz-plot-d/

Accessible

2022

Human

brain

heart

kidney

liver

lung

testis

bulk

short

I_2

II_1

IV_6

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
ExoPLOT: Representation of alternative splicing in human tissues and developmental stages with transposed element (TE) involvement.	10.1016/j.ygeno.2022.110434	unknown	prenatal postnatal	unknown	ExoPLOT interactively screens transposable-element exonization and alternative-splicing read support across 313 human tissue and developmental RNA-seq samples.

TranscriptAchilles

https://biotecnun.unav.es/app/TranscriptAchilles

Accessible

2019

Human

central nervous system

bulk

short

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
TranscriptAchilles: a genome-wide platform to predict isoform biomarkers of gene essentiality in cancer.	10.1093/gigascience/giz021	cancer central nervous system astrocytoma grade IV	unknown	central nervous system astrocytoma cell line	The live TranscriptAchilles application has preloaded data for 412 cancer cell lines and supports cell-line selection, essential-gene analysis and transcript-expression biomarker prediction.

ChickenGTEx

https://ngdc.cncb.ac.cn/chickengtex/

Accessible

2026

Chicken

brain

amygdala

cerebellum

mesencephalon

retina

bulk

short

II_1

III_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
The ChickenGTEx portal: a pan-tissue catalogue of regulatory variants shaping transcriptomic and phenotypic diversity.	10.1038/s41588-025-02155-9 10.1093/nar/gkaf731 10.1038/s41467-025-67245-y	unknown	unknown	neural crest cell retinal cell cerebellar cell	ChickenGTEx supports variant, gene and tissue search and exposes alternative-splicing variation, exon expression and cis-sQTL browse modules.

Splicing Signature Database

—

Not accessible

2023

Human

tumor

bulk

short

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Splicing signature database development to delineate cancer pathways using literature mining and transcriptome machine learning.	10.1016/j.csbj.2023.02.052	cancer	adult	unknown	The publication documents database search and visualization of cancer alternative-splicing signatures, pathway rankings, PSI heatmaps and clinical profiles for individual events.

IDeAS

https://www.biosino.org/ideas

Not accessible

2024

Human

brain

bulk

short

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
IDeAS: an interactive database for dysregulated alternative splicing in cancers across Chinese and western patients.	10.1093/jmcb/mjad074	cancer glioma	adult	unknown	The official IDeAS endpoint is online but temporarily suspended for infrastructure upgrade and database optimization; IDeAS provides gene-level cancer AS-event queries and PSI profiles.

SASdb

http://www.gdbioinfo.top/sasdb/

Accessible

2026

Human

brain

heart

liver

lung

bulk

short

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
SASdb: a comprehensive database for sex-biased alternative splicing profiles in human tissues.	10.1186/s13293-026-00861-5	non-small cell lung cancer	adult	unknown	The official SASdb endpoint responds with the SASdb application title, and the database provides gene/tissue searches for sex-biased AS-event classes, PSI values and tissue-specific profiles.

NMD AS database

https://nadifkasrilab.shinyapps.io/SpliNEx

Accessible

2026

Human

brain

bulk

short

II_1

II_2

IV_4

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Mapping NMD-coupled alternative splicing in iPSC-derived brain cells: a resource for therapeutic discovery	10.64898/2026.01.19.700316	neurodevelopmental disorder	developmental	neural progenitor neuron	SpliNEx exposes gene expression, alternative-splicing searches, and event-detail views with usage, NMD sensitivity, splice junctions, and related events.

BigBrain RNA-seq Portal

https://bigbrain.nygenome.org/

Accessible

2025

Human

cortex

caudate

putamen

bulk

short

II_1

II_2

III_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Mapping genetic effects on splicing in ten thousand post-mortem brain samples reveals novel mediators of neurological disease risk	10.1101/2025.09.25.25336663	neurological disease	adult	neuron	The live BigBrain RNA-seq Portal provides dedicated sQTL, eQTL, edQTL, and download modules for interactive exploration of brain RNA-seq results.

iMPI

https://impi.omicsbio.info/

Accessible

2026

Human

brain

tumor

bulk

short

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
iMPI: An Integrative Database for MicroProteins Encoded by Intron Retention in Tumors.	10.1002/pmic.70142	cancer glioblastoma pediatric brain tumor	adult pediatric	cancer cell line	iMPI is a user-facing database of tumor introns retained as candidate coding iORFs, with searchable intron records and coding, proteomic, localization, and structure evidence.

RadSpliceDB

https://radsplicedb.com.cn/

Accessible

2025

Human

brain

tumor

bulk

short

I_1

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
RadSpliceDB: A Comprehensive Database of Radiotherapy Prognosis-Related Splicing Isoforms.	10.1177/15578666251363380	cancer glioblastoma lower-grade glioma radiotherapy response	adult	unknown	RadSpliceDB searches 49,587 radiotherapy-prognosis splicing events and 180,149 isoforms and reports splice type, exon coordinates, PSI, functional annotation, and survival results.

DIGGER 2.0

https://exbio.wzw.tum.de/digger/

Accessible

2025

Human

Mouse

unknown

bulk

short

I_1

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
DIGGER 2.0: digging into the functional impact of differential splicing on human and mouse disorders.	10.1093/nar/gkaa768 10.1093/nar/gkaf384	multiple sclerosis	unknown	unknown	DIGGER 2.0 provides queryable isoform-, exon- and network-level views and analyzes alternative-splicing events through exon-mapped interaction data.

scTML

http://sctml.xglab.tech/

Accessible

2025

Human

tumor

single_cell

short

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
scTML: a pan-cancer single-cell landscape of multiple mutation types.	10.1093/nar/gkae898	cancer	unknown	cancer cell patient-derived xenograft cell circulating tumor cell	The live scTML portal reports 75 datasets and 5,784 alternative-splicing entries and provides mutation, association, comparison, and download modules.

PerturbAtlas

https://perturbatlas.kratoss.site/

Accessible

2025

Eukaryota

astrocytes

forebrain neurons

whole brain

myeloid cells

cerebellum

brain endotheleium cells

nucleus accumbens

neurons

forebrain

ipsilateral midbrain

somatosensory cortex

microglia

hippocampus

forebrain synapse

cortex

blood brain barrier endothelial cells

back left brain

dorsal brain

forebrain hippocampus

endothelial cells from brain

hindbrain

frontal cortex

midbrain

brain stem

substantia nigra

cerebral cortex

brain macrophages

medial prefrontal cortex

orbital frontal cortex

dorsal forebrain

midbrain contralateral

hemibrain

pericytes from brain

olfactory bulb

hippocampal neurons

somatic compartment of dorsal root ganglion neurons

hypothalamus

sciatic nerve

bulk

short

I_2

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
PerturbAtlas: a comprehensive atlas of public genetic perturbation bulk RNA-seq datasets.	10.1093/nar/gkae851 10.1101/2024.07.28.605482	genetic perturbation	unknown	unknown	PerturbAtlas searches 122,801 samples across 7,778 studies and exposes alternative-splicing, PSI, splice-site, isoform, and differential-transcript results.

Cattle BodyMap Transcriptome Database

https://cattlegenomics.online/cattle_bodymap/

Accessible

2025

Bos taurus

muscle

liver

brain

heart

rumen

testis

bulk

short

I_1

I_2

II_1

IV_3

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
A Cattle BodyMap of Transcriptome across 52 Tissues and 3 Developmental Stages Reveals New Genetic Insights into Beef Production Traits	10.1101/2025.07.21.665934	beef production traits	fetal juvenile adult	unknown	The live Cattle BodyMap reports 52 tissues, three developmental stages, and 215,754 splicing events, with dedicated splicing and lncRNA search tabs.

SnapMine

https://snapmine.idies.jhu.edu/

Accessible

2025

—

Human

Mouse

brain

spinal cord

skeletal muscle

bulk

short

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Large-scale RNA-Seq mining reveals ciclopirox olamine induces TDP-43 cryptic exons.	10.1038/s41467-025-61812-7	amyotrophic lateral sclerosis frontotemporal dementia TDP-43 proteinopathy	adult	motor neuron	The live SnapMine interface provides Junction PSI Query and Gene Expression Query tabs, coordinate fields, dataset selection, and Calculate PSI controls.

Human Neural Retina Proteogenomic Atlas

https://genome-euro.ucsc.edu/s/tabeariepe/retina_atlas

Accessible

2024

—

Human

neural retina

bulk

long

short

I_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
A proteogenomic atlas of the human neural retina	10.3389/fcell.2024.1341005	inherited retinal disease	adult	photoreceptor cell bipolar cell ganglion cell Müller glial cell	The authors' UCSC session exposes nearly 60,000 long-read neural-retina transcript isoforms with known and novel splice-junction structures and proteomic-support tracks.

SexAnnoDB

https://ccsm.uth.edu/SexAnnoDB

Accessible

2024

Human

tumor

bulk

short

II_1

III_1

III_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
SexAnnoDB, a knowledgebase of sex-specific regulations from multi-omics data of human cancers.	10.1186/s13293-024-00638-8	cancer	adult	unknown	The live SexAnnoDB provides gene, drug, cancer, and help searches and documents exon-skipping PSI, cis-sQTL, sQTM, and RBP-exon-skipping networks.

Human Cortex Transcript Atlas

—

Not accessible

2024

Human

cerebral cortex

bulk

long

I_1

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
An atlas of expressed transcripts in the prenatal and postnatal human cortex	10.1101/2024.05.24.595768	neurodevelopmental disorder	prenatal postnatal adult aging	cortical neuron glial cell	The study reports an online atlas of full-length human cortical transcript structures and abundance from prenatal life to old age, including novel isoforms and coding sequences.

HumanMultiomics

https://canceddalab.shinyapps.io/DShuman

Accessible

2024

Human

cerebral cortex

hippocampus

bulk

short

I_2

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Integrative multi-omic analysis reveals conserved cell-projection deficits in human Down syndrome brains.	10.1016/j.neuron.2024.05.002	Down syndrome	adult	unknown	The live HumanMultiomics Shiny app includes Gene, Transcript, Protein, miRNA, and Alternative splicing tabs for Down-syndrome human brain data.

CAFuncAPA

https://relab.xidian.edu.cn/CAFuncAPA/

Accessible

2023

Human

brain

tumor

bulk

short

I_1

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
CAFuncAPA: a knowledgebase for systematic functional annotations of APA events in human cancers.	10.1093/narcan/zcad004	cancer glioblastoma lower-grade glioma	adult	unknown	The live CAFuncAPA homepage provides cancer-type and gene search plus APA-event functional views, including splicing-factor effects, expression and downstream analyses.

extended catalogue of TASS

https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hubUrl=https%3A%2F%2Fraw.githubusercontent.com%2Fmagmir71%2Ftrackhubs%2Fmaster%2FTASShub.txt

Accessible

2020

—

Human

brain

heart

liver

lung

skeletal muscle

testis

bulk

short

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
An extended catalogue of tandem alternative splice sites in human tissue transcriptomes	10.1101/2020.09.11.292722	unknown	unknown	unknown	The TASS track hub loads into the official UCSC Genome Browser, where users can search genomic loci and browse tandem alternative donor and acceptor sites with tissue evidence.

PsyMuKB

https://psymukb.net/

Accessible

2019

Human

Mouse

brain

cerebral cortex

bulk

single_cell

short

I_1

I_2

III_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
PsyMuKB: A <i>De Novo</i> Variant Knowledge Base Integrating Transcriptional and Translational Information to Identify Isoform-specific Mutations in Developmental Disorders	10.1101/715813	developmental disorder neuropsychiatric disorder	brain development	neuron neural progenitor cell	The live PsyMuKB searches variants and disorders, maps mutations to alternatively spliced mRNA/protein isoforms, and reports brain developmental and cell-type expression.

Developing Human Brain Transcript Browser

https://sciso.gandallab.org/

Accessible

2024

Human

neocortex

cortical plate

germinal zone

bulk

single_cell

long

short

I_1

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Developing Human Brain Transcript Browser	10.1101/2023.03.25.534016 10.1126/science.adh7688	neurodevelopmental and neuropsychiatric disorders	mid-gestation post-conception weeks 15-17	neuron neural progenitor cell glial cell	The live browser accepts gene queries and exposes bulk and single-cell full-length transcript isoforms with isoform-level developing-neocortex cell types.

Evo-devo Alternative Splicing

https://apps.kaessmannlab.org/alternative-splicing

Accessible

2021

161

Human

Rhesus macaque

Mouse

Rat

Rabbit

Opossum

Chicken

forebrain

hindbrain

heart

kidney

liver

ovary

testis

bulk

short

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Evo-devo: Alternative splicing	10.1038/s41588-021-00851-w	unknown	embryonic fetal juvenile adult	unknown	The live Evo-devo Shiny app supports species, gene or genomic-region searches, alternative-splicing type filters, dPSI thresholds, and developmental cross-species exploration.

Nova regulates brain-specific splicing to shape the synapse

https://splicing.rockefeller.edu/

Accessible

2005

543

Mouse

neocortex

cerebellum

midbrain

spinal cord

thymus

spleen

bulk

short

I_1

II_1

II_2

III_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Nova regulates brain-specific splicing to shape the synapse	10.1038/ng1610	unknown	unknown	unknown	The Rockefeller Nova splicing database provides Search Gene, Raw Data, Tissue Specificity, Comparative Data, Validated Exons, and Nova-2 regulated-network modules.

Setbp1S858R Alternative Splicing Shiny App

https://lasseignelab.shinyapps.io/setbp1_as/

Accessible

2026

Mouse

cerebral cortex

kidney

single_cell

short

I_1

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Setbp1S858R mouse brain	10.1101/2024.06.26.600823 10.1242/dmm.052402	Schinzel-Giedion syndrome	juvenile	inhibitory neuron excitatory neuron astrocyte oligodendrocyte microglia renal epithelial cell	The live Setbp1 Shiny app provides gene-expression and splice-junction UMAPs, alternative-splicing summaries, pseudobulk junction usage, and transcript models.

SplicingAD

https://diseaselinks.com/splicingad

Accessible

—

Human

Mouse

dorsolateral prefrontal cortex

inferior frontal gyrus

temporal cortex

substantia nigra

bulk

short

I_2

II_1

III_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
SplicingAD	—	Alzheimer disease	adult aging	neuron glial cell	SplicingAD is a live Alzheimer alternative-splicing database with Datasets, DiffSplicing, sQTL, Enrichment, and Download modules covering isoform expression, isoform ratios, and splicing events.

Brain RNA Isoform Seq

https://ebbertlab.com/brain_rna_isoform_seq.html

Accessible

2024

Human

dorsolateral frontal cortex

bulk

long

short

I_1

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
RNA isoform/transcript expression in human dorsolateral frontal cortex	10.1038/s41587-024-02245-9	Alzheimer disease	adult aging	unknown	The live Ebbert Lab Brain RNA Isoform Seq page embeds the human dorsolateral frontal cortex isoform browser for full-length RNA isoform structures and abundance.

Allen Cell Types Database

https://celltypes.brain-map.org/overview

Accessible

2019

1541

Homo sapiens

Mus musculus

middle temporal gyrus

primary motor cortex

primary visual cortex

anterior cingulate gyrus

primary somatosensory cortex

primary auditory cortex

hippocampus

lateral geniculate nucleus

single_cell

short

I_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Conserved cell types with divergent features in human versus mouse cortex	10.1038/s41586-019-1506-7	Alzheimer's disease	adult	excitatory neurons inhibitory neurons GABAergic neurons glutamatergic neurons non-neuronal cells	Browsable single-cell and single-nucleus brain expression profiles, cell taxonomies, downloads and genomic read-pileup tracks for human and mouse cortical datasets.

Gene Expression Nebulas (GEN)

https://ngdc.cncb.ac.cn/gen/

Accessible

2022

Homo sapiens

Mus musculus

Macaca fascicularis

Macaca mulatta

Callithrix jacchus

Drosophila melanogaster

Rattus norvegicus

Danio rerio

Bos taurus

Caenorhabditis elegans

Oryza sativa

Glycine max

Arabidopsis thaliana

Saccharomyces cerevisiae

Plasmodium falciparum

brain

dorsolateral prefrontal cortex

cerebral cortex

forebrain

hippocampus

brainstem

liver

skin

kidney

leaf

root

seed

bulk

single_cell

short

I_2

II_1

II_2

IV_1

IV_6

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels	10.1093/nar/gkab878	Alzheimer's disease autism spectrum disorder meningitis COVID-19 breast cancer lung cancer diabetes	iPSC neural differentiation day 0 iPSC neural differentiation day 11 iPSC neural differentiation day 31	iPSC-derived neural progenitor T cell B cell	Searchable cross-species portal integrating bulk and single-cell RNA-seq, isoform abundance, alternative-splicing, circRNA-expression and RNA-editing profiles with curated metadata.

Full-length transcript sequencing of human and mouse identifies widespread isoform diversity and alternative splicing in the cortex

http://genome.exeter.ac.uk/build/index.html

Accessible

2021

147

Homo sapiens

Mus musculus

cerebral cortex

prefrontal cortex

frontal cortex

hippocampus

striatum

bulk

long

short

I_1

I_2

II_1

II_2

IV_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing	10.1016/j.celrep.2021.110022	Alzheimer's disease autism spectrum disorder schizophrenia	fetal adult	neurons oligodendrocytes glial cells	Historical cortical isoform viewer with full-length transcript structures, abundance, splice junctions, developmental transcript usage and fusion transcripts.

APPRIS

https://appris.bioinfo.cnio.es/#/seeker

Accessible

2022

Homo sapiens

Pan troglodytes

Mus musculus

Rattus norvegicus

Sus scrofa

Bos taurus

Gallus gallus

Danio rerio

Drosophila melanogaster

Caenorhabditis elegans

frontal cortex

nervous tissue

bulk

short

I_1

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
APPRIS: selecting functionally important isoforms	10.1093/nar/gkab1058	unknown	unknown	unknown	Searchable database annotating alternative coding splice isoforms with structural, functional and conservation evidence and selecting principal isoforms.

isoCirc

https://genome.ucsc.edu/s/xinglab_chop/isoCirc

Accessible

2021

124

Homo sapiens

adipose

adrenal gland

blood

brain

heart

kidney

liver

lung

prostate

skeletal muscle

smooth muscle

testis

bulk

long

short

I_1

I_2

II_2

IV_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
isoCirc catalogs full-length circular RNA isoforms in human transcriptomes	10.1038/s41467-020-20459-8	unknown	unknown	HEK293 peripheral leukocytes	Browsable UCSC catalog of 107,147 full-length circRNA isoforms from 12 pooled human tissues and HEK293 cells, including back-splice junctions and tissue abundance.

ThorAxe

https://www.lcqb.upmc.fr/Ases

Accessible

2021

Homo sapiens

Gorilla gorilla

Macaca mulatta

Monodelphis domestica

Rattus norvegicus

Mus musculus

Bos taurus

Sus scrofa

Ornithorhynchus anatinus

Xenopus tropicalis

Danio rerio

Caenorhabditis elegans

brain

muscle

bulk

short

I_1

II_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Assessing conservation of alternative splicing with evolutionary splicing graphs	10.1101/gr.274696.120	unknown	unknown	unknown	The live Ases server runs ThorAxe from gene or Ensembl identifiers and returns cross-species transcript paths, S-exon models, AS event tables and evolutionary splicing graphs.

circASbase

http://reprod.njmu.edu.cn/cgi-bin/circASbase/

Accessible

2025

—

Homo sapiens

Mus musculus

Rattus norvegicus

Macaca mulatta

Oryctolagus cuniculus

Bos taurus

Sus scrofa

Gallus gallus

Danio rerio

Apis mellifera

Drosophila melanogaster

Arabidopsis thaliana

Oryza sativa

unknown

bulk

long

short

I_1

II_1

II_2

IV_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
circASbase: A Comprehensive Database of Alternative Splicing Events in circRNAs	10.1093/gpbjnl/qzaf121	unknown	unknown	unknown	Searchable database of 884,047 full-length circRNAs and 452,129 alternative-splicing events from 581 RNase R-treated RNA-seq samples across 13 species.

ENACTdb

https://www.iscbglab.in/enactdb/

Accessible

2024

Caenorhabditis elegans

Drosophila melanogaster

Danio rerio

Mus musculus

Homo sapiens

unknown

bulk

short

I_1

II_1

II_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Exon nomenclature and classification of transcripts database (ENACTdb): a resource for analyzing alternative splicing mediated proteome diversity	10.1093/bioadv/vbae157	unknown	unknown	unknown	Gene-searchable exon-centered database serving RefSeq transcript isoforms, exon structures, AS annotations, splice-site variation codes, intron retention and protein mappings for five organisms.

SpliceAI Lookup

https://spliceailookup.broadinstitute.org/

Accessible

2019

2408

Homo sapiens

blood

brain cortex

muscle

bulk

short

I_1

II_1

II_2

III_2

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
Predicting Splicing from Primary Sequence with Deep Learning	10.1016/j.cell.2018.12.015	unknown	unknown	fibroblasts lymphoblastoid cell lines	Variant-query service running SpliceAI, Pangolin and SAI-10k to return transcript-specific acceptor or donor scores, predicted consequences, reference transcript models and IGV.js tracks.

ASVirus

https://bddg.hznu.edu.cn/asvirus/

Accessible

2025

Blattella germanica

Bos taurus

Camelus dromedarius

Canis lupus familiaris

Tupaia belangeri chinensis

Chlorocebus aethiops

Coturnix japonica

Equus caballus

Felis catus

Gallus gallus

Homo sapiens

Laodelphax striatellus

Lates calcarifer

Macaca leonina

Macrobrachium nipponense

Mesocricetus auratus

Mus musculus

Oncorhynchus mykiss

Ovis aries

Raphanus sativus

Rattus norvegicus

Sus scrofa

blood

bone

brain

bronchial tissue

cervix

connective tissue

endometrium

eye

foreskin

heart

intestinal tract

kidney

liver

lung

lymph

mammary gland

muscle

nose

ovary

peripheral nervous system

peritoneum

pleura

skin

spleen

thymus

trachea

bulk

short

I_1

II_1

II_2

III_1

Title	Doi	Disease Association	Developmental Association	Cell Type	Description
ASVirus: A Comprehensive Knowledgebase for the Viral Alternative Splicing	10.1021/acs.jcim.4c02214	viral infectious diseases	embryo fetal	astrocytes bronchial epithelial cells fibroblasts glial cells macrophages monocytes neurons natural killer cells peripheral blood mononuclear cells T cells T helper 1 cells	Curated knowledgebase of virus-associated AS in viral and host genes with searchable events, canonical transcripts, splice variants, exons, regulatory factors, methods and references.

Search for Alternative Splicing Databases

Keywords: (Default: all databases)