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Alternative splicing databases | RNA modification data analysis

Alternative splicing (AS) is a post-transcriptional regulatory mechanism for gene expression regulation. Splicing decisions are affected by the combinatorial behavior of different splicing factors that bind to multiple binding sites in exons and…
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Yeast Intron…
Dataset

Yeast Intron Database

Gathers information about the spliceosomal introns of the yeast Saccharomyces…

Gathers information about the spliceosomal introns of the yeast Saccharomyces cerevisiae. Yeast Intron Database make an inventory of known spliceosomal introns in the yeast genome and documented used…

Manihot…
Dataset

Manihot esculenta

Offers a gene annotation of Manihot esculenta also known as cassava. The…

Offers a gene annotation of Manihot esculenta also known as cassava. The Manihot esculenta database is an Illumina-based assembly from the same genotype, AM560-2. The scaffolds have been anchored…

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EID
Dataset

EID Exon-Intron Database

Offers a comprehensive and convenient dataset of sequences for computational…

Offers a comprehensive and convenient dataset of sequences for computational biologists who study exon-intron gene structures and pre-mRNA splicing. The collection of exons and introns has been…

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SpliceInfo
Dataset

SpliceInfo

Provides occurrences of alternative-splicing (AS) modes in human genome,…

Provides occurrences of alternative-splicing (AS) modes in human genome, including exon skipping, 5’-alternative splicing, 3’-alternative splicing and intron retention. SpliceInfo uses comparison…

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U12DB
Dataset

U12DB U12 Intron Database

Contains the U12-type introns of completely sequenced eukaryotic genomes. U12DB…

Contains the U12-type introns of completely sequenced eukaryotic genomes. U12DB uses queries constructed of a combination of text fields, drop-down lists, radio buttons and check boxes. It was…

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ASG
Web

ASG Alternative Splicing Gallery

Integrates all transcripts derived from a gene into a single splicing graph.…

Integrates all transcripts derived from a gene into a single splicing graph. ASG permits users to display the splicing graph to assemble transcripts and to access their sequences. This tool…

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HOLLYWOOD
Dataset

HOLLYWOOD

This database was built upon genomic annotation of splicing patterns of known…

This database was built upon genomic annotation of splicing patterns of known genes derived from spliced alignment of complementary DNAs (cDNAs) and expressed sequence tags. Hollywood was implemented…

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AtRTD-QUASI
Dataset
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Spliceosome…
Dataset

Spliceosome Database

A database of spliceosome-associated proteins and snRNAs. SpliceosomeDB…

A database of spliceosome-associated proteins and snRNAs. SpliceosomeDB provides tools to search for spliceosome genes/proteins based on several characteristics including name(s), complex…

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H-DBAS
Dataset

H-DBAS Human-transcriptome DataBase for Alternative Splicing

A specialized database for human alternative splicing (AS) based on…

A specialized database for human alternative splicing (AS) based on H-Invitational full-length cDNAs. With the unique experimental data closely connected with intensively curated cDNA information,…

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DBASS
Dataset

DBASS

A database of new exon boundaries induced by pathogenic mutations in human…

A database of new exon boundaries induced by pathogenic mutations in human disease genes. This resource will be useful for fine-tuning splice-site prediction algorithms, better definition of…

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SynoR
Web

SynoR Genome Miner for Synonymous Regulation

Detects synonymous regulatory elements (SREs) in vertebrate genomes. SynoR is…

Detects synonymous regulatory elements (SREs) in vertebrate genomes. SynoR is based on conserved transcription factor binding sites (cTFBS) and performs genome scans for regulatory elements (REs)…

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TCGASpliceSeq
Dataset

TCGASpliceSeq

A web-based resource that provides a quick, user-friendly, highly visual…

A web-based resource that provides a quick, user-friendly, highly visual interface for exploring the alternative splicing patterns of TCGA tumors. Percent Spliced In (PSI) values for splice events on…

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RASE
Algorithm

RASE Recognition of alternatively Spliced Exons in C. elegans

Provides a support vector machine (SVM) kernel which aims to classify sequences…

Provides a support vector machine (SVM) kernel which aims to classify sequences by motifs. RASE is composed of two algorithms which allows users to identify hypothetic spliced exons thanks to…

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HEXEvent
Dataset

HEXEvent

A free database that provides a list of human internal exons and reports all…

A free database that provides a list of human internal exons and reports all their known splice events based on EST information from the UCSC Genome Browser . This list can be restricted by the user…

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GeneTack
Dataset

GeneTack

A database containing genes with frameshifts (fs-genes) predicted by GeneTack.…

A database containing genes with frameshifts (fs-genes) predicted by GeneTack. The database includes 206 991 fs-genes from 1106 complete prokaryotic genomes and 45 295 frameshifts predicted in…

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ASIP
Desktop

ASIP Alternative Splicing in Plants

Serve as a starting point for the community to perform additional experiments,…

Serve as a starting point for the community to perform additional experiments, including high-throughput methods such as oligonucleotide microarrays studies, to identify functional alternative…

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Plant…
Dataset

Plant Alternative Splicing Database

A catalog of alternatively splicing (AS) events in cereal crops. The specific…

A catalog of alternatively splicing (AS) events in cereal crops. The specific pages associated with the cereal plants offer several end-users functionalities such as querying using the PUT ID, gene…

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SpliceProt
Dataset

SpliceProt

Provides predicted alternative spliced variants translated in silico and based…

Provides predicted alternative spliced variants translated in silico and based on experimental human transcriptomic data. SpliceProt applies the ternary matrix methodology to reconstruct the…

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DEDB
Dataset

DEDB Drosophila melanogaster Exon Database

A database of Drosophila melanogaster exons obtained from FlyBase arranged in a…

A database of Drosophila melanogaster exons obtained from FlyBase arranged in a splicing graph form that permits the creation of simple rules allowing for the classification of alternative splicing…

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ASTD
Dataset

ASTD Alternative Splicing and Transcript Diversity

A value-added database of alternative splice events. ASD resources have now…

A value-added database of alternative splice events. ASD resources have now closed. Alternative splicing data has been incorporated into the Ensembl and Ensembl Genomes projects, which offer access…

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MiasDB
Dataset

MiasDB

Provides a description of molecular interactions associated with human…

Provides a description of molecular interactions associated with human alternative splicing (AS) events. MiasDB covers 938 interactions between human splicing factors, RNA elements, transcription…

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ASpedia
Dataset

ASpedia Alternative Splicing Encyclopedia

Offers an alternative splicing (AS) annotation system integrating heterogeneous…

Offers an alternative splicing (AS) annotation system integrating heterogeneous genomic information. ASpedia is a comprehensive human database that encompasses genomic features and isoform-level…

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VastDB
Dataset

VastDB Vertebrate Alternative Splicing and Transcription Database

Gathers data about regulation and functional associations of Alternative…

Gathers data about regulation and functional associations of Alternative Splicing (AS) events. VastDB provides information from about 1,470 independent RNA-seq datasets including 108 human, 139…

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SFMetaDB
Dataset

SFMetaDB

Provides metadata of RNA-Seq datasets related with splicing factors with either…

Provides metadata of RNA-Seq datasets related with splicing factors with either loss- or gain-of-function experiments. SFMetaDB presents the Accession ID, description, the number of samples,…

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IRBase
Dataset

IRBase

Offers the access of over 2000 human samples. IRBase offers an online database…

Offers the access of over 2000 human samples. IRBase offers an online database of intron retention (IR). This resource permits to assess a specified intron retention event within a tissue/cell type…

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Database for…
Dataset

Database for Bacterial Group II Introns

Provides a catalogue of full-length, non-redundant group II introns present in…

Provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank. The Database for Bacterial Group II Introns website is divided into three sections.…

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ProSAS
Dataset

ProSAS Protein Structure and Alternative Splicing

Provides a unified resource to analyze the effects of alternative splicing…

Provides a unified resource to analyze the effects of alternative splicing events on the structure of the resulting protein isoforms. ProSAS comprehensively annotates protein structures for several…

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FAST DB
Dataset

FAST DB

Designed to facilitate studies that integrate transcriptional and…

Designed to facilitate studies that integrate transcriptional and post-transcriptional events to investigate the expression regulation of human gene products.

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SASD
Dataset

SASD Synthetic Alternative Splicing Database

Allows users to detect alternative splicing isoforms and interpret them at the…

Allows users to detect alternative splicing isoforms and interpret them at the context of disease, drug, pathway, and custom gene or organ specificity set with maximum coverage and exclusive focus on…

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intropolis
Dataset

intropolis

A list of exon-exon junctions. We aligned 21,504 publicly available…

A list of exon-exon junctions. We aligned 21,504 publicly available Illumina-sequenced human RNA-seq samples from the Sequence Read Archive (SRA) to the human genome and compared detected exon-exon…

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Brain RNA-seq
Dataset

Brain RNA-seq

A transcriptome database for these eight cell types by RNA sequencing and used…

A transcriptome database for these eight cell types by RNA sequencing and used a sensitive algorithm to detect alternative splicing events in each cell type. Bioinformatic analyses identified…

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TassDB
Dataset

TassDB TAndem Splice Site DataBase

Stores extensive data about alternative splice events at donors and acceptors,…

Stores extensive data about alternative splice events at donors and acceptors, both confirmed and unconfirmed cases. TassDB offers a user-friendly interface to search for specific genes or for genes…

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EDAS
Dataset

EDAS EST Derived Alternative Splicing database

A database of alternatively spliced human genes, contains data on the alignment…

A database of alternatively spliced human genes, contains data on the alignment of proteins, mRNAs, and EST. EDAS contains information on all exons and introns observed, as well as elementary…

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Kassiopeia
Web

Kassiopeia

A database and web application for the generation, storage, and presentation of…

A database and web application for the generation, storage, and presentation of genome-wide analyses of mutually exclusive exomes. Kassiopeia provides access to the mutually exclusive exomes of…

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alternativeSpli…
Dataset

alternativeSplicingEvents.hg19

Gathers alternative splicing events extracted from MISO, VAST-TOOLS, SUPPA and…

Gathers alternative splicing events extracted from MISO, VAST-TOOLS, SUPPA and rMATS. alternativeSplicingEvents.hg19 includes a repository containing Skipped Exon (SE), Mutually Exclusive Exon (MXE),…

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SPLINTER
Desktop

SPLINTER

Analyses alternative splicing sites, interpret outcomes based on sequence…

Analyses alternative splicing sites, interpret outcomes based on sequence information, select and design primers for site validation and give visual representation of the event to guide downstream…

KIR
Dataset

KIR Kiwifruit Information Resource

Hosts a wide range of kiwifruit genomics and genetics datasets based on the…

Hosts a wide range of kiwifruit genomics and genetics datasets based on the latest and most accurate genome annotation. KIR aims to be a comprehensive online platform for users to search, visualize,…

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MIsoMine
Dataset

MIsoMine

An integrated data portal for isoform-level expression, function and network…

An integrated data portal for isoform-level expression, function and network analysis in the mouse. First, MIsoMine allows retrieval of top co-expressed isoforms in diverse tissues and experimental…

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ERISdb
Dataset

ERISdb

A database of plant splice sites and splicing signals. ERISdb is probably the…

A database of plant splice sites and splicing signals. ERISdb is probably the most comprehensive database of plant splice sites and splicing signals.

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Alternative…
Dataset

Alternative Splicing in SR Genes

Offers the extent of Alternative Splicing (AS) in serine/arginine-rich (SR)…

Offers the extent of Alternative Splicing (AS) in serine/arginine-rich (SR) genes based on a splice graph approach. AS in SR Genes is a database and the result of a large-scale comparative analysis…

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DBATE
Dataset

DBATE DataBase of Alternative Transcripts Expression

A web-based repository storing expression values and functional annotation of…

A web-based repository storing expression values and functional annotation of alternative splicing variants. The possibility to perform complex queries by cross-referencing different functional…

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Cortex AS
Dataset

Cortex AS

A database of known and novel AS events in the brain. Known AS events refers to…

A database of known and novel AS events in the brain. Known AS events refers to the AS events detected in existing gene models, cDNAs and ESTs. Novel AS events refers to the AS events for which at…

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Primate…
Dataset

Primate Orthologous Exon Database

Provides a catalog of unique, non-overlapping, orthologous exon regions in the…

Provides a catalog of unique, non-overlapping, orthologous exon regions in the genomes of human, chimpanzee, and rhesus macaque. The database can be used in analysis of multi-species RNA-seq…

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ASAP
Dataset

ASAP Alternative Splicing Annotation Project

Provides genome-wide alternative splicing analyses for insect, 15 vertebrate,…

Provides genome-wide alternative splicing analyses for insect, 15 vertebrate, and other animal species. ASAP supplies comparative genomics information in order to compare alternative splicing and…

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PALS db
Dataset

PALS db Putative Alternative Splicing database

Provides a collection of Putative Alternative Splicing (PALS). PALS db is an…

Provides a collection of Putative Alternative Splicing (PALS). PALS db is an online resource that furnishes several keyword search methods, such as identification numbers. It offers average 20.000…

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ECgene
Dataset

ECgene

It was developed to provide functional annotation for alternatively spliced…

It was developed to provide functional annotation for alternatively spliced genes. The user interfaces for functional and expression analyses have been substantially improved.

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SpliceAid-F
Dataset

SpliceAid-F

Collects into a unique resource several heterogeneous information about…

Collects into a unique resource several heterogeneous information about splicing regulatory proteins, their binding sites and context-specific activity. Information of binding sites includes the…

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ASPicDB
Dataset

ASPicDB

A database designed to provide access to reliable annotations of the…

A database designed to provide access to reliable annotations of the alternative splicing pattern of human genes, obtained by ASPic algorithm, and to the functional annotation of predicted isoforms.

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ASTRA
Dataset

ASTRA Alternative Splicing and TRanscription Archives

Stores the patterns (e.g. cassette type) of alternative splicing and…

Stores the patterns (e.g. cassette type) of alternative splicing and transcriptional initiation (ASTI). ASTRA detects these patterns with an algorithm that converts alignments between human genomic…

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SpliceDisease
Dataset

SpliceDisease

A database integrating RNA splicing and disease associations. SpliceDisease…

A database integrating RNA splicing and disease associations. SpliceDisease provides information including the change of the nucleotide in the sequence, the location of the mutation on the gene, the…

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BBBomics
Dataset

BBBomics Blood Brain Barrier omics

A comprehensive portal for blood-brain barrier transcriptomics data, obtained…

A comprehensive portal for blood-brain barrier transcriptomics data, obtained by sequencing mRNA (mRNA-seq) and microRNA (miRNA-seq) of polarized hCMEC/D3 cell monolayers. This data encompasses…

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ASMD
Dataset

ASMD Alternative Splicing Mutation Database

Represents a collection of small internal exonic mutations. The ASMD web site…

Represents a collection of small internal exonic mutations. The ASMD web site allows user to explore the connections between mutations and features of their surrounding sequences. This includes…

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