H-DBAS - Human-transcriptome DataBase for Alternative Splicing

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Analysis pages: Comparative genomics analysis, RNA-Seq analysis

H-DBAS is a unique database of alternative splicing (AS) based on H-InvDB. The features of H-DBAS is as follows;

Representative AS variants (RASVs) were identified from 8 data sets consist of 6 mammalian model organisms (human, mouse, chimpanzee, macaque, rat and dog). The contents of data sets and the corresponding species are as follows;

Equally-spliced variants (ESVs) were identified from RASVs between human and mouse, chimpanzee, macaque, rat and dog by using comparative genomics. The combinations of compared data sets are as follows;

Splice sites and splice motifs affecting SNPs can be observed in human.
RASVs affecting protein functions (protein motif, GO, subcellular localization signal and transmembrane domain) can be observed in human.
AS junctions expressed in specified cellular fractions (cytoplasm, nuclear and polysome) were detected by using RNA-Seq tags (human RefSeq).

H-DBAS: 5.0, Last update: 2010/07/30
Transcript: H-InvDB 6.2 (DDBJ 73)
Genome: UCSC hg18 (human), pt2 (chimpanzee), rm2 (macaque), mm9 (mouse), rn4 (rat), cf2 (dog)
SNP: dbSNP 128

Shimada, M. et al. (2010) A comprehensive survey of human polymorphisms at conserved splice dinucleotides and its evolutionary relationship with alternative splicing. BMC Evolutionary Biology 10:122
Takeda, J. et al. (2010) H-DBAS: human-transcriptome database for alternative splicing: update 2010. Nucleic Acids Research 38 (Database Issue), D86-D90 Latest paper of H-DBAS
Takeda, J. et al. (2008) Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs. Nucleic Acids Research 36 (20), 6386-6395
Takeda, J. et al. (2007) H-DBAS: Alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational. Nucleic Acids Research 35 (Database Issue), D104-D109
Takeda, J. et al. (2006) Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs. Nucleic Acids Research 34 (14), 3917-3928
Imanishi,T. et al. (2004) Integrative annotation of 21,037 human genes varidated by full-length cDNA clones. PLoS Biology 2 (6), 856-875

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