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, rat, chimpanzee, macaque and dog). The contents of data sets and the corresponding species are as follows;
Full-length cDNA data set: H-Invitational in H-InvDB (Human), FANTOM3 + MGC (Mouse)
mRNA data set: H-InvDB (Human and Mouse)
RNA data set: H-InvDB + RefSeq + Ensembl (Rat, Chimpanzee, Macaque and Dog)
Equally-spliced variants (ESVs) were identified from RASVs between human and mouse, rat, chimpanzee, macaque and dog by using comparative genomics. The combinations of compared data sets are as follows;
Human (Full-length cDNA) - Mouse (Full-length cDNA)
Human (mRNA) - Mouse (mRNA)
Human (mRNA) - Rat (RNA)
Human (mRNA) - Chimpanzee (RNA)
Human (mRNA) - Macaque (RNA)
Human (mRNA) - Dog (RNA)
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) of human cell were detected by using RNA-Seq tags. The translation validation of the variants having AS junctions were analyzed by compared with RefSeq junctions. The results are shown from RNA-Seq analysis page.
H-DBAS: 6, Last update: 2010/09/09
Transcript: H-InvDB 7.5 (DDBJ 78)
Genome: UCSC hg19
SNP: dbSNP 130
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
[PubMed][Full Text]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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