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H-DBAS: human-transcriptome database for alternative splicing: update 2010

Jun-ichi Takeda, Yutaka Suzuki, Ryuichi Sakate, Yoshiharu Sato, Takashi Gojobori, Tadashi Imanishi, Sumio Sugano
2009 Nucleic Acids Research  
H-DBAS ( is a specialized database for human alternative splicing (AS) based on H-Invitational full-length cDNAs.  ...  In this update, for better annotations of AS events, we correlated RNA-Seq tag information to the AS exons and splice junctions.  ...  Finally, we are grateful to all those who annotated the full-length human cDNAs at the H-Invitational and H-Invitational two conferences.  ... 
doi:10.1093/nar/gkp984 pmid:19969536 pmcid:PMC2808982 fatcat:gm4nmnbszbgmvpixzcjyc3nlri

A comprehensive survey of human polymorphisms at conserved splice dinucleotides and its evolutionary relationship with alternative splicing

Makoto K Shimada, Yosuke Hayakawa, Jun-ichi Takeda, Takashi Gojobori, Tadashi Imanishi
2010 BMC Evolutionary Biology  
We therefore surveyed validated SNPs in the database dbSNP located at splice dinucleotides of all human genes that are defined by the H-Invitational Database.  ...  2010, 10:122  ...  We also thank all the other members of the Integrated Database and Systems Biology Team of BIRC, AIST and former members of the Integrated Database Team of JBIRC for technical assistance and for providing  ... 
doi:10.1186/1471-2148-10-122 pmid:20433709 pmcid:PMC2882926 fatcat:asy72jrlifaahnbecfozupmldy

ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing

P. L. Martelli, M. D'Antonio, P. Bonizzoni, T. Castrignano, A. M. D'Erchia, P. D'Onorio De Meo, P. Fariselli, M. Finelli, F. Licciulli, M. Mangiulli, F. Mignone, G. Pavesi (+8 others)
2010 Nucleic Acids Research  
Alternative splicing is emerging as a major mechanism for the expansion of the transcriptome and proteome diversity, particularly in human and other vertebrates.  ...  We present here a new release of ASPicDB which now provides a unique annotation resource of human protein variants generated by alternative splicing.  ...  Indeed, currently available databases, such as ASD (20) , ASAP II (21), ASTALAVISTA (22) and H-DBAS (23), mostly collect information on alternative transcripts at the mRNA level, without considering  ... 
doi:10.1093/nar/gkq1073 pmid:21051348 pmcid:PMC3013677 fatcat:66dt62xgnzewjpx3hb4qdnrqsi

Function of alternative splicing

Olga Kelemen, Paolo Convertini, Zhaiyi Zhang, Yuan Wen, Manli Shen, Marina Falaleeva, Stefan Stamm
2013 Gene  
Almost all polymerase II transcripts undergo alternative pre-mRNA splicing. Here, we review the functions of alternative splicing events that have been experimentally determined.  ...  Alternative splicing changes proteins encoded by mRNAs, which has profound functional effects.  ...  McEnrue for editorial help.  ... 
doi:10.1016/j.gene.2012.07.083 pmid:22909801 pmcid:PMC5632952 fatcat:4t6cozxi2vffnnkhm6difvwhnu

Information theoretical prediction of alternative splicing with application to type-2 Diabetes Mellitus [article]

Axel Rasche, Universitätsbibliothek Der FU Berlin, Universitätsbibliothek Der FU Berlin
Considering alternative splicing, all these genes stand for ~100 000 transcripts to be analysed.  ...  In the course of my work I have developed a software pipeline for the analysis of alternative splicing and differential gene expression.  ...  An exception is the H-DBAS database which relies solely on the H-Invitational project data [143] , using manually annotated cDNA sequences.  ... 
doi:10.17169/refubium-14074 fatcat:2ewta4zwjnfkffiawob57s52ay

Methods for transcript variant discovery and alternative expression analysis : application to the study of fluorouracil resistance in colorectal cancer

Malachi Griffith
I first approached this problem by creating a microarray design platform for alternative expression analysis called 'ALEXA-array' (  ...  The scale and complexity of the transcriptome present significant barriers to (1) identifying isoforms and (2) applying knowledge to human disease research.  ...  Databases of transcript diversity derived from EST/mRNA sequences AltTrans Annotation and visualization of AS and AP (Hs, Mo.R-Se De novo annotation of genomes by analysis of short read sequences 137 H-DBAS  ... 
doi:10.14288/1.0068972 fatcat:atrxurgcgjhizfcjvkzo4gsemq

Fifth International Poplar Symposium: 'Poplars and willows: from research models to multipurpose trees for a bio-based society'

R. Tognetti, A. Massacci, G. S. Mugnozza
2011 Tree Physiology  
Acknowledgements Organizers We greatly appreciate the significant contribution of Gabriele Bucci ( Sponsors We also gratefully acknowledge and thank the following organizations who have provided generously for  ...  Analysis of transcriptome data also revealed extensive alternative splicing, and we have generated dataset of over 3000 novel intron-exon junction borders.  ...  Average H, DBA and DBH of 28 clones at 4 ages were 757 ± 28 cm, 10.8 ± 0.6 cm and 8.3 ± 0.6 cm, respectively.  ... 
doi:10.1093/treephys/tpr117 pmid:22158009 fatcat:jx4k6kx2ircafkzp6c5pmc6y6e