ASHESdb - Alternatively Spliced Human genes by Exon Skipping - A Database

 

 

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Comparisons

 

Database/ Algorithm Data Source

No. of genes/ spliced transcripts

 Organism Reference

ASDB

SWISS-PROT/ GenBank literature

 1,922 protein and 2,486 DNA sequences

Human, Mouse, Rat, Fly, Worm, Chicken, Virus, Bovine and Rabbit

1
ASAP mRNA–EST-genomic sequence alignment

7,991 genes/ 30,793 spliced transcripts

Human

2
SpliceDB EST  mapped to genomic sequence 43,337 splice junction pairs Mammalian

3
TAP EST  mapped to genomic sequence 1,124 transcripts Human and mouse 4
STACKDB Clustering of EST

270,515 clusters

Human 5
HASDB mRNA and EST 6,201 spliced transcripts Human 6
EASED

EST  and mRNA

 30,000 spliced transcripts

Human, Plant, Cow, Worm, Fly, Fish, Mouse, Rat and Frog

 7
PALSDB mRNA sequence in UniGene cluster and EST 19,936 (human) and 16,615 (mouse) UniGene clusters

Human and mouse

 8
ProSplicer Protein, mRNA, and EST sequences 21,786 genes

Human

9

ASD

EST/cDNA sequences and literature

 8,314 genes Human and mouse 10

ASHESdb

Genomic/full-length cDNA sequences

1,229 genes/ 9073 spliced transcripts

 Human

11

 

References:

  1. Dralyuk I, Brudno M, Gelfand MS, Zorn M, Dubchak I. ASDB: database of alternatively spliced genes. Nucleic Acids Res. 2000 Jan 1; 28(1):296-7. [Pubmed]
     

  2. Lee C, Atanelov L, Modrek B, Xing Y. ASAP: the Alternative Splicing Annotation Project. Nucleic Acids Res. 2003 Jan 1; 31(1):101-5. [Pubmed]
     

  3. Burset M, Seledtsov IA, Solovyev VV. SpliceDB: database of canonical and non-canonical mammalian splice sites. Nucleic Acids Res. 2001 Jan 1; 29(1):255-9. [Pubmed]
     

  4. Kan Z, Rouchka EC, Gish WR, States DJ. Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res. 2001 May; 11(5):889-900. [Pubmed]
     

  5. Christoffels A, van Gelder A, Greyling G, Miller R, Hide T, Hide W. STACK: Sequence Tag Alignment and Consensus Knowledgebase. Nucleic Acids Res. 2001 Jan 1;29(1):234-8. [Pubmed]
     

  6. Modrek B, Resch A, Grasso C, Lee C. Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res. 2001 Jul 1; 29(13):2850-9. [Pubmed] 
     

  7. Pospisil H, Herrmann A, Bortfeldt RH, Reich JG. EASED: Extended Alternatively Spliced EST Database. Nucleic Acids Res. 2004 Jan 1; 32 Database issue: D 70-4. [Pubmed]
     

  8. Huang YH, Chen YT, Lai JJ, Yang ST, Yang UC. PALS db: Putative Alternative Splicing database. Nucleic Acids Res. 2002 Jan 1; 30(1):186-90. [Pubmed]
     

  9. Huang HD, Horng JT, Lee CC, Liu BJ. ProSplicer: a database of putative alternative splicing information derived from protein, mRNA and expressed sequence tag sequence data. Genome Biol. 2003; 4(4):R29. E pub 2003 Mar 14. [Pubmed]
     

  10. Thanaraj T.A., Stamm S., Clark F., Riethoven J.J.M, Le Texier V., and Muilu J. ASD: the Alternative Splicing Database. Nucl. Acids. Res. 2004 32: D64-D69. [Pubmed]

 

   11.  Sakharkar MK, Perumal BS, Lim YP, Lee PC, Yiting Y, Kangueane P, Alternatively spliced    

         human genes by exon skipping - A database (ASHESdb), In Silico Biology, 5, 0021, Dec

         2004. [Journal Link]