Alternative Splicing Database

Question

[Sara]

Dear Friends

I need to download all proteins made via different types of alternative splicing for homo sapiens . (Exon skipping , mutually exclusive exon ,.....)

I need to separately download these proteins based on their types of alternative splicing.

Would you pls tell me from which database I can do that ?

Thanks in advance

[Niek De Klein]

Do you need to do this for all organisms?

Answer 1

[Pierre Lindenbaum]

The mysql table knownGene in the UCSC database contains the alternative transcripts:

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 \
  -e  'select * from  knownGene as K left join knownGenePep as P on K.name=P.name left join kgXref as X on X.kgId=K.name \G '


(...)
*************************** 99. row ***************************
       name: uc010nyg.1
      chrom: chr1
     strand: +
    txStart: 1109285
      txEnd: 1133313
   cdsStart: 1114595
     cdsEnd: 1133227
  exonCount: 16
 exonStarts: 1109285,1109645,1109803,1114568,1115036,1115413,1115862,1116110,1117120,1117740,1118255,1119299,1120348,1131979,1132472,1132817,
   exonEnds: 1109306,1109701,1109869,1114713,1115117,1115720,1115981,1116240,1117195,1117826,1118427,1119471,1120489,1132096,1132566,1133313,
  proteinID: Q6ZVT0
    alignID: uc010nyg.1
       name: uc010nyg.1
        seq: MDHSCTRFIHRRGPPTRTRAGFKRGKRPRIQQRPRARVSGTIPASRLHPAPASQPGPCPAPGHCPVGPAHERPMGSSQEEGLRCQPSQPDHDADGHCGPDLEGAERASATPGPPGLLNSHRPADSDDTNAAGPSAALLEGLLLGGGKPSPHSTRPGPFFYIGGSNGATIISSYCKSKGWQRIHDSRRDDYTLKWCEVKSRDSYGSFREGEQLLYQLPNNKLLTTKIGLLSTLRGRARAMSKASKVPGGVQARLEKDAAAPALEDLPWTSPGYLRPQRVLRMEEFFPETYRLDLKHEREAFFTLFDETQIWICKPTASNQGKGIFLLRNQEEVAALQAKTRSMEDDPIHHKTPFRGPQARVVQRYIQNPLLVDGRKFDVRSYLLIACTTPYMIFFGHGYARLTLSLYDPHSSDLGGHLTNQFMQKKSPLYMLLKEHTVWSMEHLNRYISDTFWKARGLAKDWVFTTLKKRMQQIMAHCFLAAKPKLDCKLGYFDLIGCDFLIDDNFKVWLLEMNSNPALHTNCEVLKEVIPGVVIETLDLVLETFRKSLRGQKMLPLLSQRRFVLLHNGEADPRPHLGGSCSLRRWPPLPTRQAKSSGPPMPHAPDQPGARRPAPPPLVPQRPRPPGPDLDSAHDGEPQAPGTEQSGTGNRHPAQEPSPGTAKEEREEPENARP
       kgID: uc010nyg.1
       mRNA: BC027945
       spID: Q6ZVT0
spDisplayID: TTL10_HUMAN
 geneSymbol: TTLL10
     refseq: NM_001130045
    protAcc: NP_001123517
description: tubulin tyrosine ligase-like family, member 10
*************************** 100. row ***************************
       name: uc001acz.1
      chrom: chr1
     strand: +
    txStart: 1115076
      txEnd: 1121241
   cdsStart: 1115433
     cdsEnd: 1120522
  exonCount: 9
 exonStarts: 1115076,1115413,1115862,1116110,1117120,1117740,1118255,1119299,1120348,
   exonEnds: 1115233,1115720,1115981,1116240,1117195,1117826,1118427,1119471,1121241,
  proteinID: Q6ZVT0-3
    alignID: uc001acz.1
       name: uc001acz.1
        seq: MGSSQEEGLRCQPSQPDHDADGHCGPDLEGAERASATPGPPGLLNSHRPADSDDTNAAGPSAALLEGLLLGGGKPSPHSTRPGPFFYIGGSNGATIISSYCKSKGWQRIHDSRRDDYTLKWCEVKSRDSYGSFREGEQLLYQLPNNKLLTTKIGLLSTLRGRARAMSKASKVPGGVQARLEKDAAAPALEDLPWTSPGYLRPQRVLRMEEFFPETYRLDLKHEREAFFTLFDETQIWICKPTASNQGKGIFLLRNQEEVAALQAKTRSMEDDPIHHKTPFRGPQARVVQRYIQNPLLVDGRKFDVRSYLLIACTTPYMIFFGHGYARLTLSLYDPHSSDLGGHLTNQFMQKKSPLYMLLKEHTVWSMEHLNRYISDTFWKARGLAKDWVFTTLKVRPLCPPVWE
       kgID: uc001acz.1
       mRNA: NM_153254
       spID: Q6ZVT0-3
spDisplayID: Q6ZVT0-3
 geneSymbol: TTLL10
     refseq: NM_153254
    protAcc: NP_694986
description: tubulin tyrosine ligase-like family, member 10
(...)

Answer 2

[Malachi Griffith]

One challenging aspect of your question is breaking down the proteins by the type of splicing event. There are many databases that specifically attempt to annotate alternative splicing events. In my experience these are not as well maintained as other resources that address the more general problem of transcript annotation (without a specific focus on alternative splicing). I would start with UCSC transcripts as recommended by Pierre or if you prefer you could use Ensembl. Ensembl has an 'alternative splicing event set'. Seven common AS patterns are automatically annotated in Ensembl:

Cassette exon (skipped exon), Intron retention, Mutually exclusive exons, Alternative 3' sites, Alternative 5' sites, Alternative first exon, Alternative last exon.

You can learn all about these annotations at the link below. You can access these alternative splicing annotations via the Ensembl genome browser, the Ensembl API, or Ensembl Biomart. For example, in Biomart, select the 'Ensembl Genes' database, then the desired species, then select 'attributes', then the 'transcript event' section. Then check the 'event type' and 'event name' fields and add other fields of info that you want.

Ensembl - identifying alternative splicing events