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
2 answers
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
(...)
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.
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Do you need to do this for all organisms?