VEP cdk5r1b Atlantic salmon
We have identified a few variants in Atlantic salmon (Salmo salar):
- chr 28, genomic coordinate 1777645, alleles C/T
- chr 28, genomic coordinate 1777906, alleles G/A
- chr 28, genomic coordinate 1786995, alleles T/G
(a) Which genes and transcripts do these variants map to?
(b) Do these variants result in a change in the proteins encoded by any of the Ensembl genes? Which genes?
Go to www.ensembl.org and click on the Variant Effect Predictor link on the homepage. Click Launch VEP.
Choose Atlantic salmon as the species and copy the following into the Paste data text box:
28 1777645 1777645 C/T var1.
28 1777906 1777906 G/A var2.
28 1786995 1786995 T/G var3.
Note: Variation data input can be done in a variety of formats. See more details here http://www.ensembl.org/info/docs/variation/vep/vep_formats.html
Click Run.
When your job is listed as Done, click View Results.
You will get a table with the consequence terms from the Sequence Ontology project (http://www.sequenceontology.org/) (i.e. synonymous, missense, downstream, intronic, 5’ UTR, 3’ UTR, etc) provided by VEP for the listed SNPs. You can also upload the VEP results as a track and view them on Location pages in Ensembl.
The variants overlaps three genes (six transcripts of psmd11b, four transcripts of cdk5r1b and one transcript of ENSSSAG00000096896 gene)
Variant 28_1777906_G/A overlaps cdk5r1b gene and resulted in amino acid change at position 109 and 116 (Ser to Leu), variant 28_1777645_C/T also overlaps cdk5r1b gene and resulted in amino acid change at position 96 and 203 (Arg to His).
