Exploring a SNP in chicken
(a) Find the page with information for the chicken SNP rs10731268.
(b) What gene(s) does rs10731268 fall within? What is its effect?
(c) Have any papers been written mentioning rs10731268? What are they about?
(d) What allele is at this position in other birds? What is the likely ancestral allele?
(a) Go to the Ensembl homepage.
Type rs10731268 in the Search box, then click Go. Click on rs10731268.
(b) Click on Genes and Regulation in the side menu (or the Genes and Regulation icon).
rs10731268 falls within ENSGALG00000001749 and is missense in two transcripts of this gene.
(c) Click on Citations in the left hand side menu.
This variant is mentioned in the paper ‘Identification and characterization of genes that control fat deposition in chickens’ from 2013 by D’Andre et al. Click on the PubMed ID 24206759 to go to the paper.
(d) Click on Phylogenetic Context in the side menu. Select Alignment: 17 sauropsids EPO and click Go.
Turkey, Japanese quail, great tit and zebrafinch all have an A in this position. This suggests that A may be the ancestral allele.