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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 2 genes: ENSGALG00010028562 and ENSGALG00010028568 (HGNC: MLLT1). This variant has a missense consequence in seven transcripts of the ENSGALG00010028562 gene, and downstream gene variant consequence in three transcripts of the ENSGALG00010028568 (HGNC: MLLT1) 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.

Japanese quail, Duck, Golden Eagle, Common canary and Zebra finch all have an A in this position. This suggests that A may be the ancestral allele.