Assistance with Identifying Human Orthologs of Catle SNPs

Question

[Star:)]

Hi all,

I have a question. I have some significant SNPs (Chr, SNP ID, and position) associated with birth weight in cattle. I am interested in translating these findings to human biology by identifying the corresponding orthologous genome position in humans.

I searched the BLAT/BLAST option of Ensemble, but I could not find my answer.

I would be happy if you could help me through this. Thanks

Answer 1

[GenoMax]

How many of these do you have? e.g. https://www.ncbi.nlm.nih.gov/gene/507069/ if you check the orthologs link you can find orthologs in many species (including cattle) here: https://www.ncbi.nlm.nih.gov/gene/675/ortholog/?scope=7742

Option 2:

Bovine genome database lets you look up homologs

http://bovinemine-v16.rnet.missouri.edu/bovinemine/template.do?name=Gene_to_human_homologues_to_pathway&scope=global

[Star:)]

Thanks for your answer and sharing your knowledge. i have around 80 SNPs on chromosomes that are different choromosomes. I would like to know, for example, which human chromosome corresponds to chr 4 on cattle. The links you put are for orthoulogus genes.

Do you have any suggestion?

[GenoMax]

This would be tricky. You could use UCSC genome browser for Bos taurus genome and look for the human chain/net alignments track. Here is an example of cattle genome showing alignments to human genome (in red color).

https://genome.ucsc.edu/cgi-bin/hgTracks?db=bosTau9&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr6%3A85405597%2D85664387&hgsid=2342601526_hT0BAlM87dTairQSBxda64AsA8hi

Different parts of human chromosomes may be similar to a particular region of cattle. Example from chr4 of cattle: https://genome.ucsc.edu/cgi-bin/hgTracks?db=bosTau9&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr4%3A49950001%2D50050000&hgsid=2342604076_Am6KkO3CliCr4A97GAPMFI1l53Ut