Finding orthologs and sequences from BioMart

Question

[hemantkiitg]

How to find Human-Mouse othologs from Ensembl BioMart and also how to obtain those sequences.

[natasha.sernova]

I found a few posts in Biostars and 1 article.

Finding a orthologous genes between human and mouse along with percent alignment?

Homologous gene matching between mouse and human

Identifying orthologous exons between human and mouse

mouse exome sequencing : disease gene prioritization?

Retrieving Dn Or Ds From Ensembl Using Biomart

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5074520/pdf/pcbi.1005170.pdf

Look at UCSC.

Mouse Sequence Compared To Human Sequence

How to get mouse-human homologues table from UCSC?

What are the human and mouse reference genome (hg19, mm9) based on IGV?

To download cds see Ensemble ftp site, mentioned in the post below:

How can i retrieve all cds from a ensembl genetree？

Answer 1

[Emily]

BioMart will allow you to get the sequences for the orthologues if you combine two queries. There are instructions on how to do this here: http://www.ensembl.org/info/data/biomart/biomart_combining_species_datasets.html