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Exporting homologues with BioMart

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Exporting homologues with BioMart

Go to Ensembl’s BioMart. For a list of Cyprinus carpio carpio (common carp) Ensembl genes, export the Oncorhynchus mykiss (rainbow trout) orthologues and their coordinates:

ENSCCRG00000054216,ENSCCRG00000032455,ENSCCRG00000022461,ENSCCRG00000066160,ENSCCRG00000028244,
ENSCCRG00000006279,ENSCCRG00000072009,ENSCCRG00000031644,ENSCCRG00000044263,ENSCCRG00000075394

Do all of these genes have a homologue in rainbow trout?

  1. Go to BioMart (you can find a shortcut in the navigation bar at the top of any Ensembl page) and click New. Choose the Ensembl Genes database. Choose the Common carp genes dataset.

  2. Click on Filters in the left panel. Expand the GENE. Enter the gene list in the Input external references ID list box. Gene stable ID(s) should already be selected by default.

  3. Click on Attributes in the left panel. Select the Homologues attributes at the top of the page. Expand the GENE section. Deselect Gene stable ID version, Transcript stable ID and Transcript stable ID version. Expand the ORTHOLOGUES [P-T] section. Select the following attributes under Rainbow trout Orthologues:
    • Rainbow trout gene stable ID
    • Rainbow trout gene name
    • Rainbow trout chromosome/scaffold start (bp)
    • Rainbow trout chromosome/scaffold end (bp)
  4. Click Results. Select View: All rows as HTML.

    All but ENSCCRG00000022461 and ENSCCRG00000075394 have a homologue in rainbow trout. Your output should also included the gene ID and name in rainbow trout and their coordinates.