Interpreting Vertebrate Homology Class Reports
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This help document answers the following questions about the Vertebrate Homology Class Report.

See also:

What's in the Vertebrate Homology Report?

The Vertebrate Homology Report contains:


What is the source of the homology assertions?

MGI loads orthology data based on the 'stringent' set from the Alliance of Genome Resources. The Alliance sets are based on a scoring system developed by the Alliance in collaboration with DIOPT.

MGI includes homology for the following selected vertebrate species from the Alliance of Genome Resources:

These are a subset of the total species represented in the Alliance. There may be stringent set orthologs in other Alliance species.


Which fields should show up in the Homology table?

For each homolog in the set, the record shows some or all information in the following table, depending on the information available.

Species | Symbol | Gene Links | Genetic Location | Genome Coordinates | Associated Human Diseases | Sequences

Species Species name of each homolog in a class.
Symbol Symbol for an homologous marker.
Gene Links Database accession IDs assigned to the marker, linked to the database where the marker record is stored.
Genetic Location The chromosome the marker is assigned to and the cM position or cytogenetic band. Location information varies depending on information available.
Genome Coordinates Genome coordinate range in base pairs, strand and the genome build number.
Associated Human Diseases Human Disease Ontology (DO) terms, linked to MGI Disease Ontology Browser. Diseases that are only annotated to complex genotypes—those involving more than one genome feature—are not listed in this summary. See also the Disease Ontology Browser.
Sequences Representative transcript and protein sequence ID, linked to the provider's web site. Check boxes permit downloading selected sequences in FASTA format or forward to BLAST at NCBI.


Can I compare regions around a feature?

Yes. Just above the table is a link to a Multiple Genome Viewer that allows you to browse and compare regions around the feature. By default the Viewer launches with genomes shown for mouse, human, and rat, but you can add other species and mouse strains.

How do I download sequences in FASTA format?

  1. Click to put a check mark next to one or more sequences.
  2. Ensure that get FASTA appears at the top of the Sequences column.
  3. Click Go. The selected sequences appear on a new page, in FASTA format.


How do I forward sequences to NCBI BLAST?

To forward sequences to NCBI BLAST:

  1. Click to put a check mark next to one or more sequences.
  2. Click on get FASTA and change the toggle to BLAST at NCBI.
  3. Click Go.