Other help topics:    For The Public

Computed Orthologs Section

Introduction

Potential orthologs or paralogs are found for the following species: mouse, human, rat, African clawed frog, fly, worm, and yeast. We use two mechanisms: species-specific Blast results, and homology gene cluster databases (HomoloGene from NCBI, and Ensembl from EBI). This dual method gives us a complete listing of potential homologs, and allows for a verification mechanism.

We use standard Blast parameters (e.g. BLOSUM62 matrix), with no SEG filtering. The top hit against each species is reported, given that the hit has above 10% identity (based on minimum sequence length) to the Molecule Page sequence. The NCBI Gene ID for the Molecule Page is used to find homologous genes listed by HomoloGene and Ensembl. We report all top Blast hits, all genes classified as an ortholog by the homology databases, and any gene Ensembl classifies as a between species paralog having higher Blast score than the Ensembl orthologs for that species. Within species paralogs are not reported.

Genes that have both Blast matches and a homology database relation (or an identical gene symbol) are classified as likely orthologs. We display these genes in an abbreviated lists, to make them easy to scan and to see all grouped together. Detailed information for those homology matches, as well as any homology match with only one set of match criteria, are shown below the short list.

Homology References

NCBI Blast Link

This is a link to the NCBI Blast Link page for the protein record used to define this Molecule Page. NCBI Blast Link contains the top Blast hits of a protein record against all NCBI proteins, like our Blast Data section, but it offers an interface for doing species-based grouping, to view results in a taxonomy tree, etc.

HomoloGene

If a HomoloGene cluster contains the gene for this Molecule Page, it is displayed with a hyperlink to the HomoloGene web page for the record.

Ensembl

Any Ensembl records related to this Molecule Page that has homology information are displayed with hyperlinks to the Ensembl web pages for the records.

Likely Orthologous Gene Categories and Other Potential Orthologs or Paralogs Categories

Species

One of the species groups mentioned above. We classify all Mus family species as "Mouse", and all Rattus family sequences as "Rat".

Gene Symbol

The official gene symbol of the Entrez Gene record for the gene, hyperlinked to the NCBI web page.

Name

The official gene name of the Entrez Gene record for the gene.

Evidence

The evidence suggesting the listed gene is an ortholog.

Homology Details

Species

One of the species groups mentioned above. We classify all Mus family species as "Mouse", and all Rattus family sequences as "Rat".

Evidence

This field shows the evidence that supports the gene homology. Top Blast hits (those with the highest score) are given special mention. HomoloGene relations are mentioned (they do not specify ortholog versus paralog), and Ensembl relations are either described as orthologs (we do not specify one-to-one, one-to-many, or many-to-many) or between species paralogs.

Gene Symbol

The official gene symbol of the Entrez Gene record for the gene.

Gene Description

The official gene name or protein title in Entrez Gene.

Entrez Gene ID

The Entrez Gene ID, hyperlinked to the NCBI web page for that record.

Related Database Records

Gene-related database records that are linked to the Entrez Gene record, such as UniGene, Ensembl, OMIM, the Human Protein Resource Database (HPRD), and the Rat Genome Database (RGD).

Protein Name

The title field of the protein database record displayed.

Protein Accession

This is an identifier of the database record. When database records have multiple accessions, this field is the primary accession (i.e. the first one in the accession list). For UniProt sequences, the accession is hyperlinked to Expasy's SwissProt/TrEMBL database browser.

E-Value

This is a statistical measure of the sequence similarity as reported by the Blast algorithm. In general, a lower E-value (i.e. one that is closer to zero) means a stronger similarity. This is hyperlinked to the NCBI Pairwise Blast tool, showing the alignment of this sequence to the Molecule Page sequence given the Blast parameters we use.

Identity %

The percent identity of the Blast alignment, based on the sequence length of the Molecule Page protein.