Searching for orthologous genes at NCBI

NCBI is testing a new way to find and retrieve orthologous vertebrate genes. To find orthologs enter a gene symbol (e.g. RAG1) or a gene symbol combined with a taxonomic group (e.g. primate RAG1). Select the matching entry from the suggestions menu or you can select the orthologs option (e.g. Rag1 orthologs) to see all orthologs. Your search will return a results link to the set of orthologs provided by NCBI’s Gene resource. Click on the results link to see information for that ortholog group (Figure 1).


Figure 1.  Search  for Rag1 orthologs showing the link to the set of RAG1 genes from vertebrates.

On the ortholog page (Figure 2), you can select transcript or protein sequences for download or alignment, use the taxonomy tree to refine your results, and drill down to the species level. You’ll find more detailed gene information with links to BLAST and GDV, NCBI’s genome browser. You also get fast access to literature from PubMed based on your selection.

Figure 2. The set of RAG1 orthologs for jawed vertebrates with links to Gene, Reference Sequences, sequence download and alignment.  The Literature tab provides relevant PubMed citations for the selected orthologs. The Taxonomy Tree allows you to quickly find detailed results for a particular species such as Rhesus monkey.

If you’re looking for a set of orthogolous genes, try this out and let us know what you think. Stay tuned for updates!

7 thoughts on “Searching for orthologous genes at NCBI

  1. >XP_009169304.1 hypothetical protein T265_05905 [Opisthorchis viverrini]

  2. Hello, is there a way I could input a list of gene name from one specie and my target specie name, then get the list of ortholog gene names?

  3. Do you have a text file that include all mammal species names in the ortholog database? Trying to write a script to extract just the species from the headers

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