Searching NCBI's Gene database
The Gene database
The Gene database is as its name suggests focussed on gene-specific data. It contains a lot more than just gene sequences: it includes nomenclature, maps, pathways, variations, phenotypes, and links to other databases. The sequence section is limited to RefSeq sequences. The Gene database assigns a Gene ID, a unique identifier to all genes with defining sequences, genes with known map positions, and genes inferred from phenotypic information. These gene identifiers are used throughout all NCBI's databases.
Exercise 1: human serpin A7
- Go to NCBI's Gene database
- Do an Advanced search for Organism: homo sapiens and Gene/Protein Name: serpin A7
- Your search is so specific that it returns only one hit so you are immediately redirected to the Gene record
| On which chromosome is the gene located ? |
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| Scroll to the "Genomic context" section (see slides). There you see that serpinA7 is located on chromosome X. |
Look at the GeneRIFs of this gene. GeneRIFs are short sentences that describe the function of a gene product that are extracted from scientific publications. NCBI encourages scientists to submit these GeneRIFs together with the Pubmed ID of the publication to the Gene database and curates the submissions. In this way you don't have to go through the scientific literature yourself to get idea about the function of a gene product.
| What is the function of the protein encoded by this gene ? |
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| Scroll down to the Bibliography section (see slides). The GeneRIFs tell you a whole lot about serpin A7. For instance, it's a liver-specific gene, that can contain a mutation in the first intron that is linked to disease. It plays a role in the release of thyroxin, a hormone. |
Check out al other info that you find here for serpin A7 and try to do a search on your favourite gene to see if you can find any new info on it.
