Problem Summary:
View the genomic context of a
gene:
Find its chromosomal location and download the genomic
sequence |
| Sample User Question |
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Although I have the transcript (mRNA) for the MLH1 gene, I would also
like to obtain the genomic sequence data, along with some upstream data. How
can I do this?
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| Analysis/Comments |
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To further study the MLH1 gene, it may be useful to identify the chromosome
region that contains the gene, download the corresponding genomic sequence data,
and order the relevant clones. The Map Viewer link for NP_000240 can
provide such information. It leads to a graphical view of the appropriate
chromosome region. The "dl" (download) link for MLH1 allows us to download the
genomic sequence data for that gene and to adjust the region to download
upstream and/or downstream data, if desired. The Maps & Options dialog box can
then be used to add the Component map, which shows the GenBank records used to
assemble that chromosome region. The GenBank records contain corresponding
clone source information, which can be used to order those clones from their
distributors for further study.
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| Flow Chart |
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RESOURCE USED: Entrez, Map Viewer
FEATURES HIGHLIGHTED: "Map Viewer" option in "Links" menu for nucleotide sequence, protein sequence, adn Gene records; "dl" (download) option in Map Viewer to download the genomic sequence in the region of interest
DETAILS:
- start at the human MLH1 RefSeq mRNA (NM_000249), human RefSeq protein (NP_000240), or Gene record (GeneID: 4292)
- follow the "Map Viewer" link in order to view the genomic context.
- Make sure "Genes_seq" is the "master map" (i.e., the rightmost map in the MapViewer graphic display).
- Then follow the "dl" (download) link to download the corresponding genomic sequence data.
NOTE: As an alternative to the first two steps above, you can BLAST an mRNA query sequence against the human genome, then press the "Genome View" button on the BLAST results page to see the alignment of your query sequence to the human genome. Then click on the accession number of the map element of interest (e.g., the NT_* contig from the reference assembly) to see a detailed view of the alignment.
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| Additional Notes |
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This exercise is also narrated as part of Entrez tutorial:
- Geer RC, Sayers EW. 2003. Entrez: making use of its power.
Brief Bioinform., 4(2):179-84 (June). PMID: 12846398
The Entrez
Tutorial page provides a brief summary of the article and a link to the full
text *.pdf file.
Please note that the search results (number of hits)
noted in the article reflect the data that were available as of March 2003. The
number of search hits will change as the databases grow, but the general search
concepts will continue to apply.
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