Chromosomal Locus From Ucsc
Hi all, i wanted to know if there was way to get chromosomal locus for a gene from UCSC. i tried looking at the table browser and could not find it in any of the linked tables.
thanks in advance.
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This is also quite easy to do using Ensembl BioMart.
Let's assume you have the HGNC gene symbols for a list of genes of which you want to know on which cytogenetic bands they are located (e.g. CASP1, CASP2, CASP3, CASP4, CASP5).
Step (1):
- Go to Ensembl BioMart.
- Select the ‘Ensembl Genes 71’ database (i.e. the current version of Ensembl at the time of writing).
- Select the ‘Homo sapiens genes (GRCH37.p10)’ dataset.
Step (2):
- Click on ‘Filters’ in the left panel.
- Expand the ‘GENE’ section by clicking on the + box.
- Select ‘ID list limit – HGNC symbol(s)’.
- Enter the list of HGNC symbols in the text box (either comma separated or as a list).
Step (3):
- Click on ‘Attributes’ in the left panel.
- Expand the ‘GENE’ section by clicking on the + box.
- Deselect ‘Ensembl Transcript ID’.
- Select ‘Associated Gene Name’ , 'Chromosome Name' and 'Band'.
Step (4):
- Click the [Results] button on the toolbar.
- Select ‘View All rows as HTML’ or export all results to a file.
Hope this helps.
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duplicate of
Genomic cordinates from UCSC
Not sure if it, that post talks about coordinates, i want chromosomal locus such as 1p21 etc..
then have a look at the table 'cytoBand'