Chromosomal Locus From Ucsc

Question

[win]

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.

[Pierre Lindenbaum]

duplicate of

Genomic cordinates from UCSC

[win]

Not sure if it, that post talks about coordinates, i want chromosomal locus such as 1p21 etc..

[Pierre Lindenbaum]

then have a look at the table 'cytoBand'

Answer 1

[Bert Overduin]

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.