Question: Chromosomal Locus From Ucsc
0
gravatar for win
5.9 years ago by
win810
India
win810 wrote:

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.

ucsc • 2.2k views
ADD COMMENTlink modified 5.9 years ago by Bert Overduin3.6k • written 5.9 years ago by win810

duplicate of

Genomic cordinates from UCSC

ADD REPLYlink written 5.9 years ago by Pierre Lindenbaum118k

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

ADD REPLYlink written 5.9 years ago by win810

then have a look at the table 'cytoBand'

ADD REPLYlink written 5.9 years ago by Pierre Lindenbaum118k
0
gravatar for Bert Overduin
5.9 years ago by
Bert Overduin3.6k
Edinburgh Genomics, The University of Edinburgh
Bert Overduin3.6k wrote:

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.

ADD COMMENTlink written 5.9 years ago by Bert Overduin3.6k
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