Find Gene Symbol/Gene Name According To Orf Accession

Question

[Bioscientist]

I have a list of ORF accession like NM_000163; I want to know their corresponding gene name I tried on UCSC genome table but cannot figure out

thx

Answer 1

[Pierre Lindenbaum]

I can find your acc in the refGene table

$ mysql  --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e 'select name,name2,chrom,txStart,txEnd from refGene where name="NM_000163"\G'
*************************** 1. row ***************************
   name: NM_000163
  name2: GHR
  chrom: chr5
txStart: 42423876
  txEnd: 42721980

Answer 2

[Woa]

Download the sequences and parse the files to get the gene names.

A: Fetch Many Files With Accession Number, Output File Format Is Coding Sequences I

This piece of code will fetch the gene name:

my @tags=qw/gene/;
my ($feat_object)=@cds_features;
my ($gene_name)=map{$feat_object->get_tag_values($_);}@tags;

Answer 3

[Bert Overduin]

You can use Ensembl BioMart for this:

Step 1:

• Go to the Ensembl homepage.
• Click on the ‘BioMart’ link on the toolbar.
• Choose the ‘Ensembl Genes 65’ database.
• Choose the ‘Homo sapiens genes (GRCh37.p5)’ dataset.

Step 2:

• Click on ‘Filters’ in the left panel.
• Expand the ‘GENE’ section by clicking on the + box.
• Select ‘ID list limit – RefSeq mRNA ID(s)’.
• Enter the list of RefSeq IDs for your genes in the text box (either comma separated or as a list).

Step 3:

• Click on ‘Attributes’ in the left panel.
• Select the ‘Features’ attributes page.
  
• Expand the ‘GENE’ section by clicking on the + box.
  
• Deselect ‘Ensembl Gene ID' and 'Ensembl Transcript ID’.
  
• Expand the ‘EXTERNAL’ section by clicking on the + box.
  
• Select ‘RefSeq mRNA’ and ‘HGNC symbol’.

Step 4:

• Click the [Results] button on the toolbar.
  
• Select ‘View All rows as HTML’ or export all results to a file. Tick the box ‘Unique results only’.

For your example this gives me:

RefSeq mRNA HGNC symbol

NM_000163 GHR

Hope this helps.