Find Gene Symbol/Gene Name According To Orf Accession
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
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3 answers
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
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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;
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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.
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