Question: finding gene name according to uniprot name and description
0
gravatar for mxlsherry1992
12 months ago by
mxlsherry199230 wrote:

Dear all,

I have a list of improtant sequences (RNA sequencing, without reference genome) and annotated them with uniprot (swissprot), then I got their uniprot name, I want to translate them into their gene name, I know uniprot website can do this, for example, if I have a uniprot name"A5FIJ3", I can easily copy and paste it in uniprot website and it shows gene name is " rpoB". However, there are many genes uniprot didn't give a gene name, I tried using NCBI and Google Scholar to search the uniprot name and their description, but no realiable results. I pasted some of the uniprot name below:

Q91453  Stonustoxin subunit beta (SNTX subunit beta)
P02993  Elongation factor 1-alpha (EF-1-alpha)
P05547  Troponin I (TnI)
P35316  Calcium-transporting ATPase sarcoplasmic/endoplasmic reticulum type (EC 7.2.2.10) (Calcium pump)
P36178  Chymotrypsin BII (EC 3.4.21.1)
P42577  Soma ferritin (EC 1.16.3.1)
P98089  Intestinal mucin-like protein (MLP) (Fragment)
Q00871  Chymotrypsin BI (EC 3.4.21.1)
Q04791  Fatty acyl-CoA hydrolase precursor, medium chain (EC 3.1.2.-) (Thioesterase B)
Q05187  Hemocyte protein-glutamine gamma-glutamyltransferase (EC 2.3.2.13) (Hemocyte transglutaminase) (TGase)
Q1HPS0  Myosin regulatory light chain 2 (MLC-2)
Q8N0N3  Beta-1,3-glucan-binding protein (GBP)
Q9U639  Heat shock 70 kDa protein cognate 4 (Hsc 70-4)
Q9U943  Apolipophorins [Cleaved into: Apolipophorin-2 (Apolipophorin II) (apoLp-2); Apolipophorin-1 (Apolipophorin I) (apoLp-1)]

So if we have a website or some method that can get the gene name ?

Thanks in advance and have a great night!!

ADD COMMENTlink modified 12 months ago by Biostar ♦♦ 20 • written 12 months ago by mxlsherry199230

The Retrieve/ID mapping tool can do this job:

uniprot_id_mapping

ADD REPLYlink modified 12 months ago • written 12 months ago by SMK1.9k

Thank you for your reply! But if I use these identifiers "P02993" "P02993", it seems can not find the gene name.:( enter image description here

enter image description here

ADD REPLYlink modified 12 months ago • written 12 months ago by mxlsherry199230

In your case 1: "A5FIJ3", "rpoB" is its gene name, which can be fetched if you select "Gene name" when using that tool (because you said: gene name). In case 2: "P02993", if you check out https://www.uniprot.org/uniprot/P02993.txt, you'll find that those functional descriptions are in "RecName", it is the full and short protein name recommended by the UniProt Consortium. In your case 1 "A5FIJ3" has short RecName: "RNAP subunit beta".

However, you can still use the Retrieve/ID mapping tool to fetch both information by selecting "to UniProtKB" in that tool: (see column "Protein names" and "Gene names")

uniprot_again

Which can be downloaded as a list in tab or excel...

ADD REPLYlink modified 12 months ago • written 12 months ago by SMK1.9k

Use NCBI EntrezDirect:

$ esearch -db protein -query "P02993" | efetch -format docsum | xtract -pattern DocumentSummary -element Caption,Title
P02993  RecName: Full=Elongation factor 1-alpha; Short=EF-1-alpha
ADD REPLYlink written 12 months ago by genomax83k

Thank u !! I think it has been solved!

ADD REPLYlink written 12 months ago by mxlsherry199230
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