Question: Question about gens name starting "LOC~"
4
gravatar for mangfu100
5.4 years ago by
mangfu100730
Korea, Republic Of
mangfu100730 wrote:

Greeting all.

I am searching novel somatic mutations using various public software and annotation tools such as annovar.

I have been using my own cancer exome data not public data 'just real patient data' and finally I completed running calling program(MuTect and annovar) and I got to discover some genes that looks disease-like to me.

One of my genes is starting with LOC and its full name is LOC100129697 and it has variation in nonsynonymous region.

I hope that this gene are related to the disease and with this hope in mind,  I ran the IGV to analyze this variation more deeply.

However, when I looked up IGV , I was surprised to see that gene name which IGV shows me is totally different from LOC100129697. 

How can I interpret this gene LOC100129697?

Is there a gene which have another nick-name?

sequencing genome • 6.5k views
ADD COMMENTlink modified 5.4 years ago by cdsouthan1.8k • written 5.4 years ago by mangfu100730

If you still come across these IDs  they are unlikely to be real proteins.  Transcripts of some desciption probably, genes maybe (but not by HGNC's defintion).  Ensembl/Havana call this out as antisence, not ORF

http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000205018;r=16:88939789-88951524;t=ENST00000378347

 

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by cdsouthan1.8k
9
gravatar for iraun
5.4 years ago by
iraun3.8k
Norway
iraun3.8k wrote:

From NCBI:
"Symbols beginning with LOC. When a published symbol is not available, and orthologs have not yet been determined, Gene will provide a symbol that is constructed as 'LOC' + the GeneID. This is not retained when a replacement symbol has been identified, although queries by the LOC term are still supported. In other words, a record with the symbol LOC12345 is equivalent to GeneID = 12345. So if the symbol changes, the record can still be retrieved on the web using LOC12345 as a query, or from any file using GeneID = 12345."

ADD COMMENTlink written 5.4 years ago by iraun3.8k
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