Confusion about different IDs

Question

[zizigolu]

Hi

You imagine I have this gene ENSG00000260958

If you search, you will find several IDs for that like

LOC105371200
AC023824.3
AC023824.6
HSALNG0111081
RP11-488I20.8
RP11-244B22
Lnc-TP53TG3F-9
Lnc-TP53TG3F-8
NONHSAG019290.2
ENST00000569557.3
ENSG00000260958.2
OTTHUMG00000176241.2
AC023824.4
ENST00000569557.2
RP11-488I20.8-002
NONHSAT142166
NONHSAT142170
105371200

I heard each molecule in central dogma has a unique and non-redundant and verified ID named RefSeq ID

For ENSG00000260958, in UCSC database, you will see RefSeq: XR_007065192.1 enter link description herewhich matches with different locus as below

RefSeq Gene LOC124903769
RefSeq: XR_007065192.1  Status: Unknown
Description: uncharacterized lncRNA
Molecule type: ncRNA
Source: Gnomon
Biotype: lncRNA
Entrez Gene: 124903769
GeneCards: LOC124903769
AceView: LOC124903769

That is really confusing :(

Please, could any one tell me what is RefSeq ID for ENSG00000260958 and if there is not one available yet, which ID is the best match for ENSG00000260958 ?

Thanks a lot

Answer 1

[GenoMax]

This is an uncharacterized location. If you search for it at NCBI you get this: https://www.ncbi.nlm.nih.gov/gene/?term=ENSG00000260958%20

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.

[zizigolu]

So you say no RefSeq available for that yet?

[GenoMax]

It does have a RefSeq accession: https://www.ncbi.nlm.nih.gov/nuccore/XR_007065192.1

But as the XR prefix indicates (LINK), it is an automatic computational predictive accession that is not experimentally verified.

Answer 2

[ATpoint]

There are many competing names for the same gene. I prefer to have a common standard which is Ensembl: https://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000260958;r=16:35207613-35284148

ENST are transcripts, ENSG are genes (for human). The others might come from different sources and/or annotation versions over the years. I would stick with Ensembl since in my hands it is the most clean and systematic source of annotations. NCBI/RefSeq is a mess in my hands.