Question: Why a gene name have more than one ensembl ID in gtf?
2
gravatar for walker
2.3 years ago by
walker30
walker30 wrote:

As described. In ensembl gtf file, I find there are different gene_ids having same gene_name.For example, gene_name is TBCE, and gene_ids are ENSG00000284770 and ENSG00000285053.

ensembl gtf • 845 views
ADD COMMENTlink modified 2.3 years ago by Emily_Ensembl21k • written 2.3 years ago by walker30

Those two ID' appear to have overlapping loci.

overlapping locus
    exon(s) of the locus overlap exon(s) of a readthrough transcript or a transcript belonging to another locus

Tagging Emily_Ensembl for additional clarification.

ADD REPLYlink written 2.3 years ago by genomax91k
3
gravatar for Emily_Ensembl
2.3 years ago by
Emily_Ensembl21k
EMBL-EBI
Emily_Ensembl21k wrote:

Looks like ENSG00000285053 is a readthrough of ENSG00000284770 and GGPS1 ENSG00000152904: http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000285053;r=1:235328570-235448952

Readthroughs are annoying because we need RefSeq to agree they exist before HGNC can give them a meaningful name (in this case it would be GGPS1-TBCE). I'll report it to the relevant people, but sadly we might not be able to get it renamed. As it is, it's just taken the name of the gene it has the most sequence similarity to, which is TBCE.

ADD COMMENTlink written 2.3 years ago by Emily_Ensembl21k

I see, but I want to know if there is any other situation? For instance, there is no overlap between ENSG00000274559 and ENSG00000234289. However, they are both named "H2BFS" in GTF.

ADD REPLYlink modified 2.3 years ago by Emily_Ensembl21k • written 2.3 years ago by namedsongming0

If you have a list you would like us to investigate, please send it in to helpdesk [at] ensembl.org.

ADD REPLYlink written 2.3 years ago by Emily_Ensembl21k

Thank you so much, I will try this later.

ADD REPLYlink written 2.3 years ago by namedsongming0
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