PGOHUM00000250821 probably not a pseudogene

Q:
This is supported as a protein coding gene based on transcript and genomic data in human, and homology data. The differences with the human reference assembly (insertions at nt 475-476 and nt 496-497 in the CDS) are supported by transcript data and alignment to the alternate (Celera) assembly. The mouse protein NP_758465.2 (Ppp1r9b, Entrez GeneID 217124) is the same length as the human protein (NP_115984.3) and 96% identical. The region where the mouse gene is located on chromosome 11 has the same genes in the same order as the location on human chromosome 17 where this gene is annotated.
A:
Thanks to Dr. Janet Weber from the Refseq project group for pointing this to us. PGOHUM00000250821 is most likely a protein-coding gene PPP1R9B. The erroneous annotations probably results due to either an error or difference in the canonical human reference genome. Please note that this locus is tagged for follow-up by the Genome Reference Consortium as a possible locus where the reference genome is incorrect (GRC Jira system as HG-191, http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/issues/chr17/ ).

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s