PGOHUM00000250823 and SETP13/SETP3 pseudogenes

Q:

Could you please investigate the support you have for PGOHUM00000250823? At NCBI, we have PGOHUM00000250823 associated with HGNCid 42932, official symbol SETP13, and RefSeq accession NG_032538.1. However, we have a nearly identical RefSeq accession NG_032022.1 associated with HGNCid 31115 and official symbol SETP3. On the current human reference assembly, GRCh38, both NG_032538.1 and NG_032022.1 align perfectly to the same locus and have no other hits of comparable quality to the reference assembly (or to alternate assemblies HuRef or CHM1_1.1). In NCBI’s latest annotation (Annotation Release 106) SETP3 was annotated on the assembly but SETP13 was not because it overlapped with SETP3. Do you have any evidence these are distinct pseudogenes? If not, NCBI’s preference would be to preserve the older nomenclature associated with SETP3 and NG_032022.1. Also, if we agree that SETP13 is redundant with SETP3 then I will proceed to notify HGNC and will CC you on that email.

A:
I looked at the PGOHUM00000250823/SETP13 locus. Our pipeline
predicted it as a pseudogene to SET with around 90% sequence identity.
When compared to SETP3 locus, SETP13 lacks sequences at both 3’ and 5’
ends, which can be aligned to the UTR regions of SET. Our pipeline
missed these sequences at both ends because it searches for homologous
sequence to CDS regions only. We are actually thinking of including
some checks of UTR alignment in our revised pipeline. Thanks for
pointing this case to us.

We have no problem to merge the SETP13 locus with SETP3.

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 )

Google photo

You are commenting using your Google 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 )

Connecting to %s