Why Has2 Gene Was Not Annotated As Heterocephalus Glaber (Naked Mole-Rat) In Genebank

Question

[smagikern]

Slight different HAS2 hyaloran synthase in naked mole rat was find in http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12234.html But in GeneBank and ncbi.nlm.nih.gov no mention about this modification. I try use BLAST at http://mr.genomics.org.cn/page/species/blast_page.jsp - 1160 score point give me scaffold146 with similary sequence. So it possible to detect.

http://www.nature.com/nature/journal/v479/n7372/full/nature10533.html - also not list this gene as one of the 39 vertebrate genes that changed uniquely in the NMR .

So Why? May be it reasonably to parse other invisible, but notoriously homologue

http://www.ensembl.org/Mus_musculus/Gene/Sequence?g=ENSMUSG00000022367;r=15:56665627-56694539;t=ENSMUST00000050544 -mouse has2 sequence

Answer 1

[cdsouthan]

I have not acessed the 2nd full paper yet but what I can establish is that naked mole rat HAS2 http://www.uniprot.org/uniprot/G5AY81 has 2 residue changes compared with mouse http://www.uniprot.org/uniprot/P70312. I can find the same mole rat sequence by BLASTP at the Chinese genome site you gave the link for (>HGL_H00000306991 [mRNA] locus=scaffold142:640423:653116:- Length = 552) but also confirm the scaffold piece you hit was for HAS3. As I think you imply the partial mole rat HAS3 http://www.uniprot.org/uniprot/G5AK52 is more diverged than the complete HAS2 but the remarks for Table 19 in the first paper "exclude gene misprediction and misannotation events" could mean they dropped it because of the truncation. HAS2 got named three times on the NCBI side, first as HAS2 in EHB01992 but HAS2-like in the XP pipeline with a one residue XP variant as the 3rd.