Ensembl gene position differ with NCBI gene

Question

[zzqr]

I found genome position of Rat gene Vom2r3 ENSRNOG00000046319 differs in Ensembl and NCBI DB. Two url as below:

---

Vom2r3 page in NCBI
Vom2r3 page in Ensembl

---

The RefSeq & RGD link in Ensembl page is same as in NCBI page. Both reference genome is Rnor_6.0. However the genome location in Ensembl is quite different with NCBI

---

Ensembl - Chromosome 1: 396,700-409,676 forward strand
NCBI - Chromosome 1: 69007591..69016444, complement

---

Anyone could explain this? And which one is right or which one to prefer?

[Devon Ryan]

It looks like Ensembl is correct, but you might ask the ensembl helpdesk if they know why there's such a huge difference.

[zzqr]

Why Ensembl? Any reason?

[Devon Ryan]

To start with, NCBI says the gene is on 1p13, but shows it on 1q12, whereas Ensembl shows it on 1p13. That and the fact that NCBI's previous release had the gene around chr1:393000 suggests that NCBI has a problem with their annotation.

Answer 1

[Denise CS]

UCSC has got the same coordinates as Ensembl i.e. 1:396,700-409,676 on Rnor_6.0. Note the region is a bit fragmented: we've got some gaps so the annotation may get revisited as the assembly improves. The other thing to note is that NCBI has used an XP/XM (predicted) entry to annotate that gene. Although the NM (curated mRNA is there, it is under a provisional status). In Ensembl you can see the mapping of the NM entry against the genome and you will be able to compare to the Ensembl annotation. If you want the Ensembl team to have a closer look, get in touch with their helpdesk as suggested by Devon. I'm guessing as soon NCBI revises the model and it is no longer provisional, all three groups will agree with each other.