Why gene: OR4F16 crossed the chromesomes in refGene?

Question

[liangzebin5566]

I have download the refGene.txt.gz from UCSC ftp site,

it confused me when I found that OR4F16(which has transcript "NM_001005277") is in different chomesome position:

1964    NM_001005277    chr5    +       180794287       180795226     180794287       18079 5226       1       180794287,      180795226,   0       OR4F16  cmpl    cmpl    0,
587     NM_001005277    chr1    +       367658  368597  367658  3685971       367658, 368597, 0       OR4F16  cmpl    cmpl    0,
589     NM_001005277    chr1    -       621095  622034  621095  6220341       621095, 622034, 0       OR4F16  cmpl    cmpl    0,

How can be a cross chomesome gene? Many thanks if you can provide any tips.

Answer 1

[Denise CS]

I'm not sure if there is such a thing as cross chromosome gene. What you could have for OR, olfactory receptor (or other gene families) is different members of that family either on the same chromosome or another (they would be paralogues of each other). I've checked OR4F16 in Ensembl and just found one location for it within the interval 1:685716-686654 in GRCh38 (for the previous assembly GRCh37 or hg19, again I have one location only). When using NM_001005277, I see it matching to only one gene in Ensembl via BioMart. I'd guess that UCSC has mapped NM_001005277 to three different locations because of the similarity between the sequence of NM_001005277 and other members of the OR4 family i.e. OR4F3 and OR4F29. Not sure of the threshold they have used to allow for that alignment. Perhaps the alignment was not too stringent? You may want to contact UCSC for more info on this. All I know is that we map NM_001005224 and NM_001005221 (not NM_001005277) to OR4F3 and OR4F29, respectively.

[liangzebin5566]

Thank you very much, I'm considering to use Ensembl instead of UCSC.

[Denise CS]

Yes, give Ensembl a go. You can have the best of both worlds, the Ensembl and the UCSC worlds.

Answer 2

[WouterDeCoster]

Weird, if I look for NM_001005277 in UCSC I find:

OR4F16 (uc011dhm.2) at chr5:180794288-180795226 - Homo sapiens olfactory receptor, family 4, subfamily F, member 16 (OR4F16), mRNA.
OR4F29 (uc010nxv.2) at chr1:621096-622034 - Homo sapiens olfactory receptor, family 4, subfamily F, member 29 (OR4F29), mRNA.
OR4F29 (uc010nxu.2) at chr1:367659-368597 - Homo sapiens olfactory receptor, family 4, subfamily F, member 29 (OR4F29), mRNA.

[liangzebin5566]

I download the refGene.txt.gz from: rsync://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ is there another way to get the file?

[WouterDeCoster]

I just searched the genome browser for NM_001005277.

[Denise CS]

Can you download it from the NCBI ftp site? Here it is. But what are you trying to do now? The original post was about NM_001005277 hitting many places in UCSC but one in Ensembl (as we report the best hit/match). So I'm a bit confused now.