Trying to figure out why TNXB isn't in Gencode v12 UCSC track

[Jessica Chong]

I think I probably do not understand things fully, but I am currently displaying hg19 with the Comprehensive gene set from ENCODE/GENCODE v12 as well as the ENSEMBL v68 track and the standard UCSC Genes track.

One of my genes of interest is TNXB.

There is nothing at this gene's position in the Gencode track while there is a shorter transcript at the same position in the Ensembl track -- although that transcript does not correspond to the 1 known transcript product (ENST00000433037) of TNXB in Ensembl Browser.

TNXB is listed as being a known protein coding gene in Ensembl and the prediction method is "manual annotation from the Havana project".

Why would this gene not be present in the UCSC Gencode/Encode track and why is the known transcript not in the UCSC Ensembl track either?

Thanks so much!

[Steve Heitner]

Hello, Jessica.

I just viewed hg19 at chr6:32,008,720-32,078,223 and I saw entries for TNXB
in the UCSC Genes, GENCODE V12, RefSeq Genes and Ensembl Genes v68 tracks.
It is possible that you were looking at one of the chr6 haplotype
chromosomes. The GENCODE V12 track does not contain any TNXB items on any
of the chr6 haplotype chromosomes, so if you were looking at a haplotype
chromosome, it would explain why you saw nothing for GENCODE V12. For more
information on haplotype chromosomes, see the "Chromosome naming scheme"
section of the hg19 gateway page
(http://genome.ucsc.edu/cgi-bin/hgGateway?db=hg19).

I also performed a search for ENST00000433037 and found it in the Ensembl
Genes v68 track at chr6_apd_hap1:3,356,184-3,368,634.

Please contact us again at gen...@soe.ucsc.edu if you have any further
questions.

---
Steve Heitner
UCSC Genome Bioinformatics Group

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[Jessica Chong]

Hi Steve,

Thanks for looking.  How odd.  

I don't think I was looking at a haplotype chromosome (the coordinate box says "chr6:31,974,978-31,982,258" and I'm viewing "UCSC Genome Browser on Human Feb. 2009 (GRCh37/hg19) Assembly")

To get there, I searched for TNXB and clicked on this link.  I can see "Homo sapiens tenascin XB (TNXB), transcript variant XB, mRNA" in the UCSC Genes track but not in GENCODE v12:

TNXB (uc021yvf.1) at chr6:31976197-31981050 - Homo sapiens tenascin XB (TNXB), transcript variant XB-S, mRNA.

I do see that if I click on the following search result instead, I see TNXB in the GENCODE v12 track and "Homo sapiens tenascin XB (TNXB), transcript variant XB, mRNA" in the UCSC track. 

TNXB (uc010jts.1) at chr6:32065573-32085471 - Homo sapiens tenascin XB (TNXB), transcript variant XB, mRNA.

But it looks like the second mRNA is actually the full-length one and is the one that has a corresponding GENCODE gene.  Does that seem right?

Jessica

[Steve Heitner]

Hello, Jessica.

I see what you mean now.  I performed a BLAT search on the DNA sequence at chr6:31,974,978-31,982,258 and both the coordinates you referenced (chr6:31,974,978-31,982,258) and the coordinates I referenced (chr6:32,008,720-32,078,223) come up as very good matches in BLAT.  This is likely why, even though the majority of the results for TNXB appear at chr6:32,008,720-32,078,223, there are still results for TNXB at chr6:31,974,978-31,982,258 in the UCSC Genes and RefSeq Genes tracks.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.

---
Steve Heitner
UCSC Genome Bioinformatics Group