coordinates of the human gene ZNF536

[FASANO Laurent]

Sir,

For the same version of the GRCh37/hg19 genome, the coordinates of the human gene ZNF536 in NCBI and UCSC are different from those in Ensembl: 

chr19: 30,863,328-31,048,965 vs. chr19: 30,719,197-31,204,445

​​​​​​​Could you please, help me to solve this point.

Best,

Laurent Fasano

[Luis Nassar]

Hello Laurent,

Thank you for your interest in the Genome Browser.

As you have noted, Ensembl/NCBI and UCSC list different coordinates for ZNF536. This is due to a few reasons.

The primary reason is that the default GRCh37/hg19 annotations we display are not the same as NCBI or Ensembl. For hg19, our default genes track is UCSC Genes, which were an in-house generated set of gene predictions. You can read more in the description page (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&c=chr19&g=knownGene). For hg19, NCBI uses refseq release 105 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Homo_sapiens/105/). Ensemble uses GENCODE release 19 (https://www.gencodegenes.org/human/release_19.html) as the default.

While all these annotations are largely similar, they are not identical. It is also worth noting that these annotations are all from 2013.

Another difference is how we display our genes when you search for them. Both Ensembl and NCBI provide a location like you have said (30,719,197-31,204,445). These are the coordinates from the beginning of the first transcript, to the end of the final transcript. This gene in particular is comprised of 5 transcripts:

ZNF536 at chr19: 30719197 - 30791576
ZNF536 at chr19:30719421 - 31039375
ZNF536 at chr19:30719461 - 30934885
ZNF536 at chr19:30863291 - 31048966
ZNF536 at chr19:31040253 - 31204445

Searching for a gene in the Genome Browser takes you to specific transcript hits, like the one you have provided (30,863,328-31,048,965). It is worth noting that we do provide more recent gene annotations, most notably our lifts of the latest GENCODE releases from hg38 to hg19. If you see all the search results for ZNF536, you will see the Comprehensive Gene Annotation Set from GENCODE Version 31lift37 (Ensembl 97) results, which is the latest release currently on hg19, has the same coordinates seen in both Ensembl and NCBI.

For more information about our different gene annotations, as well as the different group annotations, see our FAQ genes page.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

Training videos & resources: http://genome.ucsc.edu/training/index.html
Want to share the Browser with colleagues?
Host a workshop: http://bit.ly/ucscTraining

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[FASANO Laurent]

Dear Luis,

Many thanks for your helpful comments.

My question was motivated by the fact that my team described a new human syndrome linked to the TSHZ3 gene (Caubit et al., Nat Genet 2016 PMID:31060802). 

All patients we identified so far are heterozygote for TSHZ3 and I maintain updated the list; all deletion coordinates correspond to the hg19 version.

The last deletion we identified was Chr19:31163540-31984490 (hg19)

This deletion for sure uncovers TSHZ3 but it was not clear whether it also uncovers ZNF536; probably yes, if we consider the isoform ZNF536 at chr19:31040253 - 31204445.

For the future, would you recommend that I convert all « GRCh37/hg19 » coordinates for "GRCh38/hg38 »?

Best,

Laurent

Laurent Fasano, PhD

IBDM CNRS UMR 7288
Parc Scientifique de Luminy
163 avenue de Luminy
Case 907
13288 Marseille cedex 09
France

[Daniel Schmelter]

Hello Laurent,

It is worth noting that RefSeq and Gencode only release gene updates on hg38 and do not release updated data for hg19. These gene sets have changed and it may be helpful to compare your data with the most up-to-date gene sets. Many people chose to use the hg19 assembly largely because certain research data has not been converted to hg38. On our site, hg19 is still used almost twice as much as hg38.

Looking at data on both assemblies will be the most informative, especially with conflicting transcript annotations for ZNF536 given by Gencode and RefSeq. Sharing both sets of coordinates could also make your findings more accessible to researchers regardless of their assembly preference. In order to convert hg19 coordinates to hg38 from the Browser, we recommend you click View from the blue navigation bar and then click In Other Genome (Convert), selecting hg38. For converting many entries, we recommend the LiftOver tool:

http://genome.ucsc.edu/cgi-bin/hgLiftOver

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Daniel Schmelter
UCSC Genome Browser

Training videos & resources: http://genome.ucsc.edu/training/index.html
Want to share the Browser with colleagues?
Host a workshop: http://bit.ly/ucscTraining

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/353CCB10-554D-45B3-8859-4E167B440A5A%40univ-amu.fr.

[FASANO Laurent]

Thanks to all for your help.

Best regards,

Laurent

Laurent Fasano, PhD

IBDM CNRS UMR 7288
Parc Scientifique de Luminy
163 avenue de Luminy
Case 907
13288 Marseille cedex 09
France