PAR1 region X/Y Chromosomes GRCh37/hg19

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Maria Gattuso

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Jan 13, 2016, 10:15:16 AM1/13/16

to gen...@soe.ucsc.edu

Hi,

As confirmed in the UCSC Genome Browser website, in all the genome assemblies (NCBI34/hg16, NCBI35/hg17, NCBI36/hg18, GRCh37/hg19 and GRCh38/hg38), the Y chromosome contains two pseudoautosomal regions (PARs) that are taken from the corresponding regions in the X chromosome and are exact duplicates.

I am currently working on the PAR1 and I have noticed that the genomic coordinates of this region are usually identical between the X and Y chromosomes, in all the assemblies (e.g. NCBI36/hg18: PAR1 at chrX:1-2,709,520 and chrY:1-2,709,520; or

GRCh38/hg38: PAR1 at chrX:10,000-2,781,479 and chrY:10,000-2,781,479).

For my analysis, however, I have to use GRCh37/hg19, and I have realised that this is the only assembly with different genomic coordinates of the PAR1 between the X and Y chromosomes (i.e. GRCh37/hg19: PAR1 at chrX:60,001-2,699,520 and chrY:10,001-2,649,520; there is a 50 Kbp difference in the position of the PAR1 on the X and Y chromosomes).

I was wondering what is the reason for this (I am working with copy number variations, and CNV coordinates in the PAR1 should normally be interchangeable between the X and Y chromosomes).

Many thanks

Maria

Matthew Speir

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Jan 13, 2016, 5:14:26 PM1/13/16

to Maria Gattuso, gen...@soe.ucsc.edu

Hi Maria,

Thank you for your questions about the locations of the pseudoautosomal regions for the human assemblies.

These pseudoautosomal regions are defined by the groups that created these assemblies, which for both hg19 and hg38 was the Genome Reference Consortium (GRC). For example, the locations of the pseudoautosomal regions in hg38 come from the following NCBI file: ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.31_GRCh38.p5/GCF_000001405.31_GRCh38.p5_assembly_structure/Primary_Assembly/pseudoautosomal_region/par_align.gff. Additionally, the locations of the PAR in hg38 and hg19 can be found on the following GRC page as well: https://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/.

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.

Matthew Speir
UCSC Genome Bioinformatics Group