LOC106128902 AZFa HERV15yq1 recombination region [Homo sapiens (human)] - Gene

Summary

Gene symbol: LOC106128902
Gene description: AZFa HERV15yq1 recombination region
Gene type: biological region
Feature type(s): misc_recomb: meiotic, non_allelic_homologous
mobile_element
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary: This region is known to undergo non-allelic homologous recombination (NAHR) with a similar low-copy repeat region, the AZFa HERV15yq2 (azoospermia factor a human endogenous retrovirus 15 yq2) recombination region, which is located about 790-800 kb centromere-distal of this region. NAHR between the AZFa HERV15yq1 and AZFa HERV15yq2 recombination regions can result in duplications and deletions of the intervening sequences, including the DEAD (Asp-Glu-Ala-Asp) box helicase 3, Y-linked (DDX3Y) and ubiquitin specific peptidase 9, Y-linked (USP9Y, also known as DFFRY) genes. Recombination occurs within the human endogenous retrovirus 15 (HERV15) element. This region contains sub-regions that have been identified as NAHR exchange sites, ID1 (identical sequence 1) and ID2 (identical sequence 2). It also contains two meiotic recombination hotspots that overlap the NAHR exchange sites. The nearly 800 kb deletion that can occur as a result of NAHR between the HERV15yq1 and HERV15yq2 recombination regions has been observed in some individuals with AZFa, and is thought to cause a complete Sertoli-cell-only type 1 phenotype. [provided by RefSeq, Sep 2016]
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Genomic context

Location:: Yq11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	Y	NC_000024.10 (12312195..12321471)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	Y	NC_060948.1 (13219646..13228909)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	Y	NC_000024.9 (14432922..14442198)

Chromosome Y - NC_000024.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

AZFa proximal HERV15 recombination region
azoospermia factor a human endogenous retroviral yq1 recombination region

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.