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LOC106007491 DPY19L2 LCR2 recombination region 1 [ Homo sapiens (human) ]

Gene ID: 106007491, updated on 10-Oct-2023

Summary

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Gene symbol
LOC106007491
Gene description
DPY19L2 LCR2 recombination region 1
Gene type
biological region
Feature type(s)
misc_recomb: 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 (LCR), the DPY19L2 LCR1 recombination region 1, which is located 195 kb centromere-proximal to this region. NAHR between these regions results in both duplications and deletions of the intervening sequences, including the dpy-19-like 2 (DPY19L2) gene. This region is contained within a larger 28 kb low-copy repeat (LCR) region. The recombination region represented here is composed of multiple sub-regions, named sub-regions 1'-10', that have been identified as NAHR exchange sites in different individuals. The majority of recombination events have been observed in an about 600 nt region that includes sub-regions 3'-7', where there is an Alu repeat region. NAHR events that lead to deletions of the 195 kb of sequence between the DPY19L2 LCR1 and LCR2 recombination regions, which includes DPY19L2, can be a cause of globozoospermia, an autosomal recessive disorder that results in infertility in males. Another region, the DPY19L2 LCR2 recombination region 2, is also known to undergo NAHR events that can be a cause of globozoospermia, and is found about 8 kb centromere-distal to this region, within the low-copy repeat region. [provided by RefSeq, Sep 2016]
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Genomic context

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Location:
12q14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (63736026..63738246)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (63714689..63716909)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (64129806..64132026)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene dpy-19 like 2 Neighboring gene S100A11 pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6585 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:64062679-64063180 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:64063181-64063680 Neighboring gene T-box 20 pseudogene Neighboring gene DPY19L2 LCR2 recombination region 2 Neighboring gene ribosomal protein S27 pseudogene 24 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4614 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:64173754-64174029 Neighboring gene ribitol xylosyltransferase 1 Neighboring gene RXYLT1 antisense RNA 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. A Homozygous Deletion of the DPY19l2 Gene is a Cause of Globozoospermia in Men from the Republic of Macedonia. Noveski P, et al. Balkan J Med Genet, 2013 Jun. PMID 24265589, Free PMC Article
  2. Identification of a new DPY19L2 mutation and a better definition of DPY19L2 deletion breakpoints leading to globozoospermia. Ghédir H, et al. Mol Hum Reprod, 2016 Jan. PMID 26516168
  3. Fine characterisation of a recombination hotspot at the DPY19L2 locus and resolution of the paradoxical excess of duplications over deletions in the general population. Coutton C, et al. PLoS Genet, 2013 Mar. PMID 23555282, Free PMC Article
  4. A recurrent deletion of DPY19L2 causes infertility in man by blocking sperm head elongation and acrosome formation. Harbuz R, et al. Am J Hum Genet, 2011 Mar 11. PMID 21397064, Free PMC Article
  5. DPY19L2 deletion as a major cause of globozoospermia. Koscinski I, et al. Am J Hum Genet, 2011 Mar 11. PMID 21397063, Free PMC Article

See all (8) citations in PubMed

GeneRIFs: Gene References Into Functions

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

  • DPY19L2 low copy repeat 2 recombination region 1

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.

Genomic

  1. NG_042209.1 

    Range
    101..2321
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    63736026..63738246
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    63714689..63716909
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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