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LOC106007490 DPY19L2 LCR1 recombination region 1 [ Homo sapiens (human) ]

Gene ID: 106007490, updated on 10-Oct-2023

Summary

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Gene symbol
LOC106007490
Gene description
DPY19L2 LCR1 recombination region 1
Gene type
biological region
Feature type(s)
misc_feature: nucleotide_motif
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 region, the DPY19L2 LCR2 recombination region 1, which is located about 195 kb centromere-distal to this region. NAHR between these regions can result in either duplications or deletions of the intervening sequence, 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 and a 13-mer consensus linkage disequilibrium hotspot motif, predicted to be the binding site for PRDM9 A. 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 LCR1 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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See LOC106007490 in Genome Data Viewer
Location:
12q14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (63540986..63543198)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (63519644..63521858)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (63934766..63936978)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 69 Neighboring gene long intergenic non-protein coding RNA 3056 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:63812284-63813483 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4612 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4613 Neighboring gene uncharacterized LOC105369797 Neighboring gene DPY19L2 LCR1 recombination region 2 Neighboring gene dpy-19 like 2 Neighboring gene S100A11 pseudogene 4

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 (7) 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 1 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_042208.1 

    Range
    101..2313
    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
    63540986..63543198
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    63519644..63521858
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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