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LOC107303342 3p25 TatD DNase domain containing 2 Alu-mediated recombination region [ Homo sapiens (human) ]

Gene ID: 107303342, updated on 10-Oct-2023

Summary

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Gene symbol
LOC107303342
Gene description
3p25 TatD DNase domain containing 2 Alu-mediated recombination region
Gene type
biological region
Feature type(s)
misc_feature: nucleotide_motif
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 biological region overlaps the TatD DNase domain containing 2 (TATDN2) gene and is known to undergo Alu-repeat-mediated non-allelic homologous recombination (NAHR) with the 3p25 FANCD2 Alu-mediated recombination region and the 3p25 BRK1 Alu-mediated recombination region, located about 175 kb and 115 kb centromere-distal of this region on the reference genome, respectively. Recombination between these regions can result in deletion of the intervening sequences, including the von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase (VHL) gene. Deletion of the VHL gene is one cause of Von Hippel-Lindau syndrome, which is inherited in autosomal dominant manner and predisposes individuals to multiple tumors. Deletions of various size have been reported, many of which are the result of Alu-mediated recombination. The severity of the disease is dependent on both the size and location of the deletion. This recombination region is composed of two NAHR sub-regions, representing different regions in which Alu-mediated recombination has been observed, and also contains meiotic recombination hotspots. Recombination events that result in the deletion of VHL have also been reported in regions overlapping the proline rich transmembrane protein 3 (PRRT3) gene, the von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase (VHL) gene, and the interleukin 1 receptor associated kinase 2 (IRAK2) gene. [provided by RefSeq, Oct 2016]
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Genomic context

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See LOC107303342 in Genome Data Viewer
Location:
3p25
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (10253583..10272080)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (10246883..10265377)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (10295267..10313764)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene 3p25 von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase Alu-mediated recombination region Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:10184379-10184912 Neighboring gene 3p25 IRAK2 Alu-mediated recombination region Neighboring gene von Hippel-Lindau tumor suppressor Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14055 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14056 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:10210671-10211181 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19418 Neighboring gene interleukin 1 receptor associated kinase 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:10227030-10227530 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:10227531-10228031 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19419 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19420 Neighboring gene Sharpr-MPRA regulatory region 12699 Neighboring gene U6 spliceosomal RNA Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:10266988-10267770 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19421 Neighboring gene Sharpr-MPRA regulatory region 8698 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:10275792-10276394 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14057 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14058 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:10290711-10291579 Neighboring gene TatD DNase domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14059 Neighboring gene microRNA 12127 Neighboring gene long intergenic non-protein coding RNA 852 Neighboring gene ghrelin opposite strand/antisense RNA Neighboring gene ghrelin and obestatin prepropeptide

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. Genotype-phenotype correlations, and retinal function and structure in von Hippel-Lindau disease. Wittström E, et al. Ophthalmic Genet, 2014 Jun. PMID 24555745
  2. Associations between VHL genotype and clinical phenotype in familial von Hippel-Lindau disease. Huang JS, et al. Eur J Clin Invest, 2007 Jun. PMID 17537157
  3. Genotype-phenotype correlations in von Hippel-Lindau disease. Ong KR, et al. Hum Mutat, 2007 Feb. PMID 17024664
  4. Molecular characterization of large deletions in the von Hippel-Lindau (VHL) gene by quantitative real-time PCR: the hypothesis of an alu-mediated mechanism underlying VHL gene rearrangements. Casarin A, et al. Mol Diagn Ther, 2006. PMID 16884328
  5. Detection of germline deletions using real-time quantitative polymerase chain reaction in Japanese patients with von Hippel-Lindau disease. Hattori K, et al. Cancer Sci, 2006 May. PMID 16630138

See all (19) 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

  • 3p25 TATDN2 Alu-mediated 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.

Genomic

  1. NG_046758.1 

    Range
    101..18598
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    10253583..10272080
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    10246883..10265377
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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