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    LOC107303341 3p25 IRAK2 Alu-mediated recombination region [ Homo sapiens (human) ]

    Gene ID: 107303341, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC107303341
    Gene description
    3p25 IRAK2 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 interleukin 1 receptor associated kinase 2 (IRAK2) gene and is known to undergo Alu-repeat-mediated non-allelic homologous recombination (NAHR) with recombination regions that overlap the proline rich transmembrane protein 3 (PRRT3) gene, the Fanconi anemia complementation group D2 (FANCD2) gene, the BRICK1, SCAR/WAVE actin-nucleating complex subunit (BRK1) gene, and the von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase (VHL) gene. These other recombination regions are located 214 kb, 86 kb, 26 kb, and 4 kb centromere-distal to 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 multiple sub-regions, representing different regions in which Alu-mediated recombination has been observed, and also contains several overlapping meiotic recombination hotspots. Recombination events that result in the deletion of VHL have also been reported in regions overlapping the TatD DNase domain containing 2 (TATDN2) gene. [provided by RefSeq, Oct 2016]
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    Genomic context

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    Location:
    3p25
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (10160532..10201782)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (10153422..10194686)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (10202216..10243466)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124906359 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 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 3p25 TatD DNase domain containing 2 Alu-mediated recombination region Neighboring gene TatD DNase domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14059 Neighboring gene microRNA 12127

    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 (20) 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)

    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_046757.1 

      Range
      101..41351
      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
      10160532..10201782
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      10153422..10194686
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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