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LOC108167311 proximal ADA Alu-mediated recombination region [ Homo sapiens (human) ]

Gene ID: 108167311, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108167311
Gene description
proximal ADA Alu-mediated recombination region
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 biological region is contained within an intron of the adenosine deaminase (ADA) gene and is known to undergo Alu-repeat-mediated non-allelic homologous recombination (NAHR) with the distal ADA Alu-mediated recombination region, located about 3 kb centromere-distal of this region on the reference genome. Recombination between these regions can result in a deletion of the intervening sequence, including an exon and the promoter region of the ADA gene. The deletion of about 3.2 kb that results from NAHR between Alu elements results in adenosine deaminase (ADA)-deficient severe combined immunodeficiency (SCID), a syndrome characterized by a deficiency in B and T cell function. [provided by RefSeq, Jun 2016]
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Genomic context

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Location:
20q13.12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (44649731..44650034)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (46385508..46385809)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (43278372..43278675)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:43124829-43126028 Neighboring gene serine incorporator 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:43149922-43150474 Neighboring gene Sharpr-MPRA regulatory region 7879 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr20:43152936-43153812 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:43154689-43155564 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:43160105-43160605 Neighboring gene cAMP-dependent protein kinase inhibitor gamma Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17927 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17929 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17928 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:43226219-43226966 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:43229479-43229980 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:43237694-43238268 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17930 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17931 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17932 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17933 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr20:43246415-43247142 Neighboring gene adenosine deaminase intronic regulatory elements Neighboring gene adenosine deaminase Neighboring gene distal ADA Alu-mediated recombination region Neighboring gene long intergenic non-protein coding RNA 1260 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:43299119-43299620 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:43299621-43300120 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:43306608-43307108 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:43307109-43307609 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12945 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12946 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12947 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17939 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17940 Neighboring gene uncharacterized LOC124904911 Neighboring gene Sharpr-MPRA regulatory region 14821 Neighboring gene KCNK15 and WISP2 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. Severe combined immune deficiency due to a homozygous 3.2-kb deletion spanning the promoter and first exon of the adenosine deaminase gene. Berkvens TM, et al. Nucleic Acids Res, 1987 Nov 25. PMID 3684597, Free PMC Article
  2. Identification of a deletion in the adenosine deaminase gene in a child with severe combined immunodeficiency. Markert ML, et al. J Immunol, 1987 May 15. PMID 3571974
  3. Adenosine deaminase (ADA) deficiency due to deletion of the ADA gene promoter and first exon by homologous recombination between two Alu elements. Markert ML, et al. J Clin Invest, 1988 May. PMID 3366897, Free PMC Article
  4. Identical 3250-bp deletion between two AluI repeats in the ADA genes of unrelated ADA-SCID patients. Berkvens TM, et al. Genomics, 1990 Aug. PMID 1696926
  5. A common sequence motif associated with recombination hot spots and genome instability in humans. Myers S, et al. Nat Genet, 2008 Sep. PMID 19165926

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

  • proximal adenosine deaminase 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_050901.1 

    Range
    101..404
    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    44649731..44650034
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    46385508..46385809
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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