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LOC108178991 20p12 distal LINE-mediated recombination region [ Homo sapiens (human) ]

Gene ID: 108178991, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108178991
Gene description
20p12 distal LINE-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 region is located just centromere-distal to the phospholipase C beta 1 (PLCB1) gene, and is known to undergo non-allelic homologous recombination (NAHR) with another region, the 20p12 proximal LINE-mediated recombination region, which contains a similar long interspersed element (LINE) element in direct orientation relative to this region. Recombination with the 20p12 proximal LINE-mediated recombination region can result in a 486 kb deletion or duplication of the intervening sequence. Recombination breakpoints of individuals with genomic rearrangements are indicated as NAHR sub-regions on the record. [provided by RefSeq, Jun 2016]
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Genomic context

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Location:
20p12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (8108867..8114868)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (8150828..8156823)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (8089514..8095515)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 13354 Neighboring gene TMX4 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 6433 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12668 Neighboring gene HNF1, HNF4 and FOXA motif-containing MPRA enhancers 45, 51 and 106/107 Neighboring gene phosphorylase kinase regulatory subunit beta pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17536 Neighboring gene phospholipase C beta 1 Neighboring gene PLCB1 intronic transcript 1 Neighboring gene NANOG hESC enhancer GRCh37_chr20:8290037-8290646 Neighboring gene uncharacterized LOC124900459 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:8444621-8445820

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. Genome-wide analyses of LINE-LINE-mediated nonallelic homologous recombination. Startek M, et al. Nucleic Acids Res, 2015 Feb 27. PMID 25613453, Free PMC Article

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_050950.1 

    Range
    101..6102
    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
    8108867..8114868
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    8150828..8156823
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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