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LOC108178987 12p13 proximal LINE-mediated recombination region [ Homo sapiens (human) ]

Gene ID: 108178987, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108178987
Gene description
12p13 proximal 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 known to undergo non-allelic homologous recombination (NAHR) with another region, the 12p13 distal LINE-mediated recombination region, which contains a similar long interspersed element (LINE) element in direct orientation relative to this region. Recombination with the 12p13 proximal LINE-mediated recombination region can result in a 168 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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See LOC108178987 in Genome Data Viewer
Location:
12p13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (5284941..5290958)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (5291121..5297137)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (5394107..5400124)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369617 Neighboring gene uncharacterized LOC105369616 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr12:5330975-5331795 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:5341834-5342334 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:5342335-5342835 Neighboring gene Sharpr-MPRA regulatory region 8722 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:5355081-5355848 Neighboring gene long intergenic non-protein coding RNA 2443 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:5377405-5378062 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:5399277-5399846 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:5399847-5400415 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:5497373-5498572 Neighboring gene uncharacterized LOC105369618 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:5542091-5542616 Neighboring gene neurotrophin 3

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_050935.1 

    Range
    101..6118
    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
    5284941..5290958
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    5291121..5297137
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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