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LOC108175341 5p14.1 proximal LINE-mediated recombination region [ Homo sapiens (human) ]

Gene ID: 108175341, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108175341
Gene description
5p14.1 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, containing a similar long interspersed element (LINE) element nearly 300 kb centromere-distal to this region, found in direct orientation relative to this region, on the p arm of chromosome 5. Recombination with the 5p14.1 distal LINE-mediated recombination region can result in deletions and duplications 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 LOC108175341 in Genome Data Viewer
Location:
5p14.1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (25378530..25384556)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (25483712..25489742)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (25378639..25384665)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2228 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:25190769-25191268 Neighboring gene long intergenic non-protein coding RNA 2211 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:25330102-25330602 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:25330603-25331103 Neighboring gene NANOG hESC enhancer GRCh37_chr5:25441975-25442639 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:25445439-25446078 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:25446079-25446718 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:25448018-25448856 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:25500627-25501143 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:25567928-25568436 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:25568437-25568943 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:25568944-25569451 Neighboring gene uncharacterized LOC124901175 Neighboring gene NANOG hESC enhancer GRCh37_chr5:25570127-25570673 Neighboring gene RNA, U6 small nuclear 374, pseudogene

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_050915.1 

    Range
    101..6127
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    25378530..25384556
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    25483712..25489742
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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