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LOC106020711 LCR17pA recombination region [ Homo sapiens (human) ]

Gene ID: 106020711, updated on 10-Oct-2023

Summary

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Gene symbol
LOC106020711
Gene description
LCR17pA 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 region is known to undergo non-allelic homologous recombination (NAHR) with a similar low-copy repeat region, LCR17pD, which is located about 4.8 Mb centromere-proximal to this region. NAHR between these regions can result in either duplications or deletions of the intervening sequence, including the RAI1 (retinoic acid induced 1) gene. Deletion events are the cause of the autosomal dominant Smith-Magenis syndrome (SMS), while the reciprocal duplication is associated with Potocki-Lupski syndrome (PTLS), also an autosomal dominant disease. While a 3.7 Mb duplication/deletion as a result of NAHR between the distal and proximal SMS-REP regions is more commonly observed in SMS and PTLS individuals (see the distal and proximal SMS-REP recombination regions), recurrent independent recombination events between LCR17pA and LCR17pD have also been observed, with the majority of NAHR events occurring within an Alu element. This region contains both an NAHR exchange site and an overlapping meiotic recombination hotspot. [provided by RefSeq, Oct 2017]
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Genomic context

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Location:
17p12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (15843747..15844894)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (15750184..15751331)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (15747061..15748208)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene NANOG hESC enhancer GRCh37_chr17:15716437-15716999 Neighboring gene long intergenic non-protein coding RNA 2087 Neighboring gene Sharpr-MPRA regulatory region 5503 Neighboring gene uncharacterized LOC105371557 Neighboring gene SPECC1 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:15760104-15761059 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:15761456-15762052 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr17:15762053-15762649 Neighboring gene adenosine A2b receptor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:15785055-15785554 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:15831280-15831780 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:15831781-15832281 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:15848447-15849261 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:15854153-15854950 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:15869033-15869619 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:15869620-15870205 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:15870206-15870792 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:15870793-15871377 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:15871628-15872376 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:15872377-15873123 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:15881867-15882452 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr17:15882453-15883039 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:15885417-15886106 Neighboring gene zinc finger SWIM-type containing 7 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8213 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11746

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. Identification of uncommon recurrent Potocki-Lupski syndrome-associated duplications and the distribution of rearrangement types and mechanisms in PTLS. Zhang F, et al. Am J Hum Genet, 2010 Mar 12. PMID 20188345, Free PMC Article
  2. The genomic basis of disease, mechanisms and assays for genomic disorders. Stankiewicz P, et al. Genome Dyn, 2006. PMID 18724050
  3. Complex chromosome 17p rearrangements associated with low-copy repeats in two patients with congenital anomalies. Vissers LE, et al. Hum Genet, 2007 Jul. PMID 17457615, Free PMC Article
  4. Uncommon deletions of the Smith-Magenis syndrome region can be recurrent when alternate low-copy repeats act as homologous recombination substrates. Shaw CJ, et al. Am J Hum Genet, 2004 Jul. PMID 15148657, Free PMC Article
  5. Genome architecture catalyzes nonrecurrent chromosomal rearrangements. Stankiewicz P, et al. Am J Hum Genet, 2003 May. PMID 12649807, Free PMC Article

See all (6) 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)

General gene information

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Other Names

  • low copy repeat 17p A 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_042224.2 

    Range
    101..1248
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    15843747..15844894
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    15750184..15751331
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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