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LOC106736480 15q13 proximal microdeletion recombination region [ Homo sapiens (human) ]

Gene ID: 106736480, updated on 10-Oct-2023

Summary

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Gene symbol
LOC106736480
Gene description
15q13 proximal microdeletion recombination region
Gene type
biological region
Feature type(s)
misc_recomb: non_allelic_homologous
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, the 15q13 distal microdeletion recombination region, which is located nearly 2 Mb centromere-distal to this region, in direct orientation. NAHR between these recombination regions can lead to deletions of the intervening sequence, and may be associated with autism. While deletions of the intervening sequences has been observed in many affected individuals, finer mapping of the recombination regions has been limited to a small number of individuals. This recombination region partially overlaps that of a golgin A8 family member (GOLGA8 family), and the palindromic nature of the genes within this gene family has been implicated in the recombination events. [provided by RefSeq, Oct 2016]
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Genomic context

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Location:
15q13.2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (30614939..30628733)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (28408121..28421926)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (30907142..30920936)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene 15q13.2-13.3 gamma inversion proximal recombination region Neighboring gene U8 small nucleolar RNA Neighboring gene ARHGAP11B divergent transcript Neighboring gene ULK4 pseudogene 2 Neighboring gene golgin A8 family member H Neighboring gene RNA, 7SL, cytoplasmic 628, pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:30917238-30918231 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:30918882-30919057 Neighboring gene Rho GTPase activating protein 11B Neighboring gene OTU deubiquitinase 7A pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:30988059-30988666 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:30988667-30989274 Neighboring gene proximal CHRNA7 low-copy repeat recombination region Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:31000717-31001312 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:31001313-31001908 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:31066043-31066308 Neighboring gene putative golgin subfamily A member 8I Neighboring gene RNA, 7SL, cytoplasmic 82, 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. Palindromic GOLGA8 core duplicons promote chromosome 15q13.3 microdeletion and evolutionary instability. Antonacci F, et al. Nat Genet, 2014 Dec. PMID 25326701, 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_044989.1 

    Range
    101..13895
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    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    30614939..30628733
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_011332701.1 Reference GRCh38.p14 PATCHES

    Range
    2787428..2801229
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_012132920.1 Reference GRCh38.p14 PATCHES

    Range
    1899829..1913625 complement
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NT_187660.1 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    2899880..2913681
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    28408121..28421926
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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