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LOC108281114 9q34.3 TOR4A distal recombination region [ Homo sapiens (human) ]

Gene ID: 108281114, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108281114
Gene description
9q34.3 TOR4A distal recombination region
Gene type
biological region
Feature type(s)
misc_feature: nucleotide_motif
misc_recomb: meiotic, recombination_hotspot
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 found centromere-distal to the torsin family 4 member A (TOR4A) gene, and is known to undergo recombination, forming interstitial deletion on chromosome 9. Secondary structure prediction analysis indicates the possibility that this region could fold into a complex structure with hairpins, loops, and DNA bending. Clinical variability can be observed in individuals with 9q34.3 deletions, but there is a characteristic phenotype for 9q34.3 microdeletions, including distinctive craniofacial features, hypotonia, obesity, microcephaly and speech delay (CHOMS). This region contains a meiotic recombination hotspot. [provided by RefSeq, Jul 2016]
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Genomic context

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Location:
9q34.3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (137287226..137293334)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (149525273..149531254)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (140181678..140187786)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140149187-140150134 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140150135-140151082 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140157448-140158007 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140165697-140166196 Neighboring gene negative elongation factor complex member B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29349 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20604 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20605 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20606 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20607 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29350 Neighboring gene torsin family 4 member A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20608 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140191021-140191688 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140193329-140194222 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20609 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20610 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20611 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140196022-140196940 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140201529-140202446 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140204820-140205742 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140205743-140206664 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140209101-140210036 Neighboring gene NOTCH regulated ankyrin repeat protein Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20613 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20614 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140213503-140214138 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140214773-140215407 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140215408-140216041 Neighboring gene exonuclease 3'-5' domain containing 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140245426-140245935 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140245936-140246444 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:140262690-140263291 Neighboring gene MPRA-validated peak7347 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr9:140264677-140264866 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20615 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20616 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:140306223-140306402 Neighboring gene Sharpr-MPRA regulatory region 4638 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:140311837-140312663 Neighboring gene uncharacterized LOC124902354

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. Molecular mechanisms for subtelomeric rearrangements associated with the 9q34.3 microdeletion syndrome. Yatsenko SA, et al. Hum Mol Genet, 2009 Jun 1. PMID 19293338, Free PMC Article
  2. Deletion 9q34.3 syndrome: genotype-phenotype correlations and an extended deletion in a patient with features of Opitz C trigonocephaly. Yatsenko SA, et al. J Med Genet, 2005 Apr. PMID 15805160, Free PMC Article
  3. A 1-Mb critical region in six patients with 9q34.3 terminal deletion syndrome. Harada N, et al. J Hum Genet, 2004. PMID 15258833
  4. 9q34.3 deletion syndrome in three unrelated children. Iwakoshi M, et al. Am J Med Genet A, 2004 Apr 30. PMID 15054842
  5. Loss-of-function mutations in euchromatin histone methyl transferase 1 (EHMT1) cause the 9q34 subtelomeric deletion syndrome. Kleefstra T, et al. Am J Hum Genet, 2006 Aug. PMID 16826528, Free PMC Article

See all (8) 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

  • 9q34.3 torsin family 4 member A distal 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_051055.1 

    Range
    101..6209
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    137287226..137293334
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    149525273..149531254
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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