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LOC120766155 negCOR silencer S1 [ Homo sapiens (human) ]

Gene ID: 120766155, updated on 10-Oct-2023

Summary

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Gene symbol
LOC120766155
Gene description
negCOR silencer S1
Gene type
biological region
Feature type(s)
regulatory: silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic region was predicted to be a silencer based on a correlation between histone H3 lysine 27 tri-methylation overlapping a DNase I hypersensitive site (H3K27me3-DHS) and negative regulation of nearby gene expression. It was experimentally validated as a negatively correlated (negCOR) silencer that significantly represses activity of an enhancer-driven reporter gene in K562 erythroleukemia cells. A subregion was also validated as a functional repressive element by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Mar 2022]
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Genomic context

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Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (65983501..65984072)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (65963016..65963587)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (66377281..66377852)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene high mobility group AT-hook 2 Neighboring gene HMGA2 antisense RNA 1 Neighboring gene MPRA-validated peak1769 silencer Neighboring gene MPRA-validated peak1770 silencer Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:66285256-66286168 Neighboring gene hESC enhancers GRCh37_chr12:66289853-66290620 and GRCh37_chr12:66290621-66291388 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:66291389-66292155 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:66320206-66320716 Neighboring gene HNF4 motif-containing MPRA enhancer 102 Neighboring gene uncharacterized LOC124902955 Neighboring gene long intergenic non-protein coding RNA 2425 Neighboring gene microRNA 6074

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 human silencers by correlating cross-tissue epigenetic profiles and gene expression. Huang D, et al. Genome Res, 2019 Apr. PMID 30886051, Free PMC Article
  2. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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)

General gene information

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Other Names

  • Sharpr-MPRA regulatory region 11483

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_073725.1 

    Range
    101..672
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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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    65983501..65984072
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    65963016..65963587
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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