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LOC112997543 P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:84469077-84470276 [ Homo sapiens (human) ]

Gene ID: 112997543, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112997543
Gene description
P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:84469077-84470276
Gene type
biological region
Feature type(s)
regulatory: enhancer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as an active enhancer by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay in HCT116 colorectal carcinoma cells. This sequence was defined as a group 1 enhancer that depends on the BRD2, BRD4, P300/CBP, MED14 and CDK7 cofactors, with strong dependence on P300/CBP. A subregion was also validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh). [provided by RefSeq, Aug 2022]
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Genomic context

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See LOC112997543 in Genome Data Viewer
Location:
4q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (83547924..83549123)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (86878024..86879223)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (84469649..84469943)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15542 Neighboring gene solute carrier family 25 member 14 pseudogene 1 Neighboring gene abraxas 1, BRCA1 A complex subunit Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15543 Neighboring gene ribosomal protein L30 pseudogene 5 Neighboring gene Sharpr-MPRA regulatory region 7334 Neighboring gene glycerol-3-phosphate acyltransferase 3 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:84539256-84540455 Neighboring gene Sharpr-MPRA regulatory region 4612 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:84557857-84558358 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21689 Neighboring gene VISTA enhancer hs712 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:84702313-84703031 Neighboring gene uncharacterized LOC105377315 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:84771005-84771616 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:84771617-84772228 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:84775825-84777024 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:84843248-84843790 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:84843791-84844331 Neighboring gene NANOG hESC enhancer GRCh37_chr4:84917176-84917884 Neighboring gene long intergenic non-protein coding RNA 2994 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:85048206-85048769 Neighboring gene RNA, U6 small nuclear 774, 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. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, 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 4722

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_061536.2 

    Range
    101..1300
    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    83547924..83549123
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    86878024..86879223
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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