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LOC112997593 P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:5598283-5599482 [ Homo sapiens (human) ]

Gene ID: 112997593, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112997593
Gene description
P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:5598283-5599482
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 non-DNase unmatched - State 24:Quies, heterochromatin/dead zone) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 2:TssF, active promoter, flanking TSS/CpG islands). [provided by RefSeq, Aug 2022]
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Genomic context

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Location:
5p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (5598170..5599369)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (5526034..5527233)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (5598809..5599103)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101929200 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22323 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:5421524-5422036 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:5422037-5422547 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15891 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15892 Neighboring gene MT-CO1 pseudogene 31 Neighboring gene interactor of little elongation complex ELL subunit 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15893 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15894 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:5497406-5497930 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:5497931-5498453 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:5511108-5511904 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:5521050-5521695 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:5520403-5521049 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22325 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:5536038-5536538 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:5569545-5570081 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:5570631-5571270 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:5573793-5574352 Neighboring gene NANOG hESC enhancer GRCh37_chr5:5621457-5621987 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:5651964-5652474 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:5652475-5652984 Neighboring gene uncharacterized LOC105374634 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22326 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22327 Neighboring gene uncharacterized LOC105374636

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 1432

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_061592.2 

    Range
    101..1300
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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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    5598170..5599369
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    5526034..5527233
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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