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LOC113002585 BRD4-independent group 4 enhancer GRCh37_chr5:56988450-56989649 [ Homo sapiens (human) ]

Gene ID: 113002585, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113002585
Gene description
BRD4-independent group 4 enhancer GRCh37_chr5:56988450-56989649
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 4 enhancer that depends on the BRD2, P300/CBP, MED14 and CDK7 cofactors, but it has limited or no dependence on the BRD4 bromodomain protein. 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 matched - State 5:Enh, candidate strong enhancer, open chromatin) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 5:Enh). [provided by RefSeq, Aug 2022]
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Genomic context

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See LOC113002585 in Genome Data Viewer
Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (57692623..57693822)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (58521398..58522598)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (56988969..56989263)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901182 Neighboring gene lncRNA SMARCA2 (BRM) associated Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:56937789-56938367 Neighboring gene uncharacterized LOC101928505 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:56994597-56995101 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:57011915-57013114 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:57030843-57032042 Neighboring gene Sharpr-MPRA regulatory region 14061 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:57131079-57131587 Neighboring gene Sharpr-MPRA regulatory region 14379 Neighboring gene NANOG hESC enhancer GRCh37_chr5:57141460-57142040 Neighboring gene long intergenic non-protein coding RNA 2225 Neighboring gene Sharpr-MPRA regulatory region 13165 Neighboring gene uncharacterized LOC124901183 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:57363636-57364835

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 2408

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_061596.2 

    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
    57692623..57693822
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    58521398..58522598
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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