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LOC112533639 BRD4-independent group 4 enhancer GRCh37_chr17:41428482-41429681 [ Homo sapiens (human) ]

Gene ID: 112533639, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112533639
Gene description
BRD4-independent group 4 enhancer GRCh37_chr17:41428482-41429681
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. A subregion 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, where it 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. An overlapping subregion was also validated as a functional enhancer by the Sharpr-MPRA technique (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 18:Pol2, Pol2 specific locations, majority in genes but substantial portion in intergenic locations) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 6:EnhF, candidate strong enhancer, flanking open chromatin), [provided by RefSeq, Aug 2022]
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Genomic context

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See LOC112533639 in Genome Data Viewer
Location:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (43350901..43352313)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (44196846..44198254)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (41428269..41428563)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene U2 spliceosomal RNA Neighboring gene U2 spliceosomal RNA Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:41382086-41382759 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:41392761-41393398 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:41393399-41394036 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:41399501-41400008 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:41400009-41400516 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:41400517-41401024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12240 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8551 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr17:41437411-41438106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12241 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8552 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8553 Neighboring gene Sharpr-MPRA regulatory region 625 Neighboring gene U2 spliceosomal RNA Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:41445663-41446502 Neighboring gene uncharacterized LOC105371785 Neighboring gene long intergenic non-protein coding RNA 910

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 4809

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_056910.2 

    Range
    101..1513
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    43350901..43352313
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    44196846..44198254
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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