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LOC112268478 BRD4-independent group 4 enhancer GRCh37_chr14:34512642-34513841 [ Homo sapiens (human) ]

Gene ID: 112268478, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112268478
Gene description
BRD4-independent group 4 enhancer GRCh37_chr14:34512642-34513841
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 (MPRA) 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. 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). This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
14q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (34043436..34044635)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (28241227..28242426)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (34512969..34513263)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene NANOG hESC enhancer GRCh37_chr14:34400622-34401183 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:34407170-34408141 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8243 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5660 Neighboring gene uncharacterized LOC102724945 Neighboring gene uncharacterized LOC105370446 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:34433111-34433612 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8244 Neighboring gene egl-9 family hypoxia inducible factor 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8245 Neighboring gene Sharpr-MPRA regulatory region 12661 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8247 Neighboring gene EGLN3 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:34529023-34529524 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8248 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8249 Neighboring gene uncharacterized LOC105370444 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:34608249-34609068 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:34609069-34609887 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8251 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8252 Neighboring gene sulfotransferase family 1C member 2 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
  3. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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

  • ATAC-STARR-seq lymphoblastoid active region 8246
  • Sharpr-MPRA regulatory region 2297

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_056675.2 

    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    34043436..34044635
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    28241227..28242426
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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