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LOC126807554 BRD4-independent group 4 enhancer GRCh37_chr5:150473600-150474799 [ Homo sapiens (human) ]

Gene ID: 126807554, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126807554
Gene description
BRD4-independent group 4 enhancer GRCh37_chr5:150473600-150474799
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 region includes an enhancer that was validated 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. 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:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (151093995..151095238)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (151630481..151631724)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:150401597-150402796 Neighboring gene glutathione peroxidase 3 Neighboring gene TNFAIP3 interacting protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23429 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:150435866-150436392 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23430 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:150445954-150446696 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:150446697-150447439 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16518 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:150460705-150461415 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23432 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23433 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23434 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23435 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23437 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23438 Neighboring gene annexin A6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:150503406-150503906 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23439 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23441 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23442 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23443 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:150537501-150538357 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23444 Neighboring gene uncharacterized LOC107986463 Neighboring gene platelet derived growth factor receptor like 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. 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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 23436

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_083868.2 

    Range
    101..1344
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    151093995..151095238
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    151630481..151631724
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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