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LOC126807615 MED14-independent group 3 enhancer GRCh37_chr5:175815238-175816437 [ Homo sapiens (human) ]

Gene ID: 126807615, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126807615
Gene description
MED14-independent group 3 enhancer GRCh37_chr5:175815238-175816437
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 enhancers that were validated by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA). The major subregion had activity in HCT116 colorectal carcinoma cells, where it was defined as a group 3 enhancer that depends on the BRD2, BRD4, P300/CBP and CDK7 cofactors, but it has limited or no dependence on the MED14 core Mediator complex subunit. Two subregions were also shown to be active enhancers by ChIP-STARR-seq in human embryonic stem cells, where both are marked by the H3K27ac histone modification, and one is additionally associated with the NANOG transcription factor and marked by H3K4me1. This locus also includes two accessible chromatin subregions that were validated as enhancers based on their 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 (176387902..176389953)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (176932260..176934311)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene KIAA1191 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23680 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23681 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16649 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:175805661-175805825 Neighboring gene microRNA 1271 Neighboring gene ADP ribosylation factor like GTPase 10 Neighboring gene NOP16 nucleolar protein Neighboring gene HIG1 hypoxia inducible domain family member 2A Neighboring gene clathrin light chain B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16650 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16651 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16652 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:175861163-175861909 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23684 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23685 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16653 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23686 Neighboring gene uncharacterized LOC124901142 Neighboring gene Fas associated factor family member 2

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
  3. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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 23682
  • ATAC-STARR-seq lymphoblastoid active region 23683
  • H3K27ac hESC enhancer GRCh37_chr5:175814903-175815586
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:175816271-175816954

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_083929.2 

    Range
    101..2152
    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
    176387902..176389953
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    176932260..176934311
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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