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LOC126805781 MED14-independent group 3 enhancer GRCh37_chr1:89239743-89240942 [ Homo sapiens (human) ]

Gene ID: 126805781, updated on 12-Sep-2024

Summary

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Gene symbol
LOC126805781
Gene description
MED14-independent group 3 enhancer GRCh37_chr1:89239743-89240942
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. 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 shown also to be active enhancers by ChIP-STARR-seq in primed human embryonic stem cells, where both subregions are marked by the H3K27ac and H3K4me1 histone modifications and associated with the OCT4 and NANOG transcription factors. [provided by RefSeq, Oct 2022]
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Genomic context

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See LOC126805781 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (88773982..88775259)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (88617397..88618674)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (89239665..89240942)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene PKN2 antisense RNA 1 Neighboring gene uncharacterized LOC105378838 Neighboring gene Sharpr-MPRA regulatory region 5313 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1290 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1291 Neighboring gene protein kinase N2 Neighboring gene uncharacterized LOC124904213 Neighboring gene Sharpr-MPRA regulatory region 874 Neighboring gene uncharacterized LOC124904214 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:89267398-89268597 Neighboring gene RNA, U6 small nuclear 125, 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. 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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:89239665-89240262
  • OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:89240263-89240858

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_082105.2 

    Range
    101..1378
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    88773982..88775259
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    88617397..88618674
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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