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LOC126807365 MED14-independent group 3 enhancer GRCh37_chr5:37847590-37848789 [ Homo sapiens (human) ]

Gene ID: 126807365, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126807365
Gene description
MED14-independent group 3 enhancer GRCh37_chr5:37847590-37848789
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 marked by the H3K4me1 histone modification were also shown to be active enhancers by ChIP-STARR-seq in human embryonic stem cells. 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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See LOC126807365 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (37847488..37848705)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (38096555..38097772)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene WD repeat domain 70 Neighboring gene Sharpr-MPRA regulatory region 9268 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:37724134-37725333 Neighboring gene RNA, U6 small nuclear 484, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr5:37756428-37756676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:37836250-37837188 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22490 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:37839067-37840004 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22492 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22493 Neighboring gene GDNF antisense RNA 1 Neighboring gene glial cell derived neurotrophic factor Neighboring gene NANOG hESC enhancer GRCh37_chr5:37938025-37938604 Neighboring gene long intergenic non-protein coding RNA 2117 Neighboring gene long intergenic non-protein coding RNA 2110

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 22491
  • H3K4me1 hESC enhancer GRCh37_chr5:37847806-37848306
  • H3K4me1 hESC enhancer GRCh37_chr5:37848307-37848807

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_083679.2 

    Range
    101..1318
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    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
    37847488..37848705
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    38096555..38097772
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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