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LOC126807556 MED14-independent group 3 enhancer GRCh37_chr5:151042798-151043997 [ Homo sapiens (human) ]

Gene ID: 126807556, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126807556
Gene description
MED14-independent group 3 enhancer GRCh37_chr5:151042798-151043997
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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 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 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. This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress 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 (151663237..151664436)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (152202214..152203413)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene solute carrier family 36 member 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82555 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82563 Neighboring gene FAT atypical cadherin 2 Neighboring gene microRNA 6499 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23458 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:150950930-150951442 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:150974668-150975189 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:150998970-150999648 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:150999649-151000325 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:151003759-151004958 Neighboring gene uncharacterized LOC105378231 Neighboring gene uncharacterized LOC124901116 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23459 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23460 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:151063929-151064758 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:151065587-151066416 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:151066417-151067244 Neighboring gene secreted protein acidic and cysteine rich Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:151079020-151079841 Neighboring gene colorectal liver metastasis associated transcript 3 Neighboring gene RN7SK pseudogene 232

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 silent region 16524

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_083870.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    151663237..151664436
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    152202214..152203413
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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