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LOC121468016 MED14-independent group 3 enhancer GRCh37_chr14:61822129-61823328 [ Homo sapiens (human) ]

Gene ID: 121468016, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121468016
Gene description
MED14-independent group 3 enhancer GRCh37_chr14:61822129-61823328
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as an active enhancer by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay in HCT116 colorectal carcinoma cells. This sequence 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. A subregion was also validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 24:Quies, heterochromatin/dead zone) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 3:PromF, promoter flanking). [provided by RefSeq, Aug 2022]
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Genomic context

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See LOC121468016 in Genome Data Viewer
Location:
14q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (61355411..61356610)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (55562027..55563226)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (61822609..61822903)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene protein kinase C eta Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:61746518-61747481 Neighboring gene transmembrane protein 30B Neighboring gene PRKCH antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 13098 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5817 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5818 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:61788641-61789185 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:61789186-61789729 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8487 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5819 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8488 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8489 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8490 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8491 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5820 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8492 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_34674 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_34691 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_34693 and experimental_34700 Neighboring gene Sharpr-MPRA regulatory region 10871 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:61932802-61933718 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8493 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8494 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8495 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_34726 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_34735 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:61972906-61973478 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_34774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8496 Neighboring gene uncharacterized LOC105370525 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:62004017-62005216 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:62018627-62019137 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:62019138-62019647 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:62028305-62029504 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:62034963-62035464 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:62035465-62035964 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:62036356-62036548 Neighboring gene long intergenic non-protein coding RNA 1303 Neighboring gene long intergenic non-protein coding RNA 3033

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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

  • Sharpr-MPRA regulatory region 1024
  • Sharpr-MPRA regulatory region 1024/14115
  • Sharpr-MPRA regulatory region 14115

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_074685.2 

    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    61355411..61356610
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    55562027..55563226
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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