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LOC123493324 MED14-independent group 3 enhancer GRCh37_chr5:64063900-64065099 [ Homo sapiens (human) ]

Gene ID: 123493324, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123493324
Gene description
MED14-independent group 3 enhancer GRCh37_chr5:64063900-64065099
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. The major subregion 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. Two subregions marked by the H3K27ac histone modification were also shown to be active enhancers by ChIP-STARR-seq in human embryonic stem cells. An overlapping subregion was also validated as a functional repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 1:Tss, active promoter, TSS/CpG island region). 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:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (64767975..64769426)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (65588094..65589545)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (64064269..64064563)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene NANOG hESC enhancer GRCh37_chr5:63984741-63985242 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:63986301-63986801 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:64001261-64002034 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:64002035-64002806 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:64010595-64011198 Neighboring gene mitochondrial ribosomal protein L49 pseudogene 1 Neighboring gene shisa like 2B Neighboring gene uncharacterized LOC124900985 Neighboring gene SREK1 interacting protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16053 Neighboring gene MPRA-validated peak5266 silencer Neighboring gene CWC27 spliceosome associated cyclophilin Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:64235623-64236166 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:64236167-64236709 Neighboring gene MPRA-validated peak5267 silencer Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:64327460-64328659 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:64331341-64331857 Neighboring gene Sharpr-MPRA regulatory region 13369 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22601 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22603 Neighboring gene uncharacterized LOC107986419 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:64398316-64398816 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:64398817-64399317 Neighboring gene ADAM metallopeptidase with thrombospondin type 1 motif 6 Neighboring gene ribosomal protein L5 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. 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
  3. 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
  4. 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

  • ATAC-STARR-seq lymphoblastoid active region 22599
  • ATAC-STARR-seq lymphoblastoid active region 22600
  • H3K27ac hESC enhancer GRCh37_chr5:64063802-64064528
  • H3K27ac hESC enhancer GRCh37_chr5:64064529-64065253
  • Sharpr-MPRA regulatory region 1989

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_077748.3 

    Range
    101..1552
    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
    64767975..64769426
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    65588094..65589545
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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