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LOC121725078 MED14-independent group 3 enhancer GRCh37_chr2:3583482-3584681 [ Homo sapiens (human) ]

Gene ID: 121725078, updated on 12-Sep-2024

Summary

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Gene symbol
LOC121725078
Gene description
MED14-independent group 3 enhancer GRCh37_chr2:3583482-3584681
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 Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). [provided by RefSeq, Aug 2022]
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Genomic context

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See LOC121725078 in Genome Data Viewer
Location:
2p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (3535892..3537091)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (3558421..3559620)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (3583482..3584681)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene acireductone dioxygenase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11110 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11111 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3522968-3523489 Neighboring gene uncharacterized LOC124907725 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3523490-3524010 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15230 Neighboring gene ribonuclease H1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15231 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11115 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3607689-3608586 Neighboring gene RNASEH1 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15232 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15233 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:3615875-3616480 Neighboring gene uncharacterized LOC124907726 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:3616481-3617087 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:3617088-3617693 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3622403-3622978

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 11889

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_075547.2 

    Range
    101..1300
    Download
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    3535892..3537091
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    3558421..3559620
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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