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LOC112042784 MED14-independent group 3 enhancer GRCh37_chr11:121559556-121560755 [ Homo sapiens (human) ]

Gene ID: 112042784, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112042784
Gene description
MED14-independent group 3 enhancer GRCh37_chr11:121559556-121560755
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 matched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites). [provided by RefSeq, Aug 2022]
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Genomic context

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Location:
11q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (121688848..121690047)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (121715206..121716405)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (121560029..121560323)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5649 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5650 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5651 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4003 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5655 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4004 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5652 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5653 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5654 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4005 Neighboring gene SORL1 antisense RNA 1 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:121336477-121337676 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5657 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5658 Neighboring gene uncharacterized LOC105369535 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5659 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:121368848-121369348 Neighboring gene sortilin related receptor 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:121421721-121422920 Neighboring gene SORL1 eExon liver enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5660 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:121441955-121442454 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5661 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:121441453-121441954 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4006 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5662 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:121465964-121467163 Neighboring gene Sharpr-MPRA regulatory region 6864 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:121507637-121508302 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:121508303-121508966 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:121514837-121515520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5663 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:121543162-121543662 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5664 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:121673071-121673918 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:121694789-121695360 Neighboring gene uncharacterized LOC107984402 Neighboring gene VISTA enhancer hs872 Neighboring gene RNA, U6 small nuclear 256, 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

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 11087

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_056433.2 

    Range
    101..1300
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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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    121688848..121690047
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    121715206..121716405
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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