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LOC111982890 CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:11425327-11426526 [ Homo sapiens (human) ]

Gene ID: 111982890, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111982890
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:11425327-11426526
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. A subregion 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, where it was defined as a group 2 enhancer that depends on the BRD2, BRD4, P300/CBP, MED14 and CDK7 cofactors, with strong dependence on CDK7. A subregion was also validated as an enhancer by Sharpr-MPRA (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 21:Repr, strong Polycomb repression) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 21:Repr, strong Polycomb repression). Another subregion was also validated as an enhancer by ChIP-STARR-seq in naive human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
11p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (11403525..11404979)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (11492444..11493898)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (11425949..11426243)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene polypeptide N-acetylgalactosaminyltransferase 18 Neighboring gene uncharacterized LOC124902633 Neighboring gene casein kinase 2 alpha 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:11400009-11400508 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:11430413-11430914 Neighboring gene uncharacterized LOC107983976 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_18862 Neighboring gene NANOG hESC enhancer GRCh37_chr11:11530882-11531383 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:11559636-11560464 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_18916 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4454 Neighboring gene uncharacterized LOC124902632 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:11591851-11592350

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. 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

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:11425072-11425984
  • Sharpr-MPRA regulatory region 8932

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_056382.3 

    Range
    101..1555
    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    11403525..11404979
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    11492444..11493898
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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