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LOC121627952 CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:46772879-46774078 [ Homo sapiens (human) ]

Gene ID: 121627952, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121627952
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:46772879-46774078
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. 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 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 a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations). The same subregion also displayed repressive activity by Sharpr-MPRA in HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State1:Tss, active promoter, TSS/CpG island region). [provided by RefSeq, Aug 2022]
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Genomic context

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Location:
22q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (46376982..46378181)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (46861841..46863041)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (46773529..46773823)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13909 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19234 Neighboring gene G2 and S-phase expressed 1 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr22:46718535-46719734 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:46731701-46732200 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46757719-46758220 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46758221-46758720 Neighboring gene tRNA mitochondrial 2-thiouridylase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46777489-46777988 Neighboring gene cadherin EGF LAG seven-pass G-type receptor 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:46780176-46780359 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr22:46782038-46783237 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46787203-46788025 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46805763-46806264 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13911 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19237 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19238 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46838653-46839604 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46849165-46849747 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46849748-46850331 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46851429-46851929 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:46858535-46859734 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46867173-46867992 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:46868263-46868432 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46875081-46875610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19239 Neighboring gene family with sequence similarity 136 member A pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46896241-46897215 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46903004-46903964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46907166-46907666 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46910168-46911084 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46913033-46913798 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr22:46918799-46919299 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46924113-46924614 Neighboring gene VISTA enhancer hs1924 Neighboring gene long intergenic non-protein coding RNA 2925

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 9841

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_075144.2 

    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    46376982..46378181
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    46861841..46863041
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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