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LOC123864094 CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:145218575-145219774 [ Homo sapiens (human) ]

Gene ID: 123864094, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123864094
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:145218575-145219774
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 repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Aug 2022]
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Genomic context

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Location:
6q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (144897439..144898638)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (146090040..146091239)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (145218749..145219043)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene rhomboid domain containing 1 pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90719 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90731 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:144754756-144755258 Neighboring gene utrophin Neighboring gene ReSE screen-validated silencer GRCh37_chr6:144780729-144780932 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25221 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:144790768-144791444 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:144794141-144795340 Neighboring gene small nucleolar RNA, H/ACA box 98 Neighboring gene Sharpr-MPRA regulatory region 2668 Neighboring gene Sharpr-MPRA regulatory region 10150 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25222 Neighboring gene NANOG hESC enhancer GRCh37_chr6:145107948-145108449 Neighboring gene Sharpr-MPRA regulatory region 9645 Neighboring gene MPRA-validated peak6190 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr6:145134839-145135340 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:145190998-145191517 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:145272790-145273457 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:145275769-145276268 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:145298093-145298720 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:145327891-145328441 Neighboring gene NANOG hESC enhancer GRCh37_chr6:145424274-145424879 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:145456814-145458013 Neighboring gene tRNA-Gln (anticodon TTG) 4-1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25223 Neighboring gene EPM2A glucan phosphatase, laforin Neighboring gene RNA, U1 small nuclear 33, 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 14510

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_078226.2 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    144897439..144898638
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    146090040..146091239
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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