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LOC112272572 CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:97646084-97647283 [ Homo sapiens (human) ]

Gene ID: 112272572, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112272572
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:97646084-97647283
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 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 both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 13:Ctcf, distal CTCF/candidate insulator without open chromatin) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Aug 2022]
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Genomic context

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Location:
14q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (97179747..97180946)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (91411605..91412804)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (97646689..97646983)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370647 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr14:97573059-97574258 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_38968 Neighboring gene long intergenic non-protein coding RNA 2304 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr14:97732279-97733478 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8994 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8995 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8996 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:97832410-97832945 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:97832946-97833480 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr14:97845143-97845772 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8999 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:97869232-97870431 Neighboring gene NANOG hESC enhancer GRCh37_chr14:97878244-97878765 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:97906411-97906911 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9000 Neighboring gene long intergenic non-protein coding RNA 2325 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_38981 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_38982 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:98001127-98001628 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:98008053-98009252 Neighboring gene uncharacterized LOC124903378 Neighboring gene long intergenic non-protein coding RNA 2291

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 9177

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_056710.2 

    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    97179747..97180946
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    91411605..91412804
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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