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LOC126806629 CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:23958136-23959335 [ Homo sapiens (human) ]

Gene ID: 126806629, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126806629
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:23958136-23959335
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 region includes an enhancer that was validated by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) 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. This locus also includes two accessible chromatin subregions that were validated as enhancers based on their ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (23916594..23917873)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (23921370..23922649)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14140 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14141 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14142 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19600 Neighboring gene UBE2E1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19601 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14144 Neighboring gene ubiquitin conjugating enzyme E2 E1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19603 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19604 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19605 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:23906443-23907202 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:23924271-23924855 Neighboring gene ADP ribosylation factor like GTPase 4A pseudogene 4 Neighboring gene NFKB inhibitor interacting Ras like 1 Neighboring gene ribosomal protein L15 Neighboring gene uncharacterized LOC124909354 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:23987327-23987868 Neighboring gene Sharpr-MPRA regulatory region 12700 Neighboring gene nuclear receptor subfamily 1 group D member 2 Neighboring gene MPRA-validated peak4577 silencer

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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 19606
  • ATAC-STARR-seq lymphoblastoid active region 19607

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_082949.2 

    Range
    101..1380
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    23916594..23917873
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    23921370..23922649
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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