U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC126806651 CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:38205703-38206902 [ Homo sapiens (human) ]

Gene ID: 126806651, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC126806651
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:38205703-38206902
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 was validated as an active enhancer 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 three 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]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (38164212..38165411)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (38169912..38171111)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene DLEC1 cilia and flagella associated protein Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:38179733-38180676 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19680 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19681 Neighboring gene acetyl-CoA acyltransferase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38196601-38197102 Neighboring gene uncharacterized LOC101928234 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:38207186-38207801 Neighboring gene MYD88 innate immune signal transduction adaptor Neighboring gene oxidative stress responsive kinase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14207 Neighboring gene Sharpr-MPRA regulatory region 12810 Neighboring gene Sharpr-MPRA regulatory region 5010 Neighboring gene solute carrier family 22 member 13 Neighboring gene CDC42 pseudogene 7 Neighboring gene solute carrier family 22 member 14 Neighboring gene RNA, U6 small nuclear 235, pseudogene

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

General gene information

Go to the top of the page Help

Other Names

  • ATAC-STARR-seq lymphoblastoid active region 19682
  • ATAC-STARR-seq lymphoblastoid active region 19683
  • ATAC-STARR-seq lymphoblastoid active region 19684

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_082971.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    38164212..38165411
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    38169912..38171111
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases