U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC126805625 CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:14843423-14844622 [ Homo sapiens (human) ]

Gene ID: 126805625, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC126805625
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:14843423-14844622
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 an accessible chromatin subregion that was validated as an enhancer based on its 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: 1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (14516927..14518126)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (13960732..13961931)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene kazrin, periplakin interacting protein Neighboring gene MPRA-validated peak78 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:14696541-14697219 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:14699385-14700250 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:14730198-14731026 Neighboring gene KAZN antisense RNA 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:14763664-14763765 Neighboring gene uncharacterized LOC124903850 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 224 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 225 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 226 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:14898509-14899073 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 292 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:14955532-14956032 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:14956033-14956533 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:14964395-14964896 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 227 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:15004649-15004813 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:15044353-15044920 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:15052062-15052748 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:15058239-15058960 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:15058961-15059682 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:15059683-15060406 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:15061129-15061850 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:15061851-15062572 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:15068552-15069136 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:15069137-15069720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:15088664-15089164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:15089165-15089665 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:15105533-15106063 Neighboring gene tubulin folding cofactor A pseudogene 2 Neighboring gene uncharacterized LOC105376759

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 223

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_081949.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    14516927..14518126
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    13960732..13961931
    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