U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC126860540 CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:140227217-140228416 [ Homo sapiens (human) ]

Gene ID: 126860540, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC126860540
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:140227217-140228416
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: 8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (139214974..139216173)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (140335477..140336671)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 135 member B Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr8:139357155-139357654 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:139555607-139556806 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:139706354-139706854 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:139706855-139707355 Neighboring gene collagen type XXII alpha 1 chain Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19571 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:139782916-139783886 Neighboring gene MPRA-validated peak7186 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:139806119-139806619 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:139860841-139861342 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:139925385-139926230 Neighboring gene Sharpr-MPRA regulatory region 3511 Neighboring gene Sharpr-MPRA regulatory region 9382 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr8:139965113-139965801 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:139966492-139967180 Neighboring gene NANOG hESC enhancer GRCh37_chr8:140009858-140010359 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:140033795-140034296 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:140181537-140182736 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:140221580-140221764 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:140294263-140294817 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr8:140416894-140417542 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19572 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr8:140440618-140441118 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr8:140441119-140441619 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:140471614-140472148 Neighboring gene Sharpr-MPRA regulatory region 3867 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19573 Neighboring gene Sharpr-MPRA regulatory region 15097 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:140748966-140749712 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:140762149-140762649 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:140784193-140784820 Neighboring gene potassium two pore domain channel subfamily K member 9 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:140842647-140843284 Neighboring gene Sharpr-MPRA regulatory region 11049 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:140850306-140850830 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:140850831-140851354 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:140853452-140853976 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:140856599-140857122 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:140860017-140860572 Neighboring gene uncharacterized LOC107986981 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:140875463-140876436 Neighboring gene trafficking protein particle complex subunit 9

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

General gene information

Go to the top of the page Help

Other Names

  • ATAC-STARR-seq lymphoblastoid active region 28025

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_085040.1 

    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    139214974..139216173
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    140335477..140336671
    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