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LOC126863008 CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:25289826-25291025 [ Homo sapiens (human) ]

Gene ID: 126863008, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126863008
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:25289826-25291025
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]
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Genomic context

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Location:
chromosome: 20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (25309190..25310389)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (25374279..25375478)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372579 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17664 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12742 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr20:25218064-25219263 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr20:25222455-25223072 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:25227753-25228006 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12743 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12744 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12745 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17665 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12746 Neighboring gene glycogen phosphorylase B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:25274716-25275238 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:25276284-25276805 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:25280703-25281254 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:25281255-25281805 Neighboring gene abhydrolase domain containing 12, lysophospholipase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:25297613-25298222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17667 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17668 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12747 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:25310906-25311427 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25337131-25337731 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25337732-25338331 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12748 Neighboring gene peptidylprolyl isomerase A pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12749 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12750 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12751 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12752 Neighboring gene uncharacterized LOC105372581 Neighboring gene MPRA-validated peak4176 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17669 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr20:25388698-25389455 Neighboring gene GINS complex subunit 1

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 17666

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_087505.1 

    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    25309190..25310389
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    25374279..25375478
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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