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LOC126862668 CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:79846281-79847480 [ Homo sapiens (human) ]

Gene ID: 126862668, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126862668
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:79846281-79847480
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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 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. An accessible chromatin subregion was used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. That subregion was identified as a functional silencer in phorbol 12-myristate 13-acetate-treated (for megakaryocytic differentiation) K562 erythroleukemia cells. [provided by RefSeq, Jun 2023]
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Genomic context

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Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (81888405..81889604)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (82755567..82756766)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene prolyl 4-hydroxylase subunit beta Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79813353-79813852 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9153 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9154 Neighboring gene uncharacterized LOC124904086 Neighboring gene Sharpr-MPRA regulatory region 9355 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12979 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79823980-79824608 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79825239-79825867 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79825868-79826497 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79826498-79827126 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9158 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12981 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9159 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12982 Neighboring gene Rho GDP dissociation inhibitor alpha Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12983 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9161 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:79850899-79851114 Neighboring gene Aly/REF export factor Neighboring gene anaphase promoting complex subunit 11 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9162 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9163 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9164 Neighboring gene phosphate cytidylyltransferase 2, ethanolamine Neighboring gene neuropeptide B

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. Systematic identification of silencers in human cells. Pang B, et al. Nat Genet, 2020 Mar. PMID 32094911, Free PMC Article
  2. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, 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

  • ReSE screen-validated silencer GRCh37_chr17:79847284-79847448

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_087165.1 

    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    81888405..81889604
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    82755567..82756766
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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