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LOC126807607 CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:173390440-173391639 [ Homo sapiens (human) ]

Gene ID: 126807607, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126807607
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:173390440-173391639
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 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. A subregion was also validated as an enhancer by ChIP-STARR-seq in naive human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. [provided by RefSeq, Dec 2022]
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Genomic context

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Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (173963437..173964636)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (174503781..174504980)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986482 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23666 Neighboring gene long intergenic non-protein coding RNA 1485 Neighboring gene Sharpr-MPRA regulatory region 2476 Neighboring gene CRISPRi-validated cis-regulatory element chr5.4552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23667 Neighboring gene Sharpr-MPRA regulatory region 12964 Neighboring gene CRISPRi-validated cis-regulatory element chr5.4558 Neighboring gene Sharpr-MPRA regulatory region 12084 Neighboring gene CRISPRi-validated cis-regulatory element chr5.4561 Neighboring gene CRISPRi-validated cis-regulatory element chr5.4562 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:173301919-173302077 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23668 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23669 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:173317123-173317624 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:173317625-173318124 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23670 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23671 Neighboring gene Sharpr-MPRA regulatory region 4386 Neighboring gene cytoplasmic polyadenylation element binding protein 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23672 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:173368663-173369301 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:173394847-173395510 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23673 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:173408357-173408858 Neighboring gene chromosome 5 open reading frame 47 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:173446513-173447102 Neighboring gene ribosomal protein L12 pseudogene 22

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. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:173390534-173391416

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_083921.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    173963437..173964636
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    174503781..174504980
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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