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LOC126862177 CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:74476518-74477717 [ Homo sapiens (human) ]

Gene ID: 126862177, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126862177
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:74476518-74477717
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 (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. 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 HepG2 liver carcinoma cells. 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, Jun 2023]
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Genomic context

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Location:
chromosome: 15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (74184177..74185376)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (72050097..72051296)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903523 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9744 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74464796-74465784 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74465785-74466772 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74466773-74467761 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74468869-74469385 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_40888 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74473477-74474013 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74485815-74486316 Neighboring gene immunoglobulin superfamily containing leucine rich repeat Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_40898 Neighboring gene signaling receptor and transporter of retinol STRA6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74492227-74492862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74492863-74493496 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74495400-74496033 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74497519-74498180 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74498181-74498842 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74500829-74501490 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74504651-74505191 Neighboring gene coiled-coil domain containing 33 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:74510918-74511127 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74515727-74516464 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74516465-74517202 Neighboring gene uncharacterized LOC105370893 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:74524367-74525566 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74526358-74526954 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74531317-74531912 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74531913-74532508 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74536295-74536796 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74537297-74538296 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74555642-74556474 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74556475-74557305 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74569034-74569758 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74569759-74570483 Neighboring gene VISTA enhancer hs2614 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74593043-74593864 Neighboring gene uncharacterized LOC124903525 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9747 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74611467-74612377

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
  3. 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 9745
  • ReSE screen-validated silencer GRCh37_chr15:74476685-74476839

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_086675.1 

    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    74184177..74185376
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_021160016.1 Reference GRCh38.p14 PATCHES

    Range
    11602..12801
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    72050097..72051296
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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