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LOC126862568 CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:40934948-40936147 [ Homo sapiens (human) ]

Gene ID: 126862568, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126862568
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:40934948-40936147
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 includes enhancers that were validated by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay. In HCT116 colorectal carcinoma cells, a subregion was defined as a group 2 enhancer that depends on the BRD2, BRD4, P300/CBP, MED14 and CDK7 cofactors, with strong dependence on CDK7. Another subregion was also validated as an enhancer by ChIP-STARR-seq in naive human embryonic stem cells, where it is marked by the H3K4me1 histone modification. [provided by RefSeq, Jan 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 (42782930..42784666)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (43640070..43641806)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene RAMP2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8547 Neighboring gene receptor activity modifying protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12222 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:40925642-40926189 Neighboring gene Sharpr-MPRA regulatory region 12532 Neighboring gene vacuolar protein sorting 25 homolog Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:40932701-40933658 Neighboring gene WNK lysine deficient protein kinase 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12223 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12224 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12225 Neighboring gene cytochrome c oxidase assembly factor 3 Neighboring gene cyclin N-terminal domain containing 1 Neighboring gene beclin 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. 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

  • H3K4me1 hESC enhancer GRCh37_chr17:40936053-40936684

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_087065.2 

    Range
    101..1837
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    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
    42782930..42784666
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    43640070..43641806
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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