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LOC126859787 CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:130935046-130936245 [ Homo sapiens (human) ]

Gene ID: 126859787, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126859787
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:130935046-130936245
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 associates with the NANOG transcription factor. [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC126859787 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (130613901..130615440)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (131808655..131810194)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene sterile alpha motif domain containing 3 Neighboring gene uncharacterized LOC112267974 Neighboring gene MPRA-validated peak6122 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17539 Neighboring gene transmembrane protein 200A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25060 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:130838308-130839507 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25061 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17540 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:130923105-130924304 Neighboring gene Sharpr-MPRA regulatory region 149 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:130953902-130954652 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:131022881-131023397 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:131032856-131033370 Neighboring gene uncharacterized LOC105378002 Neighboring gene uncharacterized LOC105378003

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

  • NANOG hESC enhancer GRCh37_chr6:130936084-130936585

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_084288.2 

    Range
    101..1640
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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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    130613901..130615440
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    131808655..131810194
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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