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LOC126806596 CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:6531900-6533099 [ Homo sapiens (human) ]

Gene ID: 126806596, updated on 12-Sep-2024

Summary

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Gene symbol
LOC126806596
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:6531900-6533099
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. The major subregion had activity 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. Two subregions were also shown to be active enhancers by ChIP-STARR-seq in human embryonic stem cells, where both are associated with the OCT4 and NANOG transcription factors and are marked by the H3K27ac and H3K4me1 histone modifications. [provided by RefSeq, Oct 2022]
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Genomic context

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See LOC126806596 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (6489941..6491412)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (6484915..6486387)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (6531628..6533099)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376942 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:6325607-6326107 Neighboring gene uncharacterized LOC124909341 Neighboring gene uncharacterized LOC105376944 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_70950 Neighboring gene MPRA-validated peak4528 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19389 Neighboring gene GRM7 antisense RNA 3 Neighboring gene YWHAQ pseudogene Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:6810923-6811530 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:6811531-6812137 Neighboring gene mitochondrial ribosomal protein S36 pseudogene 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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:6531628-6532288
  • OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:6532289-6532947

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_082916.2 

    Range
    101..1572
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    6489941..6491412
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    6484915..6486387
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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