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LOC126806875 CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:172309739-172310938 [ Homo sapiens (human) ]

Gene ID: 126806875, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126806875
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:172309739-172310938
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 (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. 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, May 2023]
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Genomic context

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See LOC126806875 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (172591949..172593148)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (175377008..175378206)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:172165405-172166172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:172167124-172167624 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:172167625-172168125 Neighboring gene MPRA-validated peak4924 silencer Neighboring gene growth hormone secretagogue receptor Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20826 Neighboring gene TNF superfamily member 10 Neighboring gene TBPL1 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 3413 Neighboring gene long intergenic non-protein coding RNA 2068 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20828 Neighboring gene Sharpr-MPRA regulatory region 2749 Neighboring gene Sharpr-MPRA regulatory region 14501 Neighboring gene solute carrier family 31 member 1 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:172330773-172331274 Neighboring gene neutral cholesterol ester hydrolase 1 Neighboring gene uncharacterized LOC124909457

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. 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 20827

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_083195.1 

    Range
    101..1300
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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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    172591949..172593148
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    175377008..175378206
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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