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LOC126861040 CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:112219715-112220914 [ Homo sapiens (human) ]

Gene ID: 126861040, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126861040
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:112219715-112220914
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 an enhancer that was validated 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 two accessible chromatin subregions that were validated as enhancers based on their 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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Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (110459957..110461197)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (111343775..111345015)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378482 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4020 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4021 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:112190742-112191347 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4022 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4023 Neighboring gene high mobility group box 3 pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4028 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4027 Neighboring gene DUSP5 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:112256187-112256710 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2815 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2816 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2817 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2818 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4029 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4030 Neighboring gene dual specificity phosphatase 5

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 4025
  • ATAC-STARR-seq lymphoblastoid active region 4026

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_085539.2 

    Range
    101..1341
    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    110459957..110461197
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    111343775..111345015
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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