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LOC126807515 CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:133771909-133773108 [ Homo sapiens (human) ]

Gene ID: 126807515, updated on 12-Sep-2024

Summary

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Gene symbol
LOC126807515
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:133771909-133773108
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 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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See LOC126807515 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (134436218..134437417)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (134960042..134961241)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (133771909..133773108)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak5476 silencer Neighboring gene ribosomal protein S10 pseudogene 11 Neighboring gene long intergenic non-protein coding RNA 2999 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:133774131-133774646 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:133774647-133775160 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:133787376-133787561 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23147 Neighboring gene RNA, U6 small nuclear 456, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:133841857-133842511 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:133844767-133845440 Neighboring gene long intergenic non-protein coding RNA 1843

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 within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. 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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 23145
  • ATAC-STARR-seq lymphoblastoid active region 23146

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_083829.1 

    Range
    101..1300
    Download
    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    134436218..134437417
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    134960042..134961241
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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