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LOC126861783 CDK7 strongly-dependent group 2 enhancer GRCh37_chr13:52922389-52923588 [ Homo sapiens (human) ]

Gene ID: 126861783, updated on 12-Sep-2024

Summary

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Gene symbol
LOC126861783
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr13:52922389-52923588
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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 a silencer based on its ability to repress 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 LOC126861783 in Genome Data Viewer
Location:
chromosome: 13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (52348254..52349453)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (51563086..51564285)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (52922389..52923588)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr13:52796837-52797005 Neighboring gene TPTE2 pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:52907715-52908216 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:52908217-52908716 Neighboring gene long intergenic non-protein coding RNA 2333 Neighboring gene uncharacterized LOC105370207 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:52951563-52952064 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:52952065-52952564 Neighboring gene thrombospondin type 1 domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5384 Neighboring gene RNY4 pseudogene 24 Neighboring gene vacuolar protein sorting 36 homolog Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:53024355-53024935

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 silent region 5383

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_086281.1 

    Range
    101..1300
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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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    52348254..52349453
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    51563086..51564285
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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