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LOC126807620 CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:176728411-176729610 [ Homo sapiens (human) ]

Gene ID: 126807620, updated on 12-Sep-2024

Summary

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Gene symbol
LOC126807620
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:176728411-176729610
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 LOC126807620 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 (177301410..177302609)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (177844645..177845844)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (176728411..176729610)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene nuclear receptor binding SET domain protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176692158-176693050 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176693051-176693942 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:176696443-176697642 Neighboring gene ribosomal protein L21 pseudogene 60 Neighboring gene protein arginine methyltransferase 1 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176722701-176723202 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176723203-176723702 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:176727388-176727581 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16677 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176730775-176731652 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23699 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23700 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23701 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23702 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23703 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176737000-176737866 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23704 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16680 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16681 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23705 Neighboring gene Sharpr-MPRA regulatory region 13731 Neighboring gene PRELI domain containing 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176746939-176747440 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176747441-176747940 Neighboring gene RAB24, member RAS oncogene family Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176751079-176751579 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:176753137-176754080 Neighboring gene MAX dimerization protein 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176763024-176763649 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176765883-176766836 Neighboring gene lectin, mannose binding 2 Neighboring gene ribosomal protein S20 pseudogene 17

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 23695

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_083934.1 

    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
    177301410..177302609
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    177844645..177845844
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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