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LOC126806551 CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:232261821-232263020 [ Homo sapiens (human) ]

Gene ID: 126806551, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126806551
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:232261821-232263020
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 LOC126806551 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (231397110..231398309)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (231881560..231882759)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene armadillo repeat containing 9 Neighboring gene ribosomal protein S28 pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17280 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:232181499-232182000 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:232182001-232182500 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232196977-232197934 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232201084-232201584 Neighboring gene Sharpr-MPRA regulatory region 9410 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232233755-232234401 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232234402-232235049 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232235050-232235696 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232235697-232236344 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:232240900-232241463 Neighboring gene microRNA 4777 Neighboring gene Sharpr-MPRA regulatory region 14998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17281 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232256876-232257459 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232258043-232258625 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232258626-232259207 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17282 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12425 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232263273-232263820 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232263821-232264366 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232266008-232266553 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:232275119-232275724 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:232275725-232276329 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12426 Neighboring gene uncharacterized LOC124907997 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:232278424-232279184 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232279185-232279944 Neighboring gene UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232283151-232283652 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:232285114-232285614 Neighboring gene zinc finger and BTB domain containing 8 opposite strand pseudogene 2

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 17283

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_082871.1 

    Range
    101..1300
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    231397110..231398309
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    231881560..231882759
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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