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LOC126861598 CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:92987036-92988235 [ Homo sapiens (human) ]

Gene ID: 126861598, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126861598
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:92987036-92988235
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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Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (92593260..92594459)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (92570742..92571941)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6748 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4701 Neighboring gene uncharacterized LOC124903118 Neighboring gene MPRA-validated peak1885 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6749 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6750 Neighboring gene MPRA-validated peak1886 silencer Neighboring gene uncharacterized LOC105369905 Neighboring gene MTCH2 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4702 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6751 Neighboring gene uncharacterized LOC124902983 Neighboring gene MPRA-validated peak1887 silencer Neighboring gene Sharpr-MPRA regulatory region 11325 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6753 Neighboring gene pleckstrin homology and RhoGEF domain containing G7 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:93139520-93140719 Neighboring gene MPRA-validated peak1888 silencer Neighboring gene early endosome antigen 1

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 6752

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_086097.1 

    Range
    101..1300
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    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    92593260..92594459
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    92570742..92571941
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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