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LOC126861498 CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:33079663-33080862 [ Homo sapiens (human) ]

Gene ID: 126861498, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126861498
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:33079663-33080862
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. A subregion was also identified as an uncharacterized cis-regulatory element (CRE) that lacked a promoter, enhancer or CTCF-bound insulator chromatin signature. That subregion was validated as a silencer that could repress activity of a super core promoter (SCP1) by STARR-seq MPRAs in K562 erythroleukemia cells. [provided by RefSeq, Apr 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 (32926729..32927928)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (32802686..32803885)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:32907771-32908410 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:32908411-32909050 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:32909051-32909690 Neighboring gene MPRA-validated peak1668 silencer Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:32939152-32940351 Neighboring gene tyrosyl-tRNA synthetase 2 Neighboring gene NANOG hESC enhancer GRCh37_chr12:32986943-32987472 Neighboring gene plakophilin 2 Neighboring gene MPRA-validated peak1670 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:33031083-33031607 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:33043314-33043814 Neighboring gene ribosomal protein L35a pseudogene 27 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4340 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4341 Neighboring gene argininosuccinate synthetase 1 pseudogene 14 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:33333175-33334374 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:33467193-33467363 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:33591665-33592481 Neighboring gene synaptotagmin 10

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. Candidate silencer elements for the human and mouse genomes. Doni Jayavelu N, et al. Nat Commun, 2020 Feb 26. PMID 32103011, Free PMC Article
  2. Differential cofactor dependencies define distinct types of human enhancers. Neumayr C, et al. Nature, 2022 Jun. PMID 35650434, 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

  • MPRA-validated peak1671 silencer

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_085997.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    32926729..32927928
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    32802686..32803885
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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