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LOC111822949 CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:91412350-91413549 [ Homo sapiens (human) ]

Gene ID: 111822949, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111822949
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:91412350-91413549
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It 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. Two overlapping subregions were also validated as functional enhancers by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 20:ReprD, Polycomb repression with Duke DNase/promoter and conservation enriched) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). This enhancer region is in the vicinity of the FURIN (furin, paired basic amino acid cleaving enzyme) gene, which is involved in SARS-CoV-2 infection, where it overlaps an intron relative to some FURIN splice variants and is in the 5' regulatory region relative to other splice variants. This locus also includes two accessible chromatin subregions that were validated as enhancers based on their 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]
Annotation information
Note: This locus has been reviewed for its involvement in coronavirus biology, and is regulatory element in the vicinity of coronavirus related gene(s).
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Genomic context

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Location:
15q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (90869120..90870319)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (88628362..88629569)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (91412909..91413283)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370969 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:91383569-91384223 Neighboring gene Sharpr-MPRA regulatory region 4312 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:91388069-91388685 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10092 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10093 Neighboring gene RNA, 7SL, cytoplasmic 363, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6828 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6829 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10096 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10097 Neighboring gene furin, paired basic amino acid cleaving enzyme Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10098 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6830 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10099 Neighboring gene FES proto-oncogene, tyrosine kinase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10100 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6831 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6832 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10101 Neighboring gene mannosidase alpha class 2A member 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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article
  3. 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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 10094
  • ATAC-STARR-seq lymphoblastoid active region 10095
  • Sharpr-MPRA regulatory region 3826
  • Sharpr-MPRA regulatory region 8172
  • Sharpr-MPRA regulatory regions 3826 and 8172

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_056219.2 

    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    90869120..90870319
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    88628362..88629569
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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