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LOC112590812 CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:59348667-59349866 [ Homo sapiens (human) ]

Gene ID: 112590812, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112590812
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:59348667-59349866
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 in HCT116 colorectal carcinoma cells. This sequence 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 validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin), with weaker activity in K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 5:Enh). [provided by RefSeq, Aug 2022]
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Genomic context

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Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (58882995..58884194)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (58761441..58762640)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (59348769..59349063)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene JUN divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:59279600-59280596 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:59280597-59281592 Neighboring gene uncharacterized LOC101926907 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 936 Neighboring gene uncharacterized LOC107984961 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1092 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1093 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:59351096-59351291 Neighboring gene long intergenic non-protein coding RNA 2777 Neighboring gene Sharpr-MPRA regulatory region 10312 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 937 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:59387615-59388116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:59388117-59388616 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1094 Neighboring gene NANOG hESC enhancer GRCh37_chr1:59446941-59447485 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:59448521-59449021 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:59448020-59448520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1095 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1096 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1097 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1098 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1099 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1100 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1101 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1102 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1103 Neighboring gene PHB1 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1104 Neighboring gene long intergenic non-protein coding RNA 1358 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1105 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1106 Neighboring gene VISTA enhancer hs1485 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:59542215-59542758 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:59543303-59543846 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:59543847-59544388

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

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

  • Sharpr-MPRA regulatory region 2604

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_060602.2 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    58882995..58884194
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    58761441..58762640
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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