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LOC126862244 CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:99211661-99212860 [ Homo sapiens (human) ]

Gene ID: 126862244, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126862244
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:99211661-99212860
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 includes enhancers that were validated by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay. In HCT116 colorectal carcinoma cells, a subregion was defined as a group 2 enhancer that depends on the BRD2, BRD4, P300/CBP, MED14 and CDK7 cofactors, with strong dependence on CDK7. Another subregion was also validated as an enhancer by ChIP-STARR-seq in naive human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
chromosome: 15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (98668432..98670007)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (96432809..96434384)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene zinc finger CCHC-type containing 9 pseudogene Neighboring gene protein FAM169B Neighboring gene ReSE screen-validated silencer GRCh37_chr15:99031875-99032074 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:99056319-99056501 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:99122390-99122890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:99122891-99123391 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:99135615-99136114 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:99143721-99144221 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:99143220-99143720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:99148269-99148769 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:99189870-99190491 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6854 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6855 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6856 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6857 Neighboring gene Sharpr-MPRA regulatory region 7544 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:99204502-99205312 Neighboring gene Sharpr-MPRA regulatory region 1749 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:99213965-99214690 Neighboring gene IGF1R antisense imprinted non-protein coding RNA Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:99243457-99243958 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:99243959-99244458 Neighboring gene insulin like growth factor 1 receptor Neighboring gene ReSE screen-validated silencer GRCh37_chr15:99247546-99247726 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:99256117-99256819 Neighboring gene VISTA enhancer hs1932 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:99277618-99278148 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:99301249-99301750 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:99301751-99302250 Neighboring gene uncharacterized LOC124903560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:99316261-99316843 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:99316844-99317425 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:99319525-99320432 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:99320433-99321339 Neighboring gene microRNA 4714

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. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:99212511-99213236

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_086742.2 

    Range
    101..1676
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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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    98668432..98670007
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    96432809..96434384
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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