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LOC126862472 CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:4906716-4907915 [ Homo sapiens (human) ]

Gene ID: 126862472, updated on 12-Sep-2024

Summary

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Gene symbol
LOC126862472
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:4906716-4907915
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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See LOC126862472 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (5003421..5004620)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (4893745..4894944)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (4906716..4907915)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903901 Neighboring gene calmodulin binding transcription activator 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8059 Neighboring gene CAMTA2 antisense RNA 1 Neighboring gene inhibitor of CDK, cyclin A1 interacting protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8060 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8061 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8062 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4902950-4903561 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4903562-4904172 Neighboring gene kinesin family member 1C Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8063 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:4923264-4924463 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4925730-4926294 Neighboring gene KIF1C antisense RNA 1 Neighboring gene uncharacterized LOC105371501 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11564 Neighboring gene solute carrier family 52 member 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. 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 Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • MPRA-validated peak2701 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_086970.1 

    Range
    101..1300
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    5003421..5004620
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    4893745..4894944
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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