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LOC126807383 CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:49963094-49964293 [ Homo sapiens (human) ]

Gene ID: 126807383, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126807383
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:49963094-49964293
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 includes enhancers that were validated by the STARR-seq (self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA). 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 associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress 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]
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Genomic context

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Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (50666912..50668459)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (51486078..51487625)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22542 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15998 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15999 Neighboring gene embigin Neighboring gene peptidylprolyl isomerase A like 4G pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16000 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16001 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22543 Neighboring gene poly(ADP-ribose) polymerase family member 8 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:50218379-50218890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:50258938-50259475 Neighboring gene uncharacterized LOC124901181 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:50265501-50266022 Neighboring gene long intergenic non-protein coding RNA 2106

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. 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
  3. 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

  • ATAC-STARR-seq lymphoblastoid silent region 16002
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:49962746-49963658

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_083697.2 

    Range
    101..1648
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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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    50666912..50668459
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    51486078..51487625
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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