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LOC126806996 CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:19777224-19778423 [ Homo sapiens (human) ]

Gene ID: 126806996, updated on 10-Oct-2023

Summary

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Gene symbol
LOC126806996
Gene description
CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:19777224-19778423
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 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. This locus also includes a subregion containing a Neanderthal adaptively introgressed genetic variant. That subregion was validated as an enhancer by MPRAs in K562 erythroleukemia cells, with activity observed for both the introgressed and non-introgressed 4:19777845 variant alleles. [provided by RefSeq, Sep 2023]
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Genomic context

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See LOC126806996 in Genome Data Viewer
Location:
chromosome: 4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (19775601..19776800)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (19758261..19759460)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene RNA, 5S ribosomal pseudogene 157 Neighboring gene long intergenic non-protein coding RNA 2438 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_77337 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:19431070-19431946 Neighboring gene uncharacterized LOC105374511 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_77374 Neighboring gene ribosomal protein L21 pseudogene 46 Neighboring gene uncharacterized LOC105374513

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

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

  • Neanderthal introgressed variant-containing enhancer experimental_77522

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_083317.1 

    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    19775601..19776800
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    19758261..19759460
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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