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    LOC126863290 CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:94544817-94546016 [ Homo sapiens (human) ]

    Gene ID: 126863290, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC126863290
    Gene description
    CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:94544817-94546016
    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 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 validated as an enhancer by ChIP-STARR-seq in naive human embryonic stem cells, where it associates with the NANOG transcription factor. [provided by RefSeq, Dec 2022]
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    Genomic context

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    Location:
    chromosome: X
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (95289818..95291017)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (93735501..93736700)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985710 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:94117653-94118233 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:94142296-94142796 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:94162743-94163280 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:94163281-94163816 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:94347448-94348142 Neighboring gene microRNA 548m Neighboring gene uncharacterized LOC124905288 Neighboring gene calmodulin 1 pseudogene 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. 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

    • NANOG hESC enhancer GRCh37_chrX:94545373-94545897

    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_087786.1 

      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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      95289818..95291017
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      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      93735501..93736700
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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