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    LOC126862617 CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:62782294-62783493 [ Homo sapiens (human) ]

    Gene ID: 126862617, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC126862617
    Gene description
    CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:62782294-62783493
    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 primed human embryonic stem cells, where it is marked by the H3K4me1 histone modification. [provided by RefSeq, Jan 2023]
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    Genomic context

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    Location:
    chromosome: 17
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (64786110..64787375)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (65655863..65657128)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ARHGAP27P1-BPTFP1-KPNA2P3 readthrough, transcribed pseudogene Neighboring gene bromodomain PHD finger transcription factor pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:62773916-62774585 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:62774586-62775254 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8849 Neighboring gene Rho GTPase activating protein 27 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8850 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:62781097-62781856 Neighboring gene microRNA 6080 Neighboring gene pleckstrin homology and RUN domain containing M1 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:62794173-62794673 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:62817908-62818408 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:62821718-62822218 Neighboring gene microRNA 4315-2 Neighboring gene RNA, U7 small nuclear 115 pseudogene

    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

    • H3K4me1 hESC enhancer GRCh37_chr17:62782228-62782728

    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_087114.2 

      Range
      101..1366
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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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      64786110..64787375
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      65655863..65657128
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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