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    LOC126861405 CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:133916360-133917559 [ Homo sapiens (human) ]

    Gene ID: 126861405, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC126861405
    Gene description
    CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:133916360-133917559
    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: 11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (134046116..134047664)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (134088900..134090448)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2730 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:133890717-133891220 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:133894031-133894833 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:133896267-133896838 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:133896839-133897409 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:133901031-133901530 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:133902231-133902958 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:133902959-133903686 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:133906753-133907724 Neighboring gene long intergenic non-protein coding RNA 2731 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:133915510-133916010 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:133923324-133924176 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4092 Neighboring gene junctional adhesion molecule 3 Neighboring gene uncharacterized LOC124902797 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:133994434-133994972 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:133994973-133995509 Neighboring gene PTP4A2 pseudogene 2

    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_chr11:133916011-133916511

    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_085904.2 

      Range
      101..1649
      Download
      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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      134046116..134047664
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      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      134088900..134090448
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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