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    LOC126861715 BRD4-independent group 4 enhancer GRCh37_chr13:27824999-27826198 [ Homo sapiens (human) ]

    Gene ID: 126861715, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC126861715
    Gene description
    BRD4-independent group 4 enhancer GRCh37_chr13:27824999-27826198
    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 (MPRA). This sequence was defined as a group 4 enhancer that depends on the BRD2, P300/CBP, MED14 and CDK7 cofactors in HCT116 colorectal carcinoma cells, but it has limited or no dependence on the BRD4 bromodomain protein. Two subregions were also shown to be active enhancers by ChIP-STARR-seq in human embryonic stem cells, where both are associated with the OCT4 and NANOG transcription factors and are marked by the H3K27ac and H3K4me1 histone modifications. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate 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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    See LOC126861715 in Genome Data Viewer
    Location:
    chromosome: 13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (27250862..27252061)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (26471577..26472776)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (27824999..27826198)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903137 Neighboring gene long intergenic non-protein coding RNA 412 Neighboring gene ribosomal protein L21 Neighboring gene small nucleolar RNA, C/D box 102 Neighboring gene small nucleolar RNA, H/ACA box 27

    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 within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. 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

    See Variation Viewer (GRCh37.p13)

    General gene information

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    Other Names

    • ATAC-STARR-seq lymphoblastoid active region 7501
    • OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:27825017-27825602
    • OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:27825603-27826188

    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_086213.1 

      Range
      101..1300
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      27250862..27252061
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      26471577..26472776
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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