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    LOC128926823 CapStarr-seq enhancer MGSCv37_chr11:109357315-109357468 [ Mus musculus (house mouse) ]

    Gene ID: 128926823, updated on 8-Feb-2024

    Summary

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    Gene symbol
    LOC128926823
    Gene description
    CapStarr-seq enhancer MGSCv37_chr11:109357315-109357468
    Gene type
    biological region
    Feature type(s)
    regulatory: enhancer
    RefSeq status
    REVIEWED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Rr369417
    Summary
    This locus includes a subregion that was identified as a candidate cis-regulatory module (CRM) in developing mouse thymocytes based on a combination of DNase I hypersensitivity and transcription factor binding. That CRM was validated as an active enhancer by high-throughput CapStarr-seq reporter assays showing weak activity in P5424 T cells and NIH3T3 fibroblasts. This locus also includes a B cell regulatory element that was identified by FAIRE-seq (formaldehyde-assisted isolation of regulatory elements sequencing), and which was validated as an enhancer by STARR-seq (self-transcribing active regulatory region sequencing) in lipopolysaccharide-activated mouse splenic B cells. [provided by RefSeq, Oct 2023]
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    Genomic context

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    See LOC128926823 in Genome Data Viewer
    Location:
    chromosome: 11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (109386623..109386980)

    Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E380 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:109287298-109287521 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:109293875-109294028 Neighboring gene STARR-positive B cell enhancer ABC_E10727 Neighboring gene STARR-positive B cell enhancer ABC_E5293 Neighboring gene archaelysin family metallopeptidase 2 Neighboring gene predicted gene, 45916 Neighboring gene solute carrier family 16 (monocarboxylic acid transporters), member 6 Neighboring gene STARR-positive B cell enhancer ABC_E5294 Neighboring gene STARR-positive B cell enhancer ABC_E7088 Neighboring gene arylsulfatase G Neighboring gene STARR-positive B cell enhancer ABC_E1846 Neighboring gene predicted gene, 22378 Neighboring gene STARR-positive B cell enhancer ABC_E7089 Neighboring gene predicted gene, 39442 Neighboring gene WD repeat domain, phosphoinositide interacting 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. High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq. Vanhille L, et al. Nat Commun, 2015 Apr 15. PMID 25872643
    2. Gene regulatory networks STARR-ing B cells. Martínez de Paz A, et al. Nat Immunol, 2020 Feb. PMID 31873293, Free PMC Article
    3. Charting the cis-regulome of activated B cells by coupling structural and functional genomics. Chaudhri VK, et al. Nat Immunol, 2020 Feb. PMID 31873292

    GeneRIFs: Gene References Into Functions

    General gene information

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    Other Names

    • STARR-positive B cell enhancer ABC_E5295
    • regulatory region 369417

    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_152464.2 

      Range
      101..458
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000077.7 Reference GRCm39 C57BL/6J

      Range
      109386623..109386980
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version