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    Sox2ot SOX2 overlapping transcript (non-protein coding) [ Mus musculus (house mouse) ]

    Gene ID: 320478, updated on 9-Dec-2024

    Summary

    Official Symbol
    Sox2otprovided by MGI
    Official Full Name
    SOX2 overlapping transcript (non-protein coding)provided by MGI
    Primary source
    MGI:MGI:2444112
    See related
    Ensembl:ENSMUSG00000105265 AllianceGenome:MGI:2444112
    Gene type
    ncRNA
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    B230215L15Rik
    Summary
    Is expressed in several structures, including brain; genitourinary system; hemolymphoid system gland; neural ectoderm; and sensory organ. Orthologous to human SOX2-OT (SOX2 overlapping transcript). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in whole brain E14.5 (RPKM 8.2), frontal lobe adult (RPKM 8.1) and 6 other tissues See more
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    Genomic context

    See Sox2ot in Genome Data Viewer
    Location:
    3 A3; 3 16.56 cM
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (34614530..34732142)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (34560381..34677993)

    Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 38505 Neighboring gene VISTA enhancer mm1529 Neighboring gene predicted gene 20515 Neighboring gene predicted gene, 34599 Neighboring gene STARR-seq mESC enhancer starr_07369 Neighboring gene Sox2 5' regulatory region Neighboring gene microRNA 1897 Neighboring gene Sox2 SRR2 enhancer Neighboring gene SRR18 enhancer downstream of Sox2 Neighboring gene N-4 enhancer downstream of Sox2 Neighboring gene STARR-seq mESC enhancer starr_07376 Neighboring gene SRY (sex determining region Y)-box 2 Neighboring gene STARR-seq mESC enhancer starr_07377 Neighboring gene STARR-seq mESC enhancer starr_07378 Neighboring gene predicted gene, 34941 Neighboring gene predicted gene 3143

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
     
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
     
    Component Evidence Code Pubs
    is_active_in cellular_component ND
    No biological Data available
    more info
     

    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.

    RNA

    1. NR_015580.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      BC057611
      Related
      ENSMUST00000197977.6

    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_000069.7 Reference GRCm39 C57BL/6J

      Range
      34614530..34732142
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_177170.2: Suppressed sequence

      Description
      NM_177170.2: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.