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    sox2ot SOX2 overlapping transcript [ Danio rerio (zebrafish) ]

    Gene ID: 103909645, updated on 4-Jan-2025

    Summary

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    Official Symbol
    sox2otprovided by ZNC
    Official Full Name
    SOX2 overlapping transcriptprovided by ZNC
    Primary source
    ZFIN:ZDB-LNCRNAG-091125-1
    See related
    AllianceGenome:ZFIN:ZDB-LNCRNAG-091125-1
    Gene type
    ncRNA
    RefSeq status
    MODEL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    si:ch73-334e23.1
    Summary
    Is expressed in several structures, including central nervous system; eye; posterior lateral mesoderm; posterior neural tube; and rostral blood island. Orthologous to human SOX2-OT (SOX2 overlapping transcript). [provided by Alliance of Genome Resources, Jan 2025]
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    Genomic context

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    See sox2ot in Genome Data Viewer
    Location:
    chromosome: 22
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 22 NC_007133.7 (37276315..37526445, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 22 NC_007133.6 (37412545..37591938, complement)

    Chromosome 22 - NC_007133.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC137488986 Neighboring gene ATPase phospholipid transporting 11B Neighboring gene uncharacterized LOC110438287 Neighboring gene SRY-box transcription factor 2 Neighboring gene DnaJ (Hsp40) homolog, subfamily C, member 19 Neighboring gene FMR1 autosomal homolog 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Detection of long non-coding RNA homology, a comparative study on alignment and alignment-free metrics. Noviello TMR, et al. BMC Bioinformatics, 2018 Nov 6. PMID 30400819, Free PMC Article
    2. Complex architecture and regulated expression of the Sox2ot locus during vertebrate development. Amaral PP, et al. RNA, 2009 Nov. PMID 19767420, Free PMC Article
    3. Key sequence features of CRISPR RNA for dual-guide CRISPR-Cas9 ribonucleoprotein complexes assembled with wild-type or HiFi Cas9. Okada K, et al. Nucleic Acids Res, 2022 Mar 21. PMID 35166844, Free PMC Article
    4. Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database. Pasquier J, et al. BMC Genomics, 2016 May 18. PMID 27189481, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Other Names

    • SOX2 overlapping transcript (non-protein coding)

    NCBI Reference Sequences (RefSeq)

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    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007133.7 Reference GRCz11 Primary Assembly

      Range
      37276315..37526445 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RNA

    1. XR_011008309.1 RNA Sequence

    2. XR_002456526.2 RNA Sequence

    3. XR_002456525.2 RNA Sequence

    4. XR_659656.4 RNA Sequence

    5. XR_011008310.1 RNA Sequence

    6. XR_002456524.2 RNA Sequence

    7. XR_002456527.2 RNA Sequence

    8. XR_002456529.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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