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    SOX2-OT SOX2 overlapping transcript [ Homo sapiens (human) ]

    Gene ID: 347689, updated on 15-Jun-2019

    Summary

    Official Symbol
    SOX2-OTprovided by HGNC
    Official Full Name
    SOX2 overlapping transcriptprovided by HGNC
    Primary source
    HGNC:HGNC:20209
    See related
    MIM:616338
    Gene type
    ncRNA
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SOX2OT; NCRNA00043
    Summary
    This gene produces alternatively spliced long non-coding RNAs. These RNAs were observed to be upregulated in tumor cells and positively correlated to expression of the SRY-box 2 gene. Overexpression of these transcripts may promote cell proliferation. [provided by RefSeq, Dec 2017]
    Expression
    Restricted expression toward brain (RPKM 80.2) See more

    Genomic context

    See SOX2-OT in Genome Data Viewer
    Location:
    3q26.33
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (181056680..181742228)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (180774468..181460016)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene FMR1 autosomal homolog 1 Neighboring gene DnaJ heat shock protein family (Hsp40) member C19 Neighboring gene VISTA enhancer hs192 Neighboring gene RNA, U6 small nuclear 4, pseudogene Neighboring gene FAU pseudogene 2 Neighboring gene uncharacterized LOC102724604 Neighboring gene ribosomal protein L7a pseudogene 25 Neighboring gene SOX2 5' regulatory region Neighboring gene SRR2 enhancer downstream of SOX2 Neighboring gene SRY-box 2 Neighboring gene RNA, 7SL, cytoplasmic 703, pseudogene Neighboring gene RNA, 5S ribosomal pseudogene 150

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Phenotypes

    NHGRI GWAS Catalog

    Description
    A genome-wide association study of anorexia nervosa.
    NHGRI GWA Catalog
    Biological insights from 108 schizophrenia-associated genetic loci.
    NHGRI GWA Catalog

    General gene information

    Markers

    Other Names

    • SOX2 overlapping transcript (non-coding RNA)
    • SOX2 overlapping transcript (non-protein coding)

    Clone Names

    • DKFZp761J1324

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    multicellular organism development IEA
    Inferred from Electronic Annotation
    more info
     

    NCBI Reference Sequences (RefSeq)

    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_004053.3 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) has an alternate exon in place of the first four exons compared to variant 1.
      Source sequence(s)
      AC117415, AK022826, DA366949, JN711430
    2. NR_075089.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) has an alternate in place of the first four exons and lacks an alternate 3' exon compared to variant 1.
      Source sequence(s)
      AC117415, DA366949, JN711430
    3. NR_075090.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) has an alternate in place of the first four exons and lacks two alternate 3' exons compared to variant 1.
      Source sequence(s)
      AC117415, DA366949, JN882275
    4. NR_075091.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript.
      Source sequence(s)
      AC117415, DA281835, JQ408703
    5. NR_075092.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate 3' exon compared to variant 1.
      Source sequence(s)
      AC117415, DA281835, JN711430
    6. NR_075093.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has an alternate in place of the first two exons and lacks two alternate 3' exons compared to variant 1.
      Source sequence(s)
      AC117415, DA310380

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

      Range
      181056680..181742228
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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