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Aliases for SOX2-OT Gene

Subcategory (RNA class) for SOX2-OT Gene

antisense

Quality Score for this RNA gene is

3

Aliases for SOX2-OT Gene

  • SOX2 Overlapping Transcript 2 3
  • SOX2 Overlapping Transcript (Non-Protein Coding) 2 3
  • SOX2 Overlapping Transcript (Non-Coding RNA) 3
  • Non-Protein Coding RNA 43 2
  • NCRNA00043 3
  • SOX2OT 3

External Ids for SOX2-OT Gene

ORGUL Members for SOX2-OT Gene

Previous HGNC Symbols for SOX2-OT Gene

  • SOX2OT

Previous GeneCards Identifiers for SOX2-OT Gene

  • GC03P181328
  • GC03P180723

Summaries for SOX2-OT Gene

GeneCards Summary for SOX2-OT Gene

SOX2-OT (SOX2 Overlapping Transcript) is an RNA Gene, and is affiliated with the antisense RNA class.

Gene Wiki entry for SOX2-OT Gene

No data available for Entrez Gene Summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SOX2-OT Gene

Genomics for SOX2-OT Gene

Genomic Location for SOX2-OT Gene

Start:
180,989,770 bp from pter
End:
181,836,880 bp from pter
Size:
847,111 bases
Orientation:
Plus strand

Genomic View for SOX2-OT Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SOX2-OT Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SOX2-OT Gene

No data available for Regulatory Elements for SOX2-OT Gene

Proteins for SOX2-OT Gene

Post-translational modifications for SOX2-OT Gene

No Post-translational modifications

No data available for DME Specific Peptides for SOX2-OT Gene

Domains for SOX2-OT Gene

Gene Families for SOX2-OT Gene

HGNC:
  • LNCRNA :Long non-coding RNAs

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SOX2-OT: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for SOX2-OT Gene

Function for SOX2-OT Gene

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Phenotypes , Animal Models , miRNA , Transcription Factor Targeting and HOMER Transcription for SOX2-OT Gene

Localization for SOX2-OT Gene

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from COMPARTMENTS and Gene Ontology (GO) - Cellular Components for SOX2-OT Gene

Pathways for SOX2-OT Gene

SuperPathways for SOX2-OT Gene

No Data Available

Interacting Proteins for SOX2-OT Gene

Gene Ontology (GO) - Biological Process for SOX2-OT Gene

None

No data available for Pathways by source for SOX2-OT Gene

Transcripts for SOX2-OT Gene

Unigene Clusters for SOX2-OT Gene

SOX2 overlapping transcript (non-protein coding):
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SOX2-OT

Primer Products

  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SOX2-OT Gene

No ASD Table

Relevant External Links for SOX2-OT Gene

GeneLoc Exon Structure for
SOX2-OT
ECgene alternative splicing isoforms for
SOX2-OT

Expression for SOX2-OT Gene

mRNA expression in normal human tissues for SOX2-OT Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SOX2-OT Gene

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (11.5), Brain - Substantia nigra (7.2), Brain - Hippocampus (5.7), Brain - Amygdala (5.0), and Brain - Putamen (basal ganglia) (4.6).

SOURCE GeneReport for Unigene cluster for SOX2-OT Gene Hs.654932

genes like me logo Genes that share expressions with SOX2-OT: view

In Situ Assay Products

No data available for Protein expression and mRNA Expression by UniProt/SwissProt for SOX2-OT Gene

Orthologs for SOX2-OT Gene

This gene was present in the common ancestor of human and mouse.

Orthologs for SOX2-OT Gene

Organism Taxonomy Gene Similarity Type Details
mouse
(Mus musculus)
Mammalia Sox2ot 16
Species with no ortholog for SOX2-OT:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • chimpanzee (Pan troglodytes)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • cow (Bos Taurus)
  • dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for SOX2-OT Gene

ENSEMBL:
Gene Tree for SOX2-OT (if available)
TreeFam:
Gene Tree for SOX2-OT (if available)

Paralogs for SOX2-OT Gene

No data available for Paralogs for SOX2-OT Gene

Variants for SOX2-OT Gene

Sequence variations from dbSNP and Humsavar for SOX2-OT Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type MAF
rs725017 -- 181,483,274(-) gagtt(C/T)aaggc intron-variant
rs733422 -- 181,404,262(-) GTGTT(G/T)CTCCA intron-variant
rs735774 -- 181,530,955(-) ATATA(C/T)TGTGA intron-variant
rs746058 -- 181,512,045(+) CAGAA(G/T)TGATA intron-variant
rs753073 -- 181,408,589(+) TTTTT(C/T)CCCTT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SOX2-OT Gene

Variant ID Type Subtype PubMed ID
esv2658568 CNV Deletion 23128226
nsv878042 CNV Gain 21882294

Relevant External Links for SOX2-OT Gene

HapMap Linkage Disequilibrium report
SOX2-OT

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SOX2-OT Gene

Disorders for SOX2-OT Gene

No disorders were found for SOX2-OT Gene.

No data available for UniProtKB/Swiss-Prot for SOX2-OT Gene

Publications for SOX2-OT Gene

  1. Complex architecture and regulated expression of the Sox2ot locus during vertebrate development. (PMID: 19767420) Amaral P.P. … Mattick J.S. (RNA 2009) 2 3 23
  2. Mutations in SOX2 cause anophthalmia. (PMID: 12612584) Fantes J. … FitzPatrick D.R. (Nat. Genet. 2003) 2 3
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3
  4. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PMID: 16344560) Kimura K. … Sugano S. (Genome Res. 2006) 3
  5. Two Novel Splice Variants of SOX2OT, SOX2OT-S1, and SOX2OT-S2 are Coupregulated with SOX2 and OCT4 in Esophageal Squamous Cell Carcinoma. (PMID: 24105929) Shahryari A. … Mowla S.J. (Stem Cells 2014) 3

Products for SOX2-OT Gene

  • QIAGEN qRT-PCR Assays for microRNAs that regulate SOX2-OT
    • QuantiTect SYBR Green Assays in human,mouse,rat
    • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
    • QuantiFast Probe-based Assays in human,mouse,rat
    • Predesigned siRNA for gene silencing in human,mouse,rat for SOX2-OT
    • Block miRNA regulation of SOX2-OT using miScript Target Protectors

    Sources for SOX2-OT Gene

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