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Aliases for SOX2-OT Gene

Subcategory (RNA class) for SOX2-OT Gene

non-coding RNA

Quality Score for this RNA gene is


Aliases for SOX2-OT Gene

  • SOX2 Overlapping Transcript 2 3 5
  • 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

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 non-coding RNA class.

Gene Wiki entry for SOX2-OT Gene

Additional gene information for SOX2-OT Gene

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

Genomics for SOX2-OT Gene

Regulatory Elements for SOX2-OT Gene

Enhancers for SOX2-OT Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03H181732 0.4 dbSUPER 10.8 +745.4 745418 4.9 POLR2A SOX2 SOX2-OT ENSG00000278026 RN7SL703P
GH03H180988 1.1 ENCODE 0.7 -0.1 -84 1.8 HDGF FOXA2 PKNOX1 ARID4B SIN3A DMAP1 ZNF2 YY1 CBX5 ZNF143 LOC647253 SOX2-OT GC03P180982
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SOX2-OT on UCSC Golden Path with GeneCards custom track

Promoters for SOX2-OT Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000162646 -170 2001 HDGF PKNOX1 FOXA2 ARID4B SIN3A DMAP1 ZNF2 YY1 CBX5 ZNF207

Genomic Locations for SOX2-OT Gene

Genomic Locations for SOX2-OT Gene
847,111 bases
Plus strand

Genomic View for SOX2-OT Gene

Genes around SOX2-OT on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SOX2-OT Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SOX2-OT Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence 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 & Families for SOX2-OT Gene

Gene Families for SOX2-OT Gene

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

Phenotypes From GWAS Catalog for SOX2-OT Gene

Animal Model Products

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets 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 , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for SOX2-OT Gene

Pathways & Interactions 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


No data available for Pathways by source and SIGNOR curated interactions for SOX2-OT Gene

Drugs & Compounds for SOX2-OT Gene

No Compound Related Data Available

Transcripts for SOX2-OT Gene

Unigene Clusters for SOX2-OT Gene

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

Clone 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
ECgene alternative splicing isoforms for

Expression for SOX2-OT Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SOX2-OT Gene

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

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (x11.5), Brain - Substantia nigra (x7.2), Brain - Hippocampus (x5.7), Brain - Amygdala (x5.0), and Brain - Putamen (basal ganglia) (x4.6).

SOURCE GeneReport for Unigene cluster for SOX2-OT Gene:

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

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for SOX2-OT Gene

Orthologs for SOX2-OT Gene

Evolution for SOX2-OT Gene

Gene Tree for SOX2-OT (if available)
Gene Tree for SOX2-OT (if available)

No data available for Orthologs for SOX2-OT Gene

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
rs104893799 Pathogenic 181,712,889(+) AGGAC(C/T)AGCTG intron-variant, reference, stop-gained
rs104893800 Pathogenic 181,712,637(+) TCGAC(G/T)AGGCT intron-variant, reference, stop-gained
rs104893801 Pathogenic 181,712,608(+) TTTGT(A/C)GGAGA intron-variant, reference, stop-gained
rs104893802 Pathogenic 181,712,650(+) GCGGC(C/T)GCGAG intron-variant, reference, missense
rs104893803 Pathogenic 181,712,823(+) TGAAC(C/G/T)AGCGC intron-variant, reference, missense, stop-gained

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

Variant ID Type Subtype PubMed ID
nsv979907 CNV duplication 23825009
nsv965238 CNV duplication 23825009
nsv963382 CNV duplication 23825009
nsv955617 CNV deletion 24416366
nsv829810 CNV gain+loss 17160897
nsv829809 CNV loss 17160897
nsv820662 CNV deletion 20802225
nsv592652 CNV loss 21841781
nsv522902 CNV loss 19592680
nsv511225 CNV gain 21212237
nsv509871 OTHER sequence alteration 20534489
nsv509870 OTHER sequence alteration 20534489
nsv478524 CNV novel sequence insertion 20440878
nsv437350 CNV loss 16327808
nsv428427 CNV gain 18775914
nsv236637 CNV deletion 16902084
nsv236619 CNV deletion 16902084
nsv1149813 CNV deletion 26484159
nsv1123713 CNV deletion 24896259
nsv1074643 CNV deletion 25765185
esv997898 CNV deletion 20482838
esv3893830 CNV loss 25118596
esv3598895 CNV loss 21293372
esv3598892 CNV loss 21293372
esv3598890 CNV loss 21293372
esv3598889 CNV loss 21293372
esv3598888 CNV loss 21293372
esv3598887 CNV loss 21293372
esv3598886 CNV loss 21293372
esv3598885 CNV loss 21293372
esv3562995 CNV deletion 23714750
esv3562990 CNV deletion 23714750
esv3562988 CNV deletion 23714750
esv3251444 CNV insertion 24192839
esv2759205 CNV gain 17122850
esv2726282 CNV deletion 23290073
esv2726281 CNV deletion 23290073
esv2726280 CNV deletion 23290073
esv2726279 CNV deletion 23290073
esv2726278 CNV deletion 23290073
esv2675280 CNV deletion 23128226
esv2666419 CNV deletion 23128226
esv2660128 CNV deletion 23128226
esv2658568 CNV deletion 23128226
esv2550869 CNV deletion 19546169
esv2245575 CNV deletion 18987734
esv21911 CNV loss 19812545
esv2084028 CNV deletion 18987734
esv1445327 CNV deletion 17803354
esv1383539 CNV deletion 17803354
esv1197897 CNV insertion 17803354
dgv959e214 CNV loss 21293372
dgv2648n106 CNV deletion 24896259

Relevant External Links for SOX2-OT Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

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

Disorders for SOX2-OT Gene

Relevant External Links for SOX2-OT

Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for SOX2-OT Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas 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 PP … Mattick JS (RNA (New York, N.Y.) 2009) 2 3 22 60
  2. Mutations in SOX2 cause anophthalmia. (PMID: 12612584) Fantes J … FitzPatrick DR (Nature genetics 2003) 2 3 60
  3. Overexpression of the non-coding SOX2OT variants 4 and 7 in lung tumors suggests an oncogenic role in lung cancer. (PMID: 26846097) Saghaeian Jazi M … Mowla SJ (Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine 2016) 3 60
  4. Identification of new SOX2OT transcript variants highly expressed in human cancer cell lines and down regulated in stem cell differentiation. (PMID: 26703382) Saghaeian Jazi M … Mowla SJ (Molecular biology reports 2016) 3 60
  5. Up-regulation of long non-coding RNA Sox2ot promotes hepatocellular carcinoma cell metastasis and correlates with poor prognosis. (PMID: 26097588) Shi XM … Teng F (International journal of clinical and experimental pathology 2015) 3 60

Products for SOX2-OT Gene

Sources for SOX2-OT Gene

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