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] See more...

Aliases for SOX2-OT Gene

Subcategory (RNA class) for SOX2-OT Gene


Number of RNA Genes sources:

3 / 17

Aliases for SOX2-OT Gene

  • SOX2 Overlapping Transcript 2 3 5
  • SOX2-OT 2 5 165
  • SOX2 Overlapping Transcript (Non-Protein Coding) 2 3
  • NCRNA00043 2 3
  • SOX2 Overlapping Transcript (Non-Coding RNA) 3
  • Non-Protein Coding RNA 43 2
  • DKFZp761J1324 2
  • HSALNG0031034 164
  • 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

Entrez Gene Summary for SOX2-OT Gene

  • 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]

GeneCards Summary for SOX2-OT Gene

SOX2-OT (SOX2 Overlapping Transcript) is an RNA Gene, and is affiliated with the lncRNA class. Diseases associated with SOX2-OT include Central Nervous System Disease and Retinal Degeneration.

Gene Wiki entry for SOX2-OT Gene

Rfam classification for SOX2-OT Gene

  • SOX2 overlapping transcript exon 2
  • SOX2 overlapping transcript exon 3
  • SOX2 overlapping transcript exon 4
  • SOX2 overlapping transcript exon 1

Additional gene information for SOX2-OT Gene

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

Genomics for SOX2-OT Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SOX2-OT Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J180988 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 600.7 -0.3 -261 3 SP1 HNRNPL CREB1 GATAD2A PRDM10 REST RFX1 IKZF1 NFKBIZ POLR2A DNAJC19 SOX2-OT lnc-DNAJC19-5 TTC14 ENSG00000242068 lnc-TTC14-1 FXR1
GH03J181735 Enhancer 0.5 Ensembl CraniofacialAtlas dbSUPER 10.8 +746.2 746245 0.4 SOX2-OT ENSG00000278026 SOX2 RF00017-4184 RN7SL703P lnc-SOX2-4
GH03J181734 Enhancer 0.4 Ensembl dbSUPER 10.8 +745.0 745039 0.4 POLR2A SOX2-OT ENSG00000278026 SOX2 RF00017-4184 RN7SL703P lnc-SOX2-4
GH03J181736 Enhancer 0.3 Ensembl dbSUPER 10.8 +747.0 747039 0.4 SOX2-OT ENSG00000278026 SOX2 RF00017-4184 RN7SL703P lnc-SOX2-4
GH03J181055 Promoter/Enhancer 1 VISTA UCNEbase Ensembl 0.2 +67.4 67364 2.6 ENSG00000241231 piR-48348-049 piR-61532-205 SOX2-OT DNAJC19 SOX2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SOX2-OT on the GeneHancer Hub at the UCSC Golden Path

Genomic Locations for SOX2-OT Gene

Genomic Locations for SOX2-OT Gene
847,119 bases
Plus strand
847,111 bases
Plus strand

Genomic View for SOX2-OT Gene

Genes around SOX2-OT on UCSC Golden Path with GeneCards custom track
SOX2-OT in the GeneCards ncRNA compendium hub on the UCSC Golden Path

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

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

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

Function for SOX2-OT Gene

Phenotypes From GWAS Catalog for SOX2-OT Gene

Animal Model Products

CRISPR Products

miRNA for SOX2-OT Gene

miRTarBase miRNAs that target SOX2-OT

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

Localization for SOX2-OT Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SOX2-OT gene
Compartment Confidence
nucleus 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
cytosol 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for SOX2-OT Gene

Pathways & Interactions for SOX2-OT Gene

PathCards logo

SuperPathways for SOX2-OT Gene

No Data Available

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

GO ID Qualified GO term Evidence PubMed IDs
GO:0007275 multicellular organism development IEA --
genes like me logo Genes that share ontologies with SOX2-OT: view

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

Drugs & Compounds for SOX2-OT Gene

No Compound Related Data Available

Transcripts for SOX2-OT Gene

Non-coding RNA (ncRNA) Transcripts from RNAcentral for SOX2-OT Gene

RNAcentral Transcript ID Subcategory Length (nts) # of Sources Source Identifiers and Annotations
URS000075D6CA_9606 lncRNA 3535 3

HGNC: 20209,

RefSeq: NR_004053,

LNCipedia: SOX2-OT:94,

URS000046832C_9606 lncRNA 1342 3

Ensembl: ENST00000597347 (view in UCSC) ,

LncBook: HSALNT0064941,

LNCipedia: SOX2-OT:11,

URS0000811730_9606 lncRNA 1012 3

Ensembl: ENST00000630482 (view in UCSC) ,

LncBook: HSALNT0064929,

LNCipedia: SOX2-OT:5,

URS000056F1DC_9606 lncRNA 979 3

Ensembl: ENST00000476125 (view in UCSC) ,

LncBook: HSALNT0065009,

LNCipedia: SOX2-OT:34,

URS0000811CFC_9606 lncRNA 954 3

Ensembl: ENST00000631025 (view in UCSC) ,

LncBook: HSALNT0065063,

LNCipedia: SOX2-OT:59,

SOX2-OT in the GeneCards ncRNA compendium hub on the UCSC Golden Path

Additional transcripts not in RNAcentral for SOX2-OT Gene

15 NCBI additional mRNA sequence :

CRISPR 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

Expression for SOX2-OT Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SOX2-OT

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, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SOX2-OT Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
678529 Likely Benign: not provided 181,712,350(+) A/C FIVE_PRIME_UTR_VARIANT
681395 Likely Benign: not provided 181,713,159(+) G/A MISSENSE_VARIANT
682175 Likely Benign: not provided 181,712,341(+) G/T FIVE_PRIME_UTR_VARIANT
691384 Likely Pathogenic: Pyloric stenosis; Esophageal atresia 181,713,058(+) C/G MISSENSE_VARIANT
705427 Benign: not provided 181,712,591(+) C/A SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for SOX2-OT Gene

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

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

Additional Variant Information 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

MalaCards: The human disease database

(17) MalaCards diseases for SOX2-OT Gene - From: LncRNADisease, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
central nervous system disease
  • cns
retinal degeneration
  • degeneration of retina
squamous cell carcinoma
  • epidermoid carcinoma
lung squamous cell carcinoma
  • epidermoid cell carcinoma of the lung
  • cca
- elite association - COSMIC cancer census association via MalaCards
genes like me logo Genes that share disorders with SOX2-OT: view

No data available for 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 23
  2. LncRNA SOX2-OT is a novel prognostic biomarker for osteosarcoma patients and regulates osteosarcoma cells proliferation and motility through modulating SOX2. (PMID: 28960757) Wang Z … Lu X (IUBMB life 2017) 2 3
  3. Mutations in SOX2 cause anophthalmia. (PMID: 12612584) Fantes J … FitzPatrick DR (Nature genetics 2003) 2 3
  4. Long noncoding RNA SOX2-OT facilitates laryngeal squamous cell carcinoma development by epigenetically inhibiting PTEN via methyltransferase EZH2. (PMID: 30811870) Tai Y … Ma J (IUBMB life 2019) 3
  5. LncRNA SOX2OT alleviates the high glucose-induced podocytes injury through autophagy induction by the miR-9/SIRT1 axis. (PMID: 31301307) Zhang Y … Wu X (Experimental and molecular pathology 2019) 3

Products for SOX2-OT Gene

Sources for SOX2-OT Gene