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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

13

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

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 non-coding RNA class.

Gene Wiki entry for SOX2-OT Gene

Additional gene information for SOX2-OT Gene

No data available for 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

GeneHancer (GH) Regulatory Elements for SOX2-OT Gene

Promoters and enhancers for SOX2-OT Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03I180988 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 550.8 -0.2 -169 2 HDGF FOXA2 PKNOX1 ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 POLR2B SOX2-OT DNAJC19 LOC647253 GC03P180982
GH03I180990 Enhancer 0.4 ENCODE 550.8 +0.9 895 0.1 MEIS2 PKNOX1 ATF2 SOX2-OT DNAJC19 ENSG00000242140
GH03I181732 Enhancer 0.3 dbSUPER 10.8 +745.4 745418 4.9 POLR2A SOX2 SOX2-OT ENSG00000278026 RN7SL703P
GH03I181055 Enhancer 0.8 VISTA UCNEbase 0.2 +67.2 67163 2.2 LOC102724604 SOX2-OT DNAJC19 ENSG00000242140
GH03I181252 Enhancer 0.8 UCNEbase 0.1 +263.1 263142 0.4 PKNOX1 FEZF1 ZEB2 ZNF843 BCL11B OSR2 CTBP1 PRDM6 POLR2A RCOR1 GC03P181252 RNU6-4P LOC102724604 SOX2-OT
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

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

Genomic Locations for SOX2-OT Gene

Genomic Locations for SOX2-OT Gene
chr3:180,989,770-181,836,880
(GRCh38/hg38)
Size:
847,111 bases
Orientation:
Plus strand
chr3:180,707,558-181,554,668
(GRCh37/hg19)

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

miRNA for SOX2-OT Gene

miRTarBase miRNAs that target SOX2-OT

Clone Products

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

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

None

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
SOX2-OT
ECgene alternative splicing isoforms for
SOX2-OT

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:

Hs.654932
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

ENSEMBL:
Gene Tree for SOX2-OT (if available)
TreeFam:
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 Variation AA Info Type
rs104893799 pathogenic, Microphthalmia syndromic 3 181,712,889(+) C/T intron_variant
rs104893800 pathogenic, Microphthalmia syndromic 3 181,712,637(+) G/T intron_variant
rs104893801 pathogenic, Microphthalmia syndromic 3 181,712,608(+) C/A intron_variant
rs104893802 pathogenic, Microphthalmia syndromic 3 181,712,650(+) T/C intron_variant
rs104893803 pathogenic, Microphthalmia syndromic 3 181,712,823(+) C/G/T intron_variant

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
SOX2-OT

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

Disorders for SOX2-OT Gene

Additional Disease Information for SOX2-OT

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 58
  2. Mutations in SOX2 cause anophthalmia. (PMID: 12612584) Fantes J … FitzPatrick DR (Nature genetics 2003) 2 3 58
  3. Overexpressed long noncoding RNA Sox2ot predicts poor prognosis for cholangiocarcinoma and promotes cell proliferation and invasion. (PMID: 29246536) Li Z … Cui Y (Gene 2018) 3 58
  4. Long Noncoding RNA-Sox2OT Knockdown Alleviates Diabetes Mellitus-Induced Retinal Ganglion Cell (RGC) injury. (PMID: 27193103) Li CP … Liu XM (Cellular and molecular neurobiology 2017) 3 58
  5. Correlations between lncRNA-SOX2OT polymorphism and susceptibility to breast cancer in a Chinese population. (PMID: 28240100) Tang X … Liu J (Biomarkers in medicine 2017) 3 58

Products for SOX2-OT Gene

Sources for SOX2-OT Gene

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