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SOX2-OT Gene

RNA gene   GIFtS: 26
GCID: GC03P180723

SOX2 Overlapping Transcript (Non-Protein Coding)


(Previous symbol: SOX2OT)
  See related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Subcategory (RNA class): antisense

Quality score for this RNA gene is 3

Aliases
SOX2 Overlapping Transcript (Non-Protein Coding)1 2
SOX2OT1 2
Non-Protein Coding RNA 431
NCRNA000432

External Ids:    HGNC: 202091   Entrez Gene: 3476892   Ensembl: ENSG000002428087   
ORGUL members:         

Export aliases for SOX2-OT gene to outside databases

Previous GC identifer: GC03P181328


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for SOX2-OT Gene:
SOX2-OT (SOX2 overlapping transcript (non-protein coding)) is an RNA gene, and is affiliated with the antisense RNA class. Diseases associated with SOX2-OT include endotheliitis.

Gene Wiki entry for SOX2-OT (SOX2OT) Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000003.12  NC_018914.2  NT_005612.17  
Regulatory elements:
   Search for regulatory transcription factor binding sites for SOX2-OT
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SOX2-OT


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 3q26.33   Ensembl cytogenetic band:  3q26.33   HGNC cytogenetic band: 3q26.33

SOX2-OT Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SOX2-OT gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03P180723:  view genomic region     (about GC identifiers)

Start:
180,707,558 bp from pter      End:
181,554,668 bp from pter
Size:
847,111 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
LNCRNA: Long non-coding RNAs

  --

(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Animal Models:
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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  --

(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SOX2-OT
Interactions:

    Search GeneGlobe Interaction Network for SOX2-OT

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for SOX2-OT



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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Unigene Cluster for SOX2-OT:

SOX2 overlapping transcript (non-protein coding)
Hs.654932  [show with all ESTs]
Unigene Representative Sequence: NR_075091
Selected Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 36):
ENST00000487240(sense_overlapping) ENST00000461063(sense_overlapping) ENST00000493521(sense_overlapping) ENST00000460739(sense_overlapping) ENST00000597347(sense_overlapping)
ENST00000493116(sense_overlapping) ENST00000469278(sense_overlapping) ENST00000597828(sense_overlapping) ENST00000595313(sense_overlapping) ENST00000594942(sense_overlapping)
ENST00000598867(sense_overlapping) ENST00000497122(sense_overlapping) ENST00000472856(sense_overlapping) ENST00000498731(sense_overlapping) ENST00000476964(sense_overlapping)
ENST00000492337(sense_overlapping) ENST00000491282(sense_overlapping) ENST00000498226(sense_overlapping)
miRNA
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Additional mRNA sequence: 

AK022826.1 AL157425.1 BC016393.1 BC041898.2 JN711430.1 JN882275.1 JQ408703.1 JX504683.1 
NR_004053.3 NR_075089.1 NR_075090.1 NR_075091.1 NR_075092.1 NR_075093.1 

14 DOTS entries:

DT.120898976  DT.99929231  DT.40305974  DT.100813092  DT.95375492  DT.436628  DT.95375490  DT.103756 
DT.120898922  DT.120898938  DT.120898945  DT.75161459  DT.91653554  DT.91735688 

Selected AceView cDNA sequences (see all 64):

AI570449 AL157425 BG701492 AI051133 CA314424 BC041898 BM709735 AA813589 
BX459910 BF594264 BX442540 BM474966 BC016393 BM725940 AI056507 AA994714 
AI912222 AI497629 AK022826 BX508181 BI916139 Z40539 BG715434 CF456582 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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Expression evidence for SOX2-OT:none

SOX2-OT expression in normal human tissues (normalized intensities)      SOX2-OT embryonic expression: see
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GGGAATTAAA
SOX2-OT Expression
About this image


SOX2-OT expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 2) fully expand
 
 Endothelium (Cardiovascular System)
         Endothelial Cells Blood Brain Barrier
 
 Brain (Nervous System)
         Endothelial Cells Blood Brain Barrier
SOX2-OT Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.654932
    Custom PCR Arrays for SOX2-OT
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SOX2-OT

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of human and mouse.

Orthologs for SOX2-OT gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Sox2ot5 SOX2 overlapping transcript (non-protein coding)   --   3 (16.56 cM) 34104438 


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

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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  --

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for SOX2-OT (see all 10804)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 3 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs105782661,2
C--180688092(+) aaaaa-/A/AAA 
        
GATGG
2 -- int11NA 2
rs18056441,2
C,F,H--180772475(+) GTTTAA/GCTTTA 2 -- us2k116Minor allele frequency- G:0.04MN EA NS NA WA 1704
rs802636091,2
C,F--180772613(+) GCCAGC/TACAGG 2 -- us2k12Minor allele frequency- T:0.01WA NA 238
rs1908376731,2
--180772675(+) GCCTTC/GATACT 2 -- us2k10--------
rs1122246171,2
C,F--180772725(+) TGGAAA/TCAGTT 2 -- us2k11Minor allele frequency- T:0.00CSA 1
rs18052011,2
C,F,H--180772747(-) TCTTTC/GTCTAT 2 -- us2k116Minor allele frequency- G:0.38MN EA NS WA NA CSA 859
rs1129378071,2
C--180772801(+) ATCCTC/TGTTTG 2 -- us2k10--------
rs1830380671,2
--180773073(+) AGATAC/TTGTTC 2 -- us2k10--------
rs1501782111,2
--180773213(+) ATGTAC/TTTTGT 2 -- us2k10--------
rs30262161,2
H--180773220(+) TTGTTG/TGCTCT 2 -- us2k13Minor allele frequency- T:0.00EA NS 300

HapMap Linkage Disequilibrium report for SOX2-OT (180707558 - 180957558 bp, first 250kb of SOX2-OT)

Structural Variations
     Database of Genomic Variants (DGV) 2 variations for SOX2-OT:    About this table    
Variant IDTypeSubtypePubMed ID
esv2658568CNV Deletion23128226
nsv878042CNV Gain21882294

Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing SOX2-OT
DNA2.0 Custom Variant and Variant Library Synthesis for SOX2-OT

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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1 disease for SOX2-OT:    About MalaCards
endotheliitis


SOX2-OT for disorders           About GeneDecksing


Export disorders for SOX2-OT gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for SOX2-OT gene integrated from 10 sources:
(articles sorted by number of sources associating them with SOX2-OT)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Complex architecture and regulated expression of the Sox2ot locus during vertebrate development. (PubMed id 19767420)1, 3, 9 Amaral P.P....Mattick J.S. (RNA 2009)
  2. Mutations in SOX2 cause anophthalmia. (PubMed id 12612584)1, 3 Fantes J.... FitzPatrick D.R. (Nat. Genet. 2003)
  3. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 347689 HGNC: 20209 AceView: SOX2OT Ensembl:ENSG00000242808 euGenes: HUgn347689
ECgene: SOX2-OT H-InvDB: SOX2-OT

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for SOX2-OT Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for SOX2-OT gene:
Search GeneIP for patents involving SOX2-OT

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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