SOX2-OT

Summary

SOX2-OT (SOX2 overlapping transcript, HGNC:20209) is a long non-coding RNA gene on chromosome 3q26.33.

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.

Source: NCBI Gene 347689 — RefSeq curated summary.

At a glance

• Gene type: non-coding (lncRNA) — no protein product; not a drug target. Variant/disease associations are omitted (they would be positional, from an overlapping protein-coding gene).

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20209
Approved symbol	SOX2-OT
Name	SOX2 overlapping transcript
Location	3q26.33
Locus type	RNA, long non-coding
Status	Approved
Aliases	DKFZp761J1324, NCRNA00043
Ensembl gene	ENSG00000242808
Ensembl biotype	lncRNA
OMIM	616338
Entrez	347689
RNAcentral	URS000075D6CA — lncRNA, 3535 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 214 — 214 lncRNA

ENST00000460739, ENST00000461063, ENST00000466034, ENST00000469278, ENST00000472856, ENST00000476125, ENST00000476964, ENST00000477928, ENST00000485035, ENST00000487240, ENST00000490005, ENST00000491282, ENST00000492337, ENST00000493116, ENST00000493521, ENST00000497122, ENST00000498226, ENST00000498731, ENST00000593330, ENST00000593549, ENST00000594942, ENST00000595084, ENST00000595287, ENST00000595313, ENST00000596250, ENST00000597347, ENST00000597651, ENST00000597828, ENST00000598474, ENST00000598867, ENST00000599082, ENST00000600386, ENST00000600778, ENST00000600801, ENST00000600962, ENST00000625581, ENST00000626299, ENST00000626619, ENST00000626802, ENST00000626948, ENST00000627501, ENST00000627530, ENST00000627738, ENST00000628211, ENST00000628343, ENST00000628347, ENST00000628496, ENST00000628810, ENST00000629112, ENST00000629273, ENST00000629552, ENST00000629781, ENST00000629830, ENST00000630150, ENST00000630482, ENST00000630553, ENST00000630887, ENST00000631025, ENST00000642218, ENST00000642301, ENST00000642429, ENST00000642652, ENST00000642685, ENST00000642823, ENST00000642922, ENST00000643131, ENST00000643236, ENST00000643667, ENST00000643769, ENST00000644304, ENST00000644358, ENST00000644582, ENST00000644732, ENST00000645423, ENST00000645583, ENST00000645960, ENST00000645983, ENST00000646056, ENST00000646296, ENST00000646508, ENST00000646683, ENST00000646698, ENST00000646712, ENST00000646841, ENST00000646949, ENST00000647034, ENST00000647055, ENST00000647179, ENST00000647552, ENST00000654538, ENST00000654649, ENST00000656613, ENST00000657986, ENST00000660576, ENST00000661842, ENST00000665033, ENST00000665112, ENST00000665187, ENST00000665485, ENST00000667332, ENST00000668295, ENST00000670501, ENST00000671456, ENST00000685088, ENST00000685509, ENST00000685767, ENST00000686214, ENST00000686782, ENST00000687464, ENST00000688647, ENST00000689495, ENST00000689942, ENST00000690586, ENST00000691318, ENST00000693669, ENST00000693697, ENST00000702225, ENST00000702256, ENST00000702337, ENST00000725556, ENST00000725557, ENST00000725558, ENST00000725559, ENST00000725560, ENST00000725561, ENST00000725562, ENST00000725563, ENST00000725564, ENST00000725565, ENST00000725566, ENST00000725567, ENST00000725568, ENST00000725569, ENST00000725570, ENST00000725571, ENST00000725572, ENST00000725573, ENST00000725574, ENST00000725575, ENST00000725576, ENST00000725577, ENST00000725578, ENST00000725579, ENST00000725580, ENST00000725581, ENST00000725582, ENST00000725583, ENST00000725584, ENST00000725585, ENST00000725586, ENST00000725587, ENST00000725588, ENST00000725589, ENST00000725590, ENST00000725591, ENST00000725592, ENST00000725593, ENST00000725594, ENST00000725595, ENST00000725596, ENST00000725597, ENST00000725598, ENST00000725599, ENST00000725600, ENST00000725601, ENST00000725602, ENST00000725603, ENST00000736084, ENST00000736085, ENST00000736086, ENST00000736087, ENST00000736088, ENST00000736089, ENST00000736090, ENST00000736091, ENST00000736092, ENST00000736093, ENST00000736094, ENST00000736095, ENST00000736096, ENST00000736097, ENST00000736098, ENST00000736099, ENST00000736100, ENST00000736101, ENST00000736102, ENST00000736103, ENST00000736104, ENST00000736105, ENST00000736106, ENST00000736107, ENST00000736108, ENST00000736109, ENST00000736110, ENST00000736111, ENST00000736112, ENST00000736113, ENST00000736114, ENST00000736115, ENST00000736116, ENST00000736117, ENST00000736118, ENST00000736119, ENST00000736120, ENST00000736121, ENST00000736122, ENST00000736123, ENST00000736124, ENST00000736125, ENST00000736126, ENST00000736127, ENST00000736128, ENST00000736129, ENST00000736130

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000460739 — 6 exons

Exon	Start	End
ENSE00001823625	181175514	181175583
ENSE00001840422	181056685	181056786
ENSE00001851364	181563720	181563928
ENSE00001883806	181699598	181699883
ENSE00001943486	181088877	181088917
ENSE00004049280	181739569	181740339

Expression profiles

Bgee: expression breadth ubiquitous, 186 present calls, max score 99.62.

FANTOM5 (CAGE): breadth broad, TPM avg 26.2130 / max 9063.7836, expressed in 421 samples.

FANTOM5 promoters (32 alternative TSS)

Promoter ID	TPM avg	Samples expressed
39991	11.1240	116
40020	4.1911	244
39992	4.0456	116
39997	0.9247	65
39987	0.8654	99
39998	0.6842	54
39978	0.6137	159
39970	0.4696	95
39995	0.4607	107
39968	0.3699	174

Top tissues by expression

253 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
corpus callosum	UBERON:0002336	99.62	gold quality
subthalamic nucleus	UBERON:0001906	99.42	gold quality
inferior vagus X ganglion	UBERON:0005363	99.40	gold quality
lateral globus pallidus	UBERON:0002476	99.38	gold quality
substantia nigra pars reticulata	UBERON:0001966	99.31	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	99.28	gold quality
spinal cord	UBERON:0002240	99.27	gold quality
medulla oblongata	UBERON:0001896	99.15	gold quality
pons	UBERON:0000988	99.03	gold quality
substantia nigra pars compacta	UBERON:0001965	98.93	gold quality
superior vestibular nucleus	UBERON:0007227	98.93	gold quality
dorsal plus ventral thalamus	UBERON:0001897	98.91	gold quality
midbrain	UBERON:0001891	98.62	gold quality
substantia nigra	UBERON:0002038	98.61	gold quality
ventral tegmental area	UBERON:0002691	98.51	gold quality
lateral nuclear group of thalamus	UBERON:0002736	98.33	gold quality
putamen	UBERON:0001874	98.08	gold quality
amygdala	UBERON:0001876	97.94	gold quality
caudate nucleus	UBERON:0001873	97.65	gold quality
Ammon’s horn	UBERON:0001954	97.22	gold quality
hypothalamus	UBERON:0001898	97.20	gold quality
nucleus accumbens	UBERON:0001882	97.03	gold quality
Brodmann (1909) area 46	UBERON:0006483	97.03	gold quality
Brodmann (1909) area 9	UBERON:0013540	96.88	gold quality
occipital lobe	UBERON:0002021	96.44	gold quality
endothelial cell	CL:0000115	96.38	gold quality
globus pallidus	UBERON:0001875	96.28	gold quality
prefrontal cortex	UBERON:0000451	96.16	gold quality
ventricular zone	UBERON:0003053	95.96	gold quality
primary visual cortex	UBERON:0002436	95.95	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-HCAD-35	yes	81.51
E-HCAD-25	yes	54.03
E-ANND-3	yes	9.95

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

Target	Regulation
SOX2	Activation

Upstream regulators (CollecTRI, top): YY1

Literature-anchored findings (GeneRIF, showing 40)

• Data suggest a part for SOX2OT spliced variants in tumor initiation and/or progression as well as regulating pluripotent state of stem cells. (PMID:24105929)
• our data suggested that Sox2ot plays an important role in regulating lung cancer cell proliferation, and may represent a novel prognostic indicator for the disease. (PMID:24927902)
• Results show that SOX2OT plays a key role in the induction and/or maintenance of SOX2 expression in breast cancer. (PMID:25006803)
• Suggest lncRNA Sox2ot plays crucial roles in promoting HCC cell migration and invasion, and might represent a novel prognostic biomarker for HCC. (PMID:26097588)
• Both Sox2ot-7 and Sox2ot-8 are highly expressed in human cancer cell lines coinciding with SOX2, one of the pluripotency regulators. (PMID:26703382)
• our findings support a potential oncogenic role for SOX2OT in non-small cell lung cancer tumor genesis (PMID:26846097)
• SOX2OT SNP rs9839776 was strongly associated with the higher expression of SOX2OT and an increased risk of breast cancer in Chinese women (PMID:28240100)
• High SOX2-OT expression is associated with pancreatic ductal adenocarcinoma. (PMID:28867247)
• LncRNA SOX2-OT is a novel prognostic biomarker for osteosarcoma patients, it regulates osteosarcoma cells proliferation and motility through SOX2 modulation, and is correlated with patients’ survival. (PMID:28960757)
• Results show that lncRNA Sox2ot was relatively overexpressed in cholangiocarcinoma tissues (CCA) and this upregulation was associated with clinical characteristics and poor prognosis of CCA patients. Its knockdown negatively regulated CCA cell lines proliferation, migration and invasion capacity. (PMID:29246536)
• The exosomal lncRNA Sox2ot plays important roles in tumor progression and may be a useful maker for pancreatic cancer prognosis. (PMID:29643475)
• Overexpressed SOX2OT promoted cell proliferation and metastasis of gastric cancer (GC) cells (SGC-7901, TMK-1) and the phosphorylation of AKT2 as well, while knockdown of SOX2OT reversed these effects. Besides that, miR-194-5p was predicted to be a target of SOX2OT and decreased expression of miR-194-5p was observed in GC tissues and cell lines. (PMID:29782828)
• High lncRNA Sox2ot expression was significantly associated with worse OS, advanced clinical stage, worse tumor differentiation, earlier distant metastasis, and earlier lymph node metastasis in various cancers. LncRNA Sox2ot expression might a promising prognostic factor in various cancers. (PMID:29787741)
• Simultaneous expression of SOX2 and SOX2OT was reported in some cancers. Regarding to the decreased expression of SOX2OT in the present study in concurrent with downregulation of SOX2 in our previous study, it seems that SOX2OT plays a tumor suppressor role in GC and may be useful biomarker for diagnosis of GC. (PMID:30198866)
• the results of the present study indicated that SOX2OT may act as an important regulator in the pathogenesis of DN by interacting with various mRNAs with critical roles in DN. (PMID:30320339)
• lncRNA SOX2-OT upregulated by IRF4 promotes cell proliferation and metastasis in cholangiocarcinoma via upregulating SOX2 and activating PI3K/AKT signaling pathway. (PMID:30556855)
• EZH2 silencing and PTEN overexpression significantly abrogated the SOX2-OT overexpression-mediated promotion of laryngeal squamous cell carcinoma (LSCC) cell malignant behavior. Collectively, our findings demonstrate that SOX2-OT inhibits PTEN expression to facilitate LSCC development through EZH2-mediated H3K27me3 (PMID:30811870)
• LncRNA SOX2-OT regulates proliferation and metastasis of nasopharyngeal carcinoma cells through miR-146b-5p/HNRNPA2B1 pathway. (PMID:31099048)
• Long non-coding RNA SOX2OT (SOX2OT) acted as a ceRNA by sponging miR-9 to facilitate sirtuin 1 (SIRT1), and thus induce autophagy. (PMID:31301307)
• the rs9839776 CT genotype may contribute to an increased risk of recurrent miscarriage in the southern Chinese population and that rs9839776 may act as a prognostic biomarker in recurrent miscarriage patients (PMID:31827385)
• Long noncoding RNA SOX2OT promotes the proliferation of pancreatic cancer by binding to FUS. (PMID:31837005)
• Long non-coding RNA SOX2OT promotes the stemness phenotype of bladder cancer cells by modulating SOX2. (PMID:32019566)
• LncRNA SOX2OT affects cervical cancer cell growth, migration and invasion by regulating SOX2. (PMID:32286144)
• LncRNA Sox2OT-V7 promotes doxorubicin-induced autophagy and chemoresistance in osteosarcoma via tumor-suppressive miR-142/miR-22. (PMID:32302291)
• Long Noncoding RNA SOX2-OT Knockdown Inhibits Proliferation and Metastasis of Prostate Cancer Cells Through Modulating the miR-452-5p/HMGB3 Axis and Inactivating Wnt/beta-Catenin Pathway. (PMID:32407168)
• Correlations between Overexpression of SOX2OT Long Non-coding RNA and Susceptibility to Breast Cancer. (PMID:32407264)
• LncRNA SOX2OT promotes temozolomide resistance by elevating SOX2 expression via ALKBH5-mediated epigenetic regulation in glioblastoma. (PMID:32439916)
• Long noncoding RNA SOX2-OT exacerbated hypoxia-induced cardiomyocytes injury by regulating activity of the miR-27a-3p/TGFbetaR1 pathway. (PMID:32528555)
• Evaluating the effect of siRNA on SOX2OT expression in the human neuron-committed teratocarcinoma NT2 cell line. (PMID:32716352)
• LncRNA SOX2-OT regulates AKT/ERK and SOX2/GLI-1 expression, hinders therapy, and worsens clinical prognosis in malignant lung diseases. (PMID:33433063)
• Tumour-derived exosomal lncRNA-SOX2OT promotes bone metastasis of non-small cell lung cancer by targeting the miRNA-194-5p/RAC1 signalling axis in osteoclasts. (PMID:34215717)
• Exosomal long non-coding RNA SOX2 overlapping transcript enhances the resistance to EGFR-TKIs in non-small cell lung cancer cell line H1975. (PMID:34244990)
• LncRNA SOX2-OT regulates miR-192-5p/RAB2A axis and ERK pathway to promote glioblastoma cell growth. (PMID:34470582)
• Long noncoding RNA SRY-box transcription factor 2 overlapping transcript participates in Parkinson’s disease by regulating the microRNA-942-5p/nuclear apoptosis-inducing factor 1 axis. (PMID:34607512)
• Exosome long non-coding RNA SOX2-OT contributes to ovarian cancer malignant progression by miR-181b-5p/SCD1 signaling. (PMID:34690112)
• SOX2-OT induced by PAI-1 promotes triple-negative breast cancer cells metastasis by sponging miR-942-5p and activating PI3K/Akt signaling. (PMID:34997317)
• Expression of SOX2OT, DANCR and TINCR long noncoding RNAs in papillary thyroid cancer and its effects on clinicopathological features. (PMID:35147200)
• LncRNA SOX2OT facilitates LPS-induced inflammatory injury by regulating intercellular adhesion molecule 1 (ICAM1) via sponging miR-215-5p. (PMID:35413439)
• Forkhead box A2-mediated lncRNA SOX2OT up-regulation alleviates oxidative stress and apoptosis of renal tubular epithelial cells by promoting SIRT1 expression in diabetic nephropathy. (PMID:36576135)
• Sox2ot /miR-9 /Cthrc1 Promote Proliferation and Migration of Schwann Cells Following Nerve Injury. (PMID:36924985)

Cross-species orthologs

0 orthologs

Protein

Non-coding RNA — no protein product; not a drug target.

Function

No curated pathway, Gene-Ontology, or interaction data.

Disease & clinical

No curated disease, variant, or cancer-driver associations.

Drugs & pharmacology

No drug or pharmacology data — not an established drug target.