U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SOX2-OT SOX2 overlapping transcript [ Homo sapiens (human) ]

Gene ID: 347689, updated on 12-Feb-2024

Summary

Go to the top of the page Help
Official Symbol
SOX2-OTprovided by HGNC
Official Full Name
SOX2 overlapping transcriptprovided by HGNC
Primary source
HGNC:HGNC:20209
See related
Ensembl:ENSG00000242808 MIM:616338; AllianceGenome:HGNC:20209
Gene type
ncRNA
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SOX2OT; NCRNA00043
Summary
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]
Expression
Restricted expression toward brain (RPKM 80.2) See more
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See SOX2-OT in Genome Data Viewer
Location:
3q26.33
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (181056680..181742228)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (183858445..184546785)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (180774468..181460016)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14927 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20879 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:180641841-180642341 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14928 Neighboring gene FMR1 autosomal homolog 1 Neighboring gene DnaJ heat shock protein family (Hsp40) member C19 Neighboring gene VISTA enhancer hs192 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:180792991-180793622 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:181010183-181011382 Neighboring gene RNA, U6 small nuclear 4, pseudogene Neighboring gene Sharpr-MPRA regulatory region 15084 Neighboring gene FAU pseudogene 2 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:181077271-181078470 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:181102468-181102968 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:181102969-181103469 Neighboring gene uncharacterized LOC102724604 Neighboring gene NANOG hESC enhancer GRCh37_chr3:181172287-181172788 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:181252985-181254184 Neighboring gene ribosomal protein L7a pseudogene 25 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:181422577-181423078 Neighboring gene SOX2 5' regulatory region Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:181430703-181431554 Neighboring gene SRR2 enhancer downstream of SOX2 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:181445376-181446114 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr3:181473577-181474268 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:181474397-181475049 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:181499765-181500277 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:181503691-181504191 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:181538013-181538512 Neighboring gene SRY-box transcription factor 2 Neighboring gene RNA, 7SL, cytoplasmic 703, pseudogene Neighboring gene RNA, 5S ribosomal pseudogene 150

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. SOX2-OT induced by PAI-1 promotes triple-negative breast cancer cells metastasis by sponging miR-942-5p and activating PI3K/Akt signaling. Zhang W, et al. Cell Mol Life Sci, 2022 Jan 7. PMID 34997317
  2. LncRNA SOX2-OT regulates miR-192-5p/RAB2A axis and ERK pathway to promote glioblastoma cell growth. Wang H, et al. Cell Cycle, 2021 Oct. PMID 34470582, Free PMC Article
  3. Exosomal long non-coding RNA SOX2 overlapping transcript enhances the resistance to EGFR-TKIs in non-small cell lung cancer cell line H1975. Zhou D, et al. Hum Cell, 2021 Sep. PMID 34244990
  4. 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. Ni J, et al. Cell Death Dis, 2021 Jul 2. PMID 34215717, Free PMC Article
  5. LncRNA SOX2-OT regulates AKT/ERK and SOX2/GLI-1 expression, hinders therapy, and worsens clinical prognosis in malignant lung diseases. Herrera-Solorio AM, et al. Mol Oncol, 2021 Apr. PMID 33433063, Free PMC Article

See all (59) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. [LncRNA SOX2OT enhances 5-fluorouracil resistance of cholangiocarcinoma cells by promoting autophagy via up-regulating SIRT1 expression].
    Title: [LncRNA SOX2OT enhances 5-fluorouracil resistance of cholangiocarcinoma cells by promoting autophagy via up-regulating SIRT1 expression].
  2. Association of lncRNA SOX2OT rs9839776 polymorphism with gastric cancer risk in Korean: Case-control study.
    Title: Association of lncRNA SOX2OT rs9839776 polymorphism with gastric cancer risk in Korean: Case-control study.
  3. Regulatory effect and mechanism of LncRNA SOX2OT in idiopathic pulmonary fibrosis.
    Title: Regulatory effect and mechanism of LncRNA SOX2OT in idiopathic pulmonary fibrosis.
  4. Sox2ot /miR-9 /Cthrc1 Promote Proliferation and Migration of Schwann Cells Following Nerve Injury.
    Title: Sox2ot /miR-9 /Cthrc1 Promote Proliferation and Migration of Schwann Cells Following Nerve Injury.
  5. Distinct gene expression patterns of SOX2 and SOX2OT variants in different types of brain tumours.
    Title: Distinct gene expression patterns of SOX2 and SOX2OT variants in different types of brain tumours.
  6. 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.
    Title: 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.
  7. LncRNA SOX2OT facilitates LPS-induced inflammatory injury by regulating intercellular adhesion molecule 1 (ICAM1) via sponging miR-215-5p.
    Title: LncRNA SOX2OT facilitates LPS-induced inflammatory injury by regulating intercellular adhesion molecule 1 (ICAM1) via sponging miR-215-5p.
  8. LncRNA SOX2-OT regulates miR-192-5p/RAB2A axis and ERK pathway to promote glioblastoma cell growth.
    Title: LncRNA SOX2-OT regulates miR-192-5p/RAB2A axis and ERK pathway to promote glioblastoma cell growth.
  9. Expression of SOX2OT, DANCR and TINCR long noncoding RNAs in papillary thyroid cancer and its effects on clinicopathological features.
    Title: Expression of SOX2OT, DANCR and TINCR long non‑coding RNAs in papillary thyroid cancer and its effects on clinicopathological features.
  10. 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.
    Title: 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.
Submit: New GeneRIF Correction See all GeneRIFs (44)

Phenotypes

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide association study of anorexia nervosa.
EBI GWAS Catalog
Biological insights from 108 schizophrenia-associated genetic loci.
EBI GWAS Catalog

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Other Names

  • SOX2 overlapping transcript (non-coding RNA)
  • SOX2 overlapping transcript (non-protein coding)

Clone Names

  • DKFZp761J1324

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

RNA

  1. NR_004053.3 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has an alternate exon in place of the first four exons compared to variant 1.
    Source sequence(s)
    AC117415, AK022826, DA366949, JN711430
    Related
    ENST00000657986.1

  2. NR_075089.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) has an alternate in place of the first four exons and lacks an alternate 3' exon compared to variant 1.
    Source sequence(s)
    AC117415, DA366949, JN711430
    Related
    ENST00000665033.1

  3. NR_075090.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) has an alternate in place of the first four exons and lacks two alternate 3' exons compared to variant 1.
    Source sequence(s)
    AC117415, DA366949, JN882275
    Related
    ENST00000476964.6

  4. NR_075091.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript.
    Source sequence(s)
    AC117415, DA281835, JQ408703

  5. NR_075092.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate 3' exon compared to variant 1.
    Source sequence(s)
    AC117415, DA281835, JN711430

  6. NR_075093.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has an alternate in place of the first two exons and lacks two alternate 3' exons compared to variant 1.
    Source sequence(s)
    AC117415, DA310380
    Related
    ENST00000646841.2

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    181056680..181742228
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    183858445..184546785
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials