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

    Gene ID: 347689, updated on 2-Nov-2024

    Summary

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    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
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    Genomic context

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    See SOX2-OT in Genome Data Viewer
    Location:
    3q26.33
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (181056680..181742228)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (183858445..184546785)
    RS_2024_09 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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Correlations between lncRNA-SOX2OT polymorphism and susceptibility to breast cancer in a Chinese population. Tang X, et al. Biomark Med, 2017 Mar. PMID 28240100
    2. Correlations between Overexpression of SOX2OT Long Non-coding RNA and Susceptibility to Breast Cancer. Dehghani-Samani M, et al. Comb Chem High Throughput Screen, 2020. PMID 32407264
    3. LncRNA Sox2OT-V7 promotes doxorubicin-induced autophagy and chemoresistance in osteosarcoma via tumor-suppressive miR-142/miR-22. Zhu K, et al. Aging (Albany NY), 2020 Apr 16. PMID 32302291, Free PMC Article
    4. Overexpression of the non-coding SOX2OT variants 4 and 7 in lung tumors suggests an oncogenic role in lung cancer. Saghaeian Jazi M, et al. Tumour Biol, 2016 Aug. PMID 26846097
    5. Enhanced expression of long non-coding RNA Sox2ot promoted cell proliferation and motility in colorectal cancer. Liu S, et al. Minerva Med, 2016 Oct. PMID 27353770

    See all (62) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Long non-coding RNA SOX2OT in tamoxifen-resistant breast cancer.
      Title: Long non-coding RNA SOX2OT in tamoxifen-resistant breast cancer.
    2. [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].
    3. 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.
    4. Regulatory effect and mechanism of LncRNA SOX2OT in idiopathic pulmonary fibrosis.
      Title: Regulatory effect and mechanism of LncRNA SOX2OT in idiopathic pulmonary fibrosis.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (45)

    Phenotypes

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    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

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Other Names

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

    Clone Names

    • DKFZp761J1324

    NCBI Reference Sequences (RefSeq)

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    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_2024_08

    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

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