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Homo sapiens SOX2 overlapping transcript (SOX2-OT), transcript variant 4, long non-coding RNA

NCBI Reference Sequence: NR_004053.3

FASTA Graphics 

LOCUS       NR_004053               3535 bp    RNA     linear   PRI 07-MAY-2024
DEFINITION  Homo sapiens SOX2 overlapping transcript (SOX2-OT), transcript
            variant 4, long non-coding RNA.
ACCESSION   NR_004053 NR_002810
VERSION     NR_004053.3
KEYWORDS    RefSeq.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 3535)
  AUTHORS   Lee,J., Kim,E.A., Kang,J., Chae,Y.S., Park,H.Y., Kang,B., Lee,S.J.,
            Lee,I.H., Park,J.Y., Park,N.J. and Jung,J.H.
  TITLE     Long non-coding RNA SOX2OT in tamoxifen-resistant breast cancer
  JOURNAL   BMC Mol Cell Biol 25 (1), 12 (2024)
   PUBMED   38649821
  REMARK    GeneRIF: Long non-coding RNA SOX2OT in tamoxifen-resistant breast
            cancer.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3535)
  AUTHORS   Xin,C., Wang,X., Li,X., Chen,Y., Wang,X., Ning,J., Yang,S. and
            Wang,Z.
  TITLE     [LncRNA SOX2OT enhances 5-fluorouracil resistance of
            cholangiocarcinoma cells by promoting autophagy via up-regulating
            SIRT1 expression]
  JOURNAL   Nan Fang Yi Ke Da Xue Xue Bao 44 (1), 187-193 (2024)
   PUBMED   38293991
  REMARK    GeneRIF: [LncRNA SOX2OT enhances 5-fluorouracil resistance of
            cholangiocarcinoma cells by promoting autophagy via up-regulating
            SIRT1 expression].
REFERENCE   3  (bases 1 to 3535)
  AUTHORS   Hong,J.H., Jin,E.H., Sung,J.K., Chang,I.A., Kang,H. and Lee,S.I.
  TITLE     Association of lncRNA SOX2OT rs9839776 polymorphism with gastric
            cancer risk in Korean: Case-control study
  JOURNAL   Medicine (Baltimore) 102 (43), e35103 (2023)
   PUBMED   37904476
  REMARK    GeneRIF: Association of lncRNA SOX2OT rs9839776 polymorphism with
            gastric cancer risk in Korean: Case-control study.
REFERENCE   4  (bases 1 to 3535)
  AUTHORS   Qiao,M., Li,D., He,Y., Cui,Q., Li,X. and Chi,H.
  TITLE     Regulatory effect and mechanism of LncRNA SOX2OT in idiopathic
            pulmonary fibrosis
  JOURNAL   Cell Mol Biol (Noisy-le-grand) 69 (7), 187-190 (2023)
   PUBMED   37715386
  REMARK    GeneRIF: Regulatory effect and mechanism of LncRNA SOX2OT in
            idiopathic pulmonary fibrosis.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 3535)
  AUTHORS   Fouani,Y., Gholipour,A., Oveisee,M., Shahryari,A., Saberi,H.,
            Mowla,S.J. and Malakootian,M.
  TITLE     Distinct gene expression patterns of SOX2 and SOX2OT variants in
            different types of brain tumours
  JOURNAL   J Genet 102 (2023)
   PUBMED   37017197
  REMARK    GeneRIF: Distinct gene expression patterns of SOX2 and SOX2OT
            variants in different types of brain tumours.
REFERENCE   6  (bases 1 to 3535)
  AUTHORS   Hou,Z., Zhao,W., Zhou,J., Shen,L., Zhan,P., Xu,C., Chang,C., Bi,H.,
            Zou,J., Yao,X., Huang,R., Yu,L. and Yan,J.
  TITLE     A long noncoding RNA Sox2ot regulates lung cancer cell
            proliferation and is a prognostic indicator of poor survival
  JOURNAL   Int J Biochem Cell Biol 53, 380-388 (2014)
   PUBMED   24927902
  REMARK    GeneRIF: 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.
REFERENCE   7  (bases 1 to 3535)
  AUTHORS   Askarian-Amiri,M.E., Seyfoddin,V., Smart,C.E., Wang,J., Kim,J.E.,
            Hansji,H., Baguley,B.C., Finlay,G.J. and Leung,E.Y.
  TITLE     Emerging role of long non-coding RNA SOX2OT in SOX2 regulation in
            breast cancer
  JOURNAL   PLoS One 9 (7), e102140 (2014)
   PUBMED   25006803
  REMARK    GeneRIF: Results show that SOX2OT plays a key role in the induction
            and/or maintenance of SOX2 expression in breast cancer.
            Publication Status: Online-Only
REFERENCE   8  (bases 1 to 3535)
  AUTHORS   Shahryari,A., Rafiee,M.R., Fouani,Y., Oliae,N.A., Samaei,N.M.,
            Shafiee,M., Semnani,S., Vasei,M. and Mowla,S.J.
  TITLE     Two novel splice variants of SOX2OT, SOX2OT-S1, and SOX2OT-S2 are
            coupregulated with SOX2 and OCT4 in esophageal squamous cell
            carcinoma
  JOURNAL   Stem Cells 32 (1), 126-134 (2014)
   PUBMED   24105929
  REMARK    GeneRIF: Data suggest a part for SOX2OT spliced variants in tumor
            initiation and/or progression as well as regulating pluripotent
            state of stem cells.
REFERENCE   9  (bases 1 to 3535)
  AUTHORS   Amaral,P.P., Neyt,C., Wilkins,S.J., Askarian-Amiri,M.E.,
            Sunkin,S.M., Perkins,A.C. and Mattick,J.S.
  TITLE     Complex architecture and regulated expression of the Sox2ot locus
            during vertebrate development
  JOURNAL   RNA 15 (11), 2013-2027 (2009)
   PUBMED   19767420
REFERENCE   10 (bases 1 to 3535)
  AUTHORS   Fantes,J., Ragge,N.K., Lynch,S.A., McGill,N.I., Collin,J.R.,
            Howard-Peebles,P.N., Hayward,C., Vivian,A.J., Williamson,K., van
            Heyningen,V. and FitzPatrick,D.R.
  TITLE     Mutations in SOX2 cause anophthalmia
  JOURNAL   Nat Genet 33 (4), 461-463 (2003)
   PUBMED   12612584
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DA366949.1, JN711430.1,
            AK022826.1 and AC117415.7.
            
            On Feb 8, 2013 this sequence version replaced NR_004053.2.
            
            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].
            
            Transcript Variant: This variant (4) has an alternate exon in place
            of the first four exons compared to variant 1.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript alignments.
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AK022826.1, SRR1803612.270349.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2145743, SAMEA2157437
                                           [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-29                DA366949.1         2-30
            30-767              JN711430.1         1-738
            768-1845            AK022826.1         556-1633
            1846-3535           AC117415.7         66594-68283         c
FEATURES             Location/Qualifiers
     source          1..3535
                     /organism="Homo sapiens"
                     /mol_type="transcribed RNA"
                     /db_xref="taxon:9606"
                     /chromosome="3"
                     /map="3q26.33"
     gene            1..3535
                     /gene="SOX2-OT"
                     /gene_synonym="NCRNA00043; SOX2OT"
                     /note="SOX2 overlapping transcript"
                     /db_xref="GeneID:347689"
                     /db_xref="HGNC:HGNC:20209"
                     /db_xref="MIM:616338"
     ncRNA           1..3535
                     /ncRNA_class="lncRNA"
                     /gene="SOX2-OT"
                     /gene_synonym="NCRNA00043; SOX2OT"
                     /product="SOX2 overlapping transcript, transcript variant
                     4"
                     /db_xref="GeneID:347689"
                     /db_xref="HGNC:HGNC:20209"
                     /db_xref="MIM:616338"
     exon            1..412
                     /gene="SOX2-OT"
                     /gene_synonym="NCRNA00043; SOX2OT"
                     /inference="alignment:Splign:2.1.0"
     exon            413..481
                     /gene="SOX2-OT"
                     /gene_synonym="NCRNA00043; SOX2OT"
                     /inference="alignment:Splign:2.1.0"
     exon            482..767
                     /gene="SOX2-OT"
                     /gene_synonym="NCRNA00043; SOX2OT"
                     /inference="alignment:Splign:2.1.0"
     exon            768..875
                     /gene="SOX2-OT"
                     /gene_synonym="NCRNA00043; SOX2OT"
                     /inference="alignment:Splign:2.1.0"
     exon            876..3535
                     /gene="SOX2-OT"
                     /gene_synonym="NCRNA00043; SOX2OT"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 aaaaatgttg aatatcaaca atgggtttca gtgctgtatt gttgagtttt gtatgaacta
       61 atctagcttc tctaaaaaaa aaaaaaaaaa aaaaaaaaag aaagaaaaga aagaaagaaa
      121 agaaagaaag aaagaaaaaa aaagaaaaga aaaaaaagag aaccacagct ttggacaaaa
      181 gtctatagcc agtgcatttg aaaactcccc ttgcaccagg gctgactgta gctgggggaa
      241 gacattttac tcatttgctc tttcctttca tacagtcagc tggtccctct tctcaggtgt
      301 agatcaccta ttataatttt acctaatttt gatactctga taaggaaagt cccaggactt
      361 atcagctggg ataggcctca cttacaagac agctctgttc agtatttgga agaaagcctg
      421 acaggtttct tcggaaaagt ggccatccat ggaatgaatg aaatgttctc tttctattcc
      481 agggattgca gtggcaaagc taggctaggt cttggaggct ggtgtaaggc gatgtgggtg
      541 aaggcaggag gctgatggaa agactggggg gaagaaaagc cgaaatggat tcacggtgcc
      601 ttggatgaag gacgagaggg gaactgcaag ctccttcaac tggttctgtc cggtgagaag
      661 tgatcaagct tgggctgaca agaggctcag ggagccctca cgttctttcg cttttttacc
      721 tgccaatcaa actgctacaa gacaacaccc tgatctggca tggacatcgc gggtccaagc
      781 ctgtagcccc aaatcggata atctctgcag ctgataacaa gcaaaagaga agccaggcaa
      841 cagccatatt aaagaagaaa acaatcaact ctgagatcca acttagaaat aatgtttcat
      901 tcaagataag gctcgtggct taggagattg tgacctggct tgcatcattc taagacttct
      961 atcgtctgtt ttcaaaaccc aaggaggacc tccttttctg tgtgatagtt cctcatgctt
     1021 tgccagccac tgggtcttta aggaagcttg ccaagagttc ccggctggga aggacagttc
     1081 gagttcatca tagacaatga gctggcacca cagtttaagt gactcaccaa cctggttgcc
     1141 cacttcaaaa tgtcaagaac cacactatct aattgaaaga actgtgtttt agcaaagtgt
     1201 aattggatcg cctggcaaga tcatctcaaa ctatgtctct gaccttgcct ttcagtggct
     1261 attttgagca caagaggaga aaggaaatga ttcctgaatt atatcttgtt tttaaaaatt
     1321 aagattaatt aatacttggt tttatgttca ttccattgta ggaacttagt gattattaca
     1381 aaacagtcaa aataggtcat agcaaaatga acgtttaaga ttaggttaaa acattcctct
     1441 gaaattttag tattcacttt tgaagtgtca attactatat ttctgtaatt tctcattttt
     1501 ttcttggctt agagtcaaga tgaaaaatga tatttgaatc aaagacattg ttttgttata
     1561 tagccactcc tttctaaaat gcaaatccac cctcccctca ccaatgcttt attctttgtg
     1621 cgcgcacaca cacacacaca cacacacaca cacacacaca cacacagaca tacacagaac
     1681 cagcacccaa atggtagagg aggtccttcc aagacttcta ggacctggat catgtaagca
     1741 gtagatgaga aaatgaagta agagatatag agtaataaca ataaaagtca atgatttcat
     1801 tttacaaaaa agtcattgtg tagtactcag atatttttaa gagcaagtat tattatgact
     1861 aaagtatatt atacttctaa attattatga ttctcatcta atttcaagcc acacataggc
     1921 gccatttgaa agcattttgt gttacaacct atcaacaaaa atcaactaat agttttataa
     1981 cgtgcatagg tttaccccat ggggaattaa aatttttatc tgcaagtatt tctgttgttg
     2041 tgagacttta ggacaagaca acatttggtg ttaacataga agaatattct atggcttttt
     2101 tagctttaaa gttcattact ctaaaataaa gtacacgtgg tatttttttc ttcctagtgt
     2161 tctcttatta tatgtagagt attttcggtt gttgttttta acgtatacat tatttttatt
     2221 aagtcatttc ataaaagata agatatatac taatagaccc ttggttttct cctaatttaa
     2281 ttatttcaag tcaagcaaaa ttgggcaatt ttctttcagg aaaaaaaaaa tattgagcat
     2341 gattttgagg taaaactgat tatttacagc atcttttctc taataggcta acatttatga
     2401 tggatcttat ttcaaagttg attattctca aagaaaagtg gagatattag aatttccgag
     2461 taaattgcat tgttttaaaa agtactttaa tgcattgttc acattgttgc cagctattga
     2521 ccaaaaaaga gaagaagaaa aaagaaataa aaaaagcagt atctgctcca aacgtcaagt
     2581 tttgcagttt gaaagacttg tacattataa ttgttttttt cttttttgga aagcagtagt
     2641 aattaatacc aaaggcatag acaatttagg gccataacct cccttccccc ctctccacct
     2701 tttttttttt tttttttttt ttttaacttt aaccatgata ggcatctctg caaggtaggt
     2761 tttaacatat ttttttccta atttttttcc ctccattcag taagaaggat aagcttttag
     2821 agtacccagt caccgtggta actgccaaaa aaattctcct gaagtttgaa gaggtcagct
     2881 agcagggtca acaaccctgg cctctctctg agctcggtct agcatgcccc agcctgcggt
     2941 tggagtgtca ggccagatct gaccctggga ggtggaccat tctggctctg atataaattt
     3001 ttcgagtcag ttcatggcct ggactctcca ggtggcctcc aaaatcgatt ttgaccccct
     3061 gaccctgtct cacggaggca tagcatccac cctaagtaag gatttagcca ggaatgacag
     3121 ctttccactg agtgttattg gggacagtat aaacagtttg gaaagcaagt aaggaggtgt
     3181 gagggctagc aatcattaaa agcacattaa aaaacaattt ttaaaaatct ttattagaga
     3241 aagttgtaaa tgcatatctg ttacagaatt cctgtgattt gtagagtttt ctagtcagtt
     3301 ttgaatataa ataggtcaca tatctttatc tttttgcata ctttgttaca aatatgcaaa
     3361 taagataggc atacttgcta caaaataggt acagcaggaa tgtaatatgt tcagaaaagg
     3421 caaactggtt attaaaacac attaacaggt aaggagtttc taatatttta aatactaaaa
     3481 ttttacatgt gtattttgaa gtttttaaaa tggaaaaata aagaaccttt aaaaa
//
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