##gff-version 3 ##sequence-region NC_001669.1 1 5243 NC_001669.1 annotation remark 1 5243 . . . accessions=NC_001669;comment=PROVISIONAL REFSEQ: This record has not yet been subject to final%0ANCBI review. The reference sequence is identical to J02400.%0A%5B2%5D mRNA.%0A%5B1%5D mRNA.%0A%5B3%5D mRNA.%0A%5B4%5D sites%3B cds start for VP1.%0A%5B8%5D direct tandem repeats.%0A%5B9%5D mRNA and DNA.%0A%5B10%5D overlap between VP1%2C VP2 and VP3 genes.%0A%5B11%5D origin of replication.%0A%5B15%5D VP1 gene.%0A%5B16%5D mRNA.%0A%5B13%5D RNA and DNA.%0A%5B29%5D RNA and DNA.%0A%5B30%5D sites-late 16S mRNA and RNA splicing.%0A%5B33%5D sites-late 16S mRNA and RNA splicing.%0A%5B40%5D small t antigen gene.%0A%5B31%5D RNA.%0A%5B18%5D T antigen binding sites.%0A%5B32%5D sites%3B 5%27 and 3%27 termini of 19s late mRNAs.%0A%5B27%5D VP2 and VP3 genes.%0A%5B26%5D sites-5%27 termini of late mRNAs.%0A%5B28%5D sites-mRNA 3%27 termini.%0A%5B38%5D sites-cDNA%2C 16S leader segments.%0A%5B35%5D sites%3B cap site for 16s and 19s late mRNAs.%0A%5B37%5D sites%3B mutations in region of origin of replication. %5B19%5D%0Asites%3B splice sites in late mRNAs.%0A%5B36%5D sites%3B early mRNAs.%0A%5B39%5D sites%3B early mRNAs and RNA splicing.%0A%5B43%5D review%3B bases 1 to 163%3B 181 to 5243.%0A%5B45%5D deletion mutant analysis.%0A%5B53%5D cDNA.%0A%5B46%5D sites-5%27 termini of early mRNAs.%0A%5B56%5D sites%3B splice sites for large T antigen mRNA. %5B57%5D deletion%0Amutant analysis.%0A%5B49%5D deletion mutant analysis.%0A%5B54%5D deletion mutant analysis.%0A%5B48%5D deletion mutant analysis.%0A%5B51%5D deletion mutant analysis.%0A%5B50%5D cDNA.%0A%5B47%5D sites%3B deletion mutant analysis over bases 4553 to 5172. %5B52%5D%0Asites%3B deletion mutant analysis of major late cap site. %5B42%5D%0Asites%3B splice sites in early mRNAs.%0A%5B%28in%29 Tooze%2CJ. %28Eds.%29%3BDNA Tumor Viruses - Second Edition Revised:%0A799-841%3BCold Sp%5D review%3B bases 1 to 163%3B 181 to 5243. %5B64%5D%0Adeletion mutant analysis.%0A%5B59%5D RNA and DNA.%0A%5B62%5D deletion and point mutants over the replication origin. %5B66%5D%0Adeletion mutants over the early promoter.%0A%5B55%5D sites%3B T antigen binding sites.%0A%5B67%5D origin-defective deletion mutants.%0A%5B63%5D early mRNA initiation sites.%0A%5B71%5D sites%3B early mRNA initiation sites and repression by T%0Aantigen.%0A%5B68%5D sites%3B poly-A at 2662%3B deletion mutants over 2533-2775. %5B85%5D%0Adeletion mutant analysis.%0A%5B83%5D early promoter analysis.%0A%5B74%5D deletion mutant analysis.%0A%5B82%5D cDNAs over this region.%0A%5B78%5D early promoter analysis.%0A%5B79%5D sites%3B promoter for early mRNAs.%0A%5B69%5D autoregulation by T antigen.%0A%5B75%5D upstream shift of early mRNA initiation site. %5B76%5D deletion%0Amutant analysis.%0A%5B84%5D sites%3B cds for agnoprotein.%0A%5B77%5D T antigen binding to a deletion mutant.%0A%5B81%5D sites%3B transcriptional enhancement by the 72 bp repeats. %5B73%5D%0AcDNAs%3B.%0A%5B80%5D sites%3B agnoprotein coding sequence.%0A%5B98%5D sites%3B mapping of the origin of replication. %5B97%5D sites%3B%0Atopoisomerase cleavage sites.%0A%5B95%5D deletion mutant analysis.%0A%5B99%5D only joints of deletion mutants.%0A%5B87%5D RNA.%0A%5B94%5D sites%3B late mRNA initiation sites.%0A%5B88%5D late promoter analysis.%0A%5B89%5D mutant analysis over origin of replication.%0A%5B92%5D T antigen binding to a deletion mutant.%0A%5B91%5D sites%3B T antigen binding sites.%0A%5B90%5D sites%3B mapping of early region promoter.%0A%5B70%5D sites%3B SV40 enhancement of beta-globin gene expression. %5B110%5D%0Amapping of the early promoter.%0A%5B105%5D sites%3B agnogene mutants.%0A%5B106%5D mutant analysis.%0A%5B108%5D mutant analysis over these regions.%0A%5B103%5D topoisomerase II.%0A%5B111%5D only joints of deletion mutants.%0A%5B102%5D transcription factor binding to early promoter. %5B112%5D%0Asites%3B 7S-K RNA of transformed cells.%0A%5B101%5D T antigen binding analysis.%0A%5B107%5D cDNA%3B late mRNA initiation.%0A%5B100%5D autoregulation by T antigen.%0A%5B109%5D early promoter analysis.%0A%5B113%5D T antigen binding sites.%0A%5B119%5D sites%3B sites-5%27 termini of late mRNAs.%0A%5B116%5D T antigen binding analysis.%0A%5B117%5D sites%3B T antigen binding sites.%0A%5B123%5D primase initiation sites.%0A%5B114%5D transcriptional enhancer analysis.%0A%5B118%5D mutant analysis at the replication origin.%0A%5B120%5D sites%3B mRNA polyadenylation signal sequences. %5B121%5D%0Achromatin structure at origin of replication%3B mutational analysis.%0A%5B122%5D sites%3B bidirectional promoter element.%0A%5B124%5D sites%3B.%0A%5B115%5D sites%3B Okazaki fragment sequences.%0A%5B128%5D sites%3B tsA3900 point mutant sequence.%0A%5B129%5D sites%3B large t-antigen binding specificity. %5B130%5D%0Atemperature-sensitive mutants.%0A%5B131%5D sites%3B recombination in poly%28GT.%0A%5B127%5D sites%3B large T-antigen binding sites.%0A%5B133%5D sites%3B SV40 early leader protein %28SELP.%0A%5B93%5D sites%3B early SV40 transcription.%0A%5B134%5D sites%3B temperature sensitive mutants in the VP1 gene. %5B7%5D%0Asites%3B ends of %27early%27 and %27late%27 mRNA.%0AKindly reviewed by K. N. Subramanian. Draft entry and computer-%0Areadable sequence for %5B134%5D kindly submitted by M.Bina%2C%0A16-FEB-1989.%0AThe E or minus strand of SV40 strain 776 is shown as it is reported%0Aby %5B41%5D and %5B34%5D using the numbering system by %5B%28in%29 Tooze%2CJ.%0A%28Eds.%29%3BDNA Tumor Viruses - Second Edition Revised: 799-841%3BCold%0ASp%5D%2C with exception%0Aof of the addition of 17 bases %28between nucleotides 164 and 165%29 to%0Atheir sequence %5B44%5D. Differences between the complete sequences as%0Apublished by %5B41%5D and %5B34%5D and this sequence are limited to the 17%0Abp change%2C the revision at 328 below%2C and the numbering. All%0Areferences tend to agree upon an independent coordinate system%2C%0Awhere map units run from 0.00 to 1.00 and the origin is defined by%0Athe sole EcoRI site%2C which is found at base 1782 below. In keeping%0Awith %5B%28in%29 Tooze%2CJ. %28Eds.%29%3BDNA Tumor Viruses - Second Edition%0ARevised: 799-841%3BCold Sp%5D%2C map units for this entry have been%0Acalculated by%0A SV %2B 3461%0A mu %3D -----------%0A 5243%0AIf the result is %3E 1%2C subtract 1 for the value. The origin of this%0Asequence%2C then%2C is at 0.66. Identical units are used for Polyoma%0Avirus.%0ADNA replication is bidirectional from an origin which has been%0Anarrowed by mutational analysis to bases 5193 to 34 %5B37%5D. Given%0Athat early mRNA transcription also arises from this region%2C the two%0Aprocesses will be%2C to some extent%2C simultaneously regulated. In%0Aaddition to the 21-bp and 72-bp repeats concerned with early%0Atranscription %28see below%29%2C the origin includes a 17-bp A %2B T-rich%0Asequence%3B further demarcation of a %27core%27 region and an %27auxiliary%27%0Aregion makes the former comprise a 17-bp palindrome %285193-5209%29%2C a%0A15-bp palindrome %285213-5227%29%2C a 27-bp palindrome %285230-13%29 and the%0AA %2B T-rich region %2815-31%29%2C and the latter the three 21-bp repeats%0A%5B89%5D. Thus the %27core%27 overlaps the T-antigen binding sites I and II%0Aand the %27auxiliary region%27 %28which is said to enhance replication%0Aefficiency%29 overlaps the T-antigen binding site III %5B89%5D.%0ATranscription of early mRNAs %2818s and 19s%29 is leftward off the E%2C%0Aor minus%2C strand and transcription of late mRNAs %2816s and 19s%29 is%0Arightward off the L%2C or plus%2C strand. In the former case%2C the%0Aannotation will show the symbols %27%28c%29%27 and %27comp strand%27 for the%0Atranscripts and products%2C and for the regulatory elements which%0Agovern them. In some references%2C the E strand has been labeled%0A%27Late%27 to indicate that it has the polarity of late mRNA%2C and the L%0Astrand %27Early%27 to indicate that it has the polarity of early mRNA.%0A%28Early mRNAs can be produced throughout the lytic cycle.%29 The%0Acharacterization of the mRNAs as 18s and 19s early and 16s and 19s%0Alate is a simplification: heterogeneity with regard to 5%27 and 3%27%0Atermini%2C splice sites%2C and abundance as a function of time in the%0Alytic cycle and regulatory events%2C have all been observed %5B32%5D%0A%5B43%5D%2C%5B82%5D%2C%5B75%5D. For the purposes of this entry%2C only the simplest%0Amajor mRNA species have been entered in the Sites. The promoter for%0Athe early mRNAs is considered to include at least bases 5185 to 250%0Aon the E strand: the T antigen binding sites %28for which the minimal%0Aspans are given %5B71%5D%29%2C the %27TATA%27 box at position 21%2C the 21-bp%0Arepeats%2C and the 72-bp repeats are all known to play a role in%0Aearly transcription. One of the effects of regulation at these%0Asites is to shift the cap site to one of at least seven positions%0Abetween bases 95 and 32 %5B75%5D. Bases 55 to 97 are also of interest%0Abecause they permit base-pairing homology with the small nuclear%0ARNA 7S-K %5B112%5D and because they bind the cell factor SP-1 %5B102%5D.%0AFor late promoter induction to occur at high efficiency two domains%0Aare required simultaneously: the minimal replication origin and the%0A72 bp repeat %5B124%5D. The origin-proximal 22 bp portion of the 72-bp%0Arepeat is sufficient for induction%2C while the origin-distal portion%0Ais dispensable %5B124%5D. If T antigen is present%2C the 21 bp repeat is%0Adispensable for induction of late promoter activity in vivo %5B124%5D.%0AThe regulatory elements for early transcription have been annotated%0Afor the %27comp strand%27. The late region induction signals are to be%0Afound in the same region as the early regulatory elements %5B124%5D.%0AThe efficacy of the 72-bp repeat in promoting transcription has%0Abeen demonstrated for both orientations %5B81%5D.%0AThe SAS-RNA is a small viral associated RNA whose function is%0Aunknown. It appears to arise through processing from some of the%0Alonger early transcripts%3B mutants in the SAS-RNA coding region%0Aremain viable %5B64%5D.%0ASeven proteins -- the small t antigen%2C the large T antigen%2C the%0Athree structural proteins%2C the early leader protein %5B133%5D%2C and the%0Aagnoprotein %28which is thought to be involved with structural%0Adevelopment %5B106%5D%29-- are known to be translated from the%0Amultiplicity of mRNAs. The existence of a middle T antigen%2C known%0Ato exist in Polyoma%2C has been suggested %5B56%5D. For a summary of%0Aother possible coding sequences%2C see %5B%28in%29 Tooze%2CJ. %28Eds.%29%3BDNA%0ATumor Viruses - Second Edition Revised: 799-841%3BCold Sp%5D. Missing%0Adata project %5B124-129%5D%2C %5B7%5D.%0A EMBL features not translated to GenBank features:%0A key from to description%0A PRM 21 15 %28C%29 TATA-box %5B3%5D%0A MSG 120 2674 major 16S RNA.%0ACOMPLETENESS: full length.;data_file_division=VRL;date=22-SEP-2016;gi=9628421;keywords=RefSeq;organism=Macaca mulatta polyomavirus 1;references=authors: Kube%2CD. and Milavetz%2CB.%0Atitle: Generation of a nucleosome-free promoter region in SV40 does not require T-antigen binding to site I%0Ajournal: Virology 172 %281%29%2C 100-105 %281989%29%0Amedline id: %0Apubmed id: 2549706%0Acomment:,authors: Behm%2CM.%2C Lowman%2CH.%2C Ng%2CS.C. and Bina%2CM.%0Atitle: Analysis of temperature-sensitive mutations in the simian virus 40 gene encoding virion protein 1%0Ajournal: Proc. Natl. Acad. Sci. U.S.A. 85 %2824%29%2C 9421-9425 %281988%29%0Amedline id: %0Apubmed id: 2849104%0Acomment:,authors: Khalili%2CK.%2C Brady%2CJ. and Khoury%2CG.%0Atitle: Translational regulation of SV40 early mRNA defines a new viral protein%0Ajournal: Cell 48 %284%29%2C 639-645 %281987%29%0Amedline id: %0Apubmed id: 3028644%0Acomment:,authors: Barrera-Saldana%2CH.%2C Takahashi%2CK.%2C Vigneron%2CM.%2C Wildeman%2CA.%2C Davidson%2CI. and Chambon%2CP.%0Atitle: All six GC-motifs of the SV40 early upstream element contribute to promoter activity in vivo and in vitro%0Ajournal: EMBO J. 4 %2813B%29%2C 3839-3849 %281985%29%0Amedline id: %0Apubmed id: 3004974%0Acomment:,authors: Stringer%2CJ.R.%0Atitle: Recombination between poly%5Bd%28GT%29.d%28CA%29%5D sequences in simian virus 40-infected cultured cells%0Ajournal: Mol. Cell. Biol. 5 %286%29%2C 1247-1259 %281985%29%0Amedline id: %0Apubmed id: 2993859%0Acomment:,authors: Scheller%2CA. and Prives%2CC.%0Atitle: Simian virus 40 and polyomavirus large tumor antigens have different requirements for high-affinity sequence-specific DNA binding%0Ajournal: J. Virol. 54 %282%29%2C 532-545 %281985%29%0Amedline id: %0Apubmed id: 2985816%0Acomment:,authors: Hutchinson%2CN.I.%2C Chang%2CL.S.%2C Pater%2CM.M.%2C Bouck%2CN.%2C Shenk%2CT.E. and di Mayorca%2CG.%0Atitle: Characterization of a new simian virus 40 mutant%2C tsA3900%2C isolated from deletion mutant tsA1499%0Ajournal: J. Virol. 53 %283%29%2C 814-821 %281985%29%0Amedline id: %0Apubmed id: 2983092%0Acomment:,authors: Hartzell%2CS.W.%2C Byrne%2CB.J. and Subramanian%2CK.N.%0Atitle: The simian virus 40 minimal origin and the 72-base-pair repeat are required simultaneously for efficient induction of late gene expression with large tumor antigen%0Ajournal: Proc. Natl. Acad. Sci. U.S.A. 81 %2820%29%2C 6335-6339 %281984%29%0Amedline id: %0Apubmed id: 6093097%0Acomment:,authors: Sadofsky%2CM. and Alwine%2CJ.C.%0Atitle: Sequences on the 3%27 side of hexanucleotide AAUAAA affect efficiency of cleavage at the polyadenylation site%0Ajournal: Mol. Cell. Biol. 4 %288%29%2C 1460-1468 %281984%29%0Amedline id: %0Apubmed id: 6149460%0Acomment:,authors: Hay%2CR.T.%2C Hendrickson%2CE.A. and DePamphilis%2CM.L.%0Atitle: Sequence specificity for the initiation of RNA-primed simian virus 40 DNA synthesis in vivo%0Ajournal: J. Mol. Biol. 175 %282%29%2C 131-157 %281984%29%0Amedline id: %0Apubmed id: 6202875%0Acomment:,authors: Lycan%2CD.E. and Danna%2CK.J.%0Atitle: S1 mapping of purified nascent transcripts of simian virus 40%0Ajournal: Mol. Cell. Biol. 4 %284%29%2C 625-633 %281984%29%0Amedline id: %0Apubmed id: 6325887%0Acomment:,authors: Pomerantz%2CB.J. and Hassell%2CJ.A.%0Atitle: Polyomavirus and simian virus 40 large T antigens bind to common DNA sequences%0Ajournal: J. Virol. 49 %283%29%2C 925-937 %281984%29%0Amedline id: %0Apubmed id: 6321773%0Acomment:,authors: Hartzell%2CS.W.%2C Byrne%2CB.J. and Subramanian%2CK.N.%0Atitle: Mapping of the late promoter of simian virus 40%0Ajournal: Proc. Natl. Acad. Sci. U.S.A. 81 %281%29%2C 23-27 %281984%29%0Amedline id: %0Apubmed id: 6320166%0Acomment:,authors: Sohn%2CU.%2C Szyszko%2CJ.%2C Coombs%2CD. and Krause%2CM.%0Atitle: 7S-K nuclear RNA from simian virus 40-transformed cells has sequence homology to the viral early promoter%0Ajournal: Proc. Natl. Acad. Sci. U.S.A. 80 %2823%29%2C 7090-7094 %281983%29%0Amedline id: %0Apubmed id: 6196783%0Acomment:,authors: Mertz%2CJ.E.%2C Murphy%2CA. and Barkan%2CA.%0Atitle: Mutants deleted in the agnogene of simian virus 40 define a new complementation group%0Ajournal: J. 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Genet. 1 %285%29%2C 457-481 %281982%29%0Amedline id: %0Apubmed id: 6296253%0Acomment:,authors: Banerji%2CJ.%2C Rusconi%2CS. and Schaffner%2CW.%0Atitle: Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences%0Ajournal: Cell 27 %282 PT 1%29%2C 299-308 %281981%29%0Amedline id: %0Apubmed id: 6277502%0Acomment:,authors: Hansen%2CU.%2C Tenen%2CD.G.%2C Livingston%2CD.M. and Sharp%2CP.A.%0Atitle: T antigen repression of SV40 early transcription from two promoters%0Ajournal: Cell 27 %283 PT 2%29%2C 603-613 %281981%29%0Amedline id: %0Apubmed id: 6101224%0Acomment:,authors: Moreau%2CP.%2C Hen%2CR.%2C Wasylyk%2CB.%2C Everett%2CR.%2C Gaub%2CM.P. and Chambon%2CP.%0Atitle: The SV40 72 base repair repeat has a striking effect on gene expression both in SV40 and other chimeric recombinants%0Ajournal: Nucleic Acids Res. 9 %2822%29%2C 6047-6068 %281981%29%0Amedline id: %0Apubmed id: 6273820%0Acomment:,authors: Jackson%2CV. and Chalkley%2CR.%0Atitle: Use of whole-cell fixation to visualize replicating and maturing simian virus 40: identification of new viral gene product%0Ajournal: Proc. Natl. Acad. Sci. 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Symp. Quant. Biol. 44 %28PT 1%29%2C 55-62 %281980%29%0Amedline id: %0Apubmed id: 6253155%0Acomment:,authors: Haegeman%2CG.%2C Iserentant%2CD.%2C Gheysen%2CD. and Fiers%2CW.%0Atitle: Characterization of the major altered leader sequence of late mRNA induced by SV40 deletion mutant d1-1811%0Ajournal: Nucleic Acids Res. 7 %287%29%2C 1799-1814 %281979%29%0Amedline id: %0Apubmed id: 231763%0Acomment:,authors: Khoury%2CG.%2C Gruss%2CP.%2C Dhar%2CR. and Lai%2CC.J.%0Atitle: Processing and expression of early SV40 mRNA: a role for RNA conformation in splicing%0Ajournal: Cell 18 %281%29%2C 85-92 %281979%29%0Amedline id: %0Apubmed id: 228860%0Acomment:,authors: Thimmappaya%2CB. and Shenk%2CT.%0Atitle: Nucleotide sequence analysis of viable deletion mutants lacking segments of the simian virus 40 genome coding for small t antigen%0Ajournal: J. Virol. 30 %283%29%2C 668-673 %281979%29%0Amedline id: %0Apubmed id: 225535%0Acomment:,location: %5B0:5243%5D%0Aauthors: Lebowitz%2CP. and Weissman%2CS.M.%0Atitle: Organization and transcription of the simian virus 40 genome%0Ajournal: Curr. Top. Microbiol. Immunol. 87%2C 43-172 %281979%29%0Amedline id: %0Apubmed id: 232871%0Acomment:,authors: Ghosh%2CP.K.%2C Reddy%2CV.B.%2C Swinscoe%2CJ.%2C Lebowitz%2CP. and Weissman%2CS.M.%0Atitle: Heterogeneity and 5%27-terminal structures of the late RNAs of simian virus 40%0Ajournal: J. Mol. Biol. 126 %284%29%2C 813-846 %281978%29%0Amedline id: %0Apubmed id: 218021%0Acomment:,authors: Subramanian%2CK.N. and Shenk%2CT.%0Atitle: Definition of the boundaries of the origin of DNA replication in simian virus 40%0Ajournal: Nucleic Acids Res. 5 %2810%29%2C 3635-3642 %281978%29%0Amedline id: %0Apubmed id: 214761%0Acomment:,authors: May%2CE.%2C Kress%2CM. and May%2CP.%0Atitle: Characterization of two SV40 early mRNAs and evidence for a nuclear %27prespliced%27 RNA species%0Ajournal: Nucleic Acids Res. 5 %289%29%2C 3083-3099 %281978%29%0Amedline id: %0Apubmed id: 212714%0Acomment:,authors: Lai%2CC.J.%2C Dhar%2CR. and Khoury%2CG.%0Atitle: Mapping the spliced and unspliced late lytic SV40 RNAs%0Ajournal: Cell 14 %284%29%2C 971-982 %281978%29%0Amedline id: %0Apubmed id: 210961%0Acomment:,authors: Haegeman%2CG. and Fiers%2CW.%0Atitle: Localization of the 5%27 terminus of late SV40 mRNA%0Ajournal: Nucleic Acids Res. 5 %287%29%2C 2359-2371 %281978%29%0Amedline id: %0Apubmed id: 209408%0Acomment:,authors: Ysebaert%2CM.%2C van Heuverswyn%2CH.%2C van de Voorde%2CA. and Fiers%2CW.%0Atitle: Nucleotide sequence of part of the simian virus 40 Hind-D restriction fragment. The presumed initiation region of the VP2 gene%0Ajournal: Eur. J. Biochem. 85 %281%29%2C 195-204 %281978%29%0Amedline id: %0Apubmed id: 205416%0Acomment:,authors: Berk%2CA.J. and Sharp%2CP.A.%0Atitle: Spliced early mRNAs of simian virus 40%0Ajournal: Proc. Natl. Acad. Sci. U.S.A. 75 %283%29%2C 1274-1278 %281978%29%0Amedline id: %0Apubmed id: 206891%0Acomment:,authors: Van de Voorde%2CA.%2C Contreras%2CR.%2C Rogiers%2CR. and Fiers%2CW.%0Atitle: The initiation region of the SV40 VP1 gene%0Ajournal: Cell 9 %281%29%2C 117-120 %281976%29%0Amedline id: %0Apubmed id: 184959%0Acomment:,authors: Subramanian%2CK.N.%2C Ghosh%2CP.K.%2C Dhar%2CR.%2C Thimmappaya%2CB.%2C Zain%2CS.B.%2C Pan%2CJ. and Weissman%2CS.M.%0Atitle: The primary structure of regions of SV 40 DNA encoding the ends of mRNA%0Ajournal: Prog. Nucleic Acid Res. Mol. Biol. 19%2C 157-164 %281976%29%0Amedline id: %0Apubmed id: 190641%0Acomment:,location: %5B0:5243%5D%0Aauthors: %0Aconsrtm: NCBI Genome Project%0Atitle: Direct Submission%0Ajournal: Submitted %2801-AUG-2000%29 National Center for Biotechnology Information%2C NIH%2C Bethesda%2C MD 20894%2C USA%0Amedline id: %0Apubmed id: %0Acomment:;sequence_version=1;source=Macaca mulatta polyomavirus 1;taxonomy=Viruses,dsDNA viruses%2C no RNA stage,Polyomaviridae;topology=circular NC_001669.1 feature source 1 5243 . + . db_xref=taxon:1891767;mol_type=genomic DNA;organism=Macaca mulatta polyomavirus 1 NC_001669.1 feature gene 1 5243 . - . db_xref=GeneID:29031022;locus_tag=SV40gp1 NC_001669.1 feature CDS 1 5243 . - 0 codon_start=1;db_xref=GI:297591898,GeneID:29031022;locus_tag=SV40gp1;note=early leader protein %28SELP%3B %5B133%5D%29;product=hypothetical protein;protein_id=YP_003708377.1;translation=MQRPRPPRPLSYSRSSEEAFLEA NC_001669.1 feature rep_origin 1 5243 . + . note=replication origin core region%3B 0.67 %5B89%5D NC_001669.1 feature protein_bind 13 52 . - . bound_moiety=large T-antigen NC_001669.1 feature regulatory 21 27 . - . note=early mRNA promoter element%3B 0.66 %5B66%5D%2C%5B78%5D%2C%5B79%5D;regulatory_class=other NC_001669.1 feature prim_transcript 31 2599 . - . note=early mRNA %28alt.%29 %5B23%5D%2C%5B71%5D%2C%5B75%5D NC_001669.1 feature prim_transcript 31 2587 . - . note=early mRNA %28alt.%29 %5B3%5D%2C%5B39%5D%2C%5B46%5D%2C%5B71%5D%2C%5B75%5D NC_001669.1 feature rep_origin 32 83 . + . note=replication origin auxiliary region%3B 0.67 %5B89%5D NC_001669.1 feature protein_bind 36 61 . - . bound_moiety=large T-antigen NC_001669.1 feature repeat_region 40 60 . - . note=21 bp non-tandem repeat I %5B110%5D%2C%5B102%5D%2C%5B112%5D NC_001669.1 feature repeat_region 62 82 . - . note=21 bp tandem repeat II %5B110%5D%2C%5B102%5D%2C%5B112%5D NC_001669.1 feature repeat_region 83 103 . - . note=21 bp tandem repeat III %5B110%5D%2C%5B102%5D%2C%5B112%5D NC_001669.1 feature repeat_region 107 178 . - . note=72 bp tandem repeat enhancer sequence A %5B83%5D%2C%5B78%5D%2C %5B81%5D%2C%5B110%5D NC_001669.1 feature variation 164 182 . + . note=gggactttccacacctggt in strain 776 %5B44%5D%3B gt in strain 777%3B 0.69 %5B41%5D%2C%5B34%5D;replace=gt NC_001669.1 feature repeat_region 179 250 . - . note=72 bp tandem repeat enhancer sequence B %5B83%5D%2C%5B78%5D%2C %5B81%5D%2C%5B110%5D NC_001669.1 feature prim_transcript 264 2676 . + . note=minor late 19s mRNA %5B38%5D%2C%5B71%5D%2C%5B75%5D NC_001669.1 feature intron 295 434 . + . note=late 19s intron %5B32%5D%2C%5B38%5D NC_001669.1 feature prim_transcript 325 2676 . + . note=major late 19s mRNA %5B17%5D%2C%5B30%5D%2C%5B38%5D%2C%5B35%5D%2C%5BProc. Natl. Acad. Sci. U.S.A. 76%2C 731-735 %281979 NC_001669.1 feature gene 335 523 . + . db_xref=GeneID:29031015;locus_tag=SV40gp2 NC_001669.1 feature CDS 335 523 . + 0 codon_start=1;db_xref=GI:297591899,GeneID:29031015;locus_tag=SV40gp2;note=agnoprotein %28lp-1%2C VCP%29%3B agnoprotein%3B involved in the localization of VP1 to the peri-nuclear region of host cells%3B involved in the release of progeny virions from the host cell%3B The polyomaviruses are non-enveloped dsDNA viruses%3B the viral genome is organized into two divergent transcriptional units known as early and late regions%3B mRNAs transcribed from the 5%27 proximal portion of the late region encode the agnoprotein%3B there is a high degree of sequence conservation between polyomaviral agnoproteins in the N-terminal and central domains;product=agnoprotein;protein_id=YP_003708378.1;translation=MVLRRLSRQASVKVRRSWTESKKTAQRLFVFVLELLLQFCEGEDTVDGKRKKPERLTEKPES NC_001669.1 feature intron 527 1462 . + . note=late 16s intron %5B30%5D%2C%5B38%5D%2C%5B19%5D NC_001669.1 feature gene 562 1620 . + . db_xref=GeneID:29031016;locus_tag=SV40gp3 NC_001669.1 feature CDS 562 1620 . + 0 codon_start=1;db_xref=GI:297591900,GeneID:29031016;locus_tag=SV40gp3;note=VP2 minor structural protein%3B VP2%2C VP3%3B 72 pentamers of VP1 comprise the outer capsid and form a T %3D 7 icosahedral lattice%3B a single copy of either VP2 or VP3 interact with each VP1 pentamer%3B VP2 is an N-terminally extended and myristoylated isoform of VP3%3B hetero-oligomers of VP2 and VP3 intergrate into the endoplasmic reticulum to facilitate transport of the genomic DNA into the nucleus%3B The polyomaviruses are non-enveloped dsDNA viruses%3B the viral genome is organized into two divergent transcriptional units known as early and late regions%3B mRNAs from the early region encode the viral small and large t-antigens%3B mRNAs from the late region encode the structural proteins%2C VP1%2C VP2 and VP3%3B the promoters of the early and late regions closely resemble host promoters and replication is therefore facilitated by host-cell machinery;product=VP2;protein_id=YP_003708379.1;translation=MGAALTLLGDLIATVSEAAAATGFSVAEIAAGEAAAAIEVQLASVATVEGLTTSEAIAAIGLTPQAYAVISGAPAAIAGFAALLQTVTGVSAVAQVGYRFFSDWDHKVSTVGLYQQPGMAVDLYRPDDYYDILFPGVQTFVHSVQYLDPRHWGPTLFNAISQAFWRVIQNDIPRLTSQELERRTQRYLRDSLARFLEETTWTVINAPVNWYNSLQDYYSTLSPIRPTMVRQVANREGLQISFGHTYDNIDEADSIQQVTERWEAQSQSPNVQSGEFIEKFEAPGGANQRTAPQWMLPLLLGLYGSVTSALKAYEDGPNKKKRKLSRGSSQKTKGTSASAKARHKRRNRSSRS NC_001669.1 feature gene 916 1620 . + . db_xref=GeneID:29031017;locus_tag=SV40gp4 NC_001669.1 feature CDS 916 1620 . + 0 codon_start=1;db_xref=GI:297591901,GeneID:29031017;locus_tag=SV40gp4;note=VP3 minor structural protein;product=hypothetical protein;protein_id=YP_003708380.1;translation=MAVDLYRPDDYYDILFPGVQTFVHSVQYLDPRHWGPTLFNAISQAFWRVIQNDIPRLTSQELERRTQRYLRDSLARFLEETTWTVINAPVNWYNSLQDYYSTLSPIRPTMVRQVANREGLQISFGHTYDNIDEADSIQQVTERWEAQSQSPNVQSGEFIEKFEAPGGANQRTAPQWMLPLLLGLYGSVTSALKAYEDGPNKKKRKLSRGSSQKTKGTSASAKARHKRRNRSSRS NC_001669.1 feature gene 1499 2593 . + . db_xref=GeneID:29031018;locus_tag=SV40gp5 NC_001669.1 feature CDS 1499 2593 . + 0 codon_start=1;db_xref=GI:297591902,GeneID:29031018;locus_tag=SV40gp5;note=VP1 major structural protein%3B VP1%3B major capsid protein of polyomavirus%3B 72 pentamers of VP1 comprise the outer capsid and form a T %3D 7 icosahedral lattice%3B VP1 contains an amino-terminal bipartite nuclear targeting signal that overlaps its DNA-binding-domain%3B The polyomaviruses are non-enveloped dsDNA viruses with a major capsid protein%2C VP1%2C that facilitates binding of genomic DNA and entry into target cells%3B the viral genome is organized into two divergent transcriptional units known as early and late regions%3B mRNAs from the early region encode the viral small and large t-antigens%3B mRNAs from the late region encode the structural proteins%2C VP1%2C VP2 and VP3;product=Major capsid protein VP1;protein_id=YP_003708381.1;translation=MKMAPTKRKGSCPGAAPKKPKEPVQVPKLVIKGGIEVLGVKTGVDSFTEVECFLNPQMGNPDEHQKGLSKSLAAEKQFTDDSPDKEQLPCYSVARIPLPNLNEDLTCGNILMWEAVTVKTEVIGVTAMLNLHSGTQKTHENGAGKPIQGSNFHFFAVGGEPLELQGVLANYRTKYPAQTVTPKNATVDSQQMNTDHKAVLDKDNAYPVECWVPDPSKNENTRYFGTYTGGENVPPVLHITNTATTVLLDEQGVGPLCKADSLYVSAVDICGLFTNTSGTQQWKGLPRYFKITLRKRSVKNPYPISFLLSDLINRRTQRVDGQPMIGMSSQVEEVRVYEDTEELPGDPDMIRYIDEFGQTTTRMQ NC_001669.1 feature variation 1626 1626 . + . locus_tag=SV40gp5;note=g in wild-type%3B a in temperature-sensitive mutant tsC260 NC_001669.1 feature variation 1667 1667 . + . locus_tag=SV40gp5;note=c in wild-type%3B a in temperature-sensitive mutant tsB228 NC_001669.1 feature variation 1680 1680 . + . locus_tag=SV40gp5;note=c in wild-type%3B g in temperature-sensitive mutant tsB218 NC_001669.1 feature variation 1718 1718 . + . locus_tag=SV40gp5;note=g in wild-type%3B a in temperature-sensitive mutant tsB%5B204%2C211%2C265%5D NC_001669.1 feature variation 1719 1719 . + . locus_tag=SV40gp5;note=c in wild-type%3B t in temperature-sensitive mutant tsB8 NC_001669.1 feature variation 1756 1756 . + . locus_tag=SV40gp5;note=a in wild-type%3B c in temperature-sensitive mutant tsB8 NC_001669.1 feature variation 1995 1995 . + . locus_tag=SV40gp5;note=g in wild-type%3B c in temperature-sensitive mutant tsB221 NC_001669.1 feature variation 2003 2003 . + . locus_tag=SV40gp5;note=g in wild-type%3B a in temperature-sensitive mutant tsB201 NC_001669.1 feature variation 2084 2084 . + . locus_tag=SV40gp5;note=c in wild-type%3B t in temperature-sensitive mutant tsBC223 NC_001669.1 feature variation 2091 2091 . + . locus_tag=SV40gp5;note=c in wild-type%3B c in temperature-sensitive mutant tsB4 NC_001669.1 feature variation 2141 2141 . + . locus_tag=SV40gp5;note=c in wild-type%3B t in temperature-sensitive mutant tsC219 NC_001669.1 feature variation 2237 2237 . + . locus_tag=SV40gp5;note=c in wild-type%3B a in temperature-sensitive mutant tsC240 NC_001669.1 feature variation 2262 2262 . + . locus_tag=SV40gp5;note=c in wild-type%3B t in temperature-sensitive mutant tsC260 NC_001669.1 feature variation 2354 2354 . + . locus_tag=SV40gp5;note=c in wild-type%3B t in temperature-sensitive mutant tsBC%5B208%2C214%2C216%2C217%2C248%2C274%5D NC_001669.1 feature variation 2367 2367 . + . locus_tag=SV40gp5;note=a in wild-type%3B c in temperature-sensitive mutant tsBC11 NC_001669.1 feature prim_transcript 2587 5236 . - . note=early mRNA %28alt.%29 %5B3%5D%2C%5B8%5D%2C%5B39%5D%2C%5B46%5D%2C%5B63%5D NC_001669.1 feature prim_transcript 2587 5230 . - . note=early mRNA %28alt.%29 %5B3%5D%2C%5B39%5D%2C%5B46%5D%2C%5B78%5D NC_001669.1 feature prim_transcript 2587 5225 . - . note=early mRNA %28alt.%29 %5B3%5D%2C%5B39%5D%2C%5B46%5D%2C%5B50%5D%2C%5B63%5D NC_001669.1 feature prim_transcript 2599 5236 . - . note=early mRNA %28alt.%29 %5B8%5D%2C%5B23%5D%2C%5B46%5D%2C%5B63%5D NC_001669.1 feature prim_transcript 2599 5230 . - . note=early mRNA %28alt.%29 %5B23%5D%2C%5B78%5D NC_001669.1 feature prim_transcript 2599 5225 . - . note=early mRNA %28alt.%29 %5B23%5D%2C%5B50%5D%2C%5B63%5D NC_001669.1 feature regulatory 2608 2613 . - . note=early mRNA polyadenyation signal on the comp strand%3B 0.16 %5B23%5D%2C%5B120%5D;regulatory_class=polyA_signal_sequence NC_001669.1 feature regulatory 2637 2642 . - . note=early mRNA polyadenyation signal on the comp strand%3B 0.16 %5B23%5D%2C%5B120%5D;regulatory_class=polyA_signal_sequence NC_001669.1 feature regulatory 2657 2662 . + . note=late mRNA polyadenyation signal%3B 0.17 %5B23%5D%2C%5B68%5D%2C %5B120%5D;regulatory_class=polyA_signal_sequence NC_001669.1 feature gene 2691 5163 . - . db_xref=GeneID:29031019;locus_tag=SV40gp6 NC_001669.1 feature CDS 2691 5163 . - 0 codon_start=1;db_xref=GI:297591903,GeneID:29031019;locus_tag=SV40gp6;note=large T antigen%3B binds to the viral origin of replication%3B regulates the transcription of early region mRNA%3B helicase activity facilitates movement of the virion DNA replication fork%3B the small T antigen shares a region in common with the large T antigen known as the J-domain%3B the J-domain is required for multiple processes including assembly%2C viral genomic DNA replication and transcription%3B The polyomaviruses are non-enveloped dsDNA viruses%3B the viral genome is organized into two divergent transcriptional units known as early and late regions%3B mRNAs from the early region encode the viral small and large t-antigens%3B the small T antigen and large T antigen are expressed upon entry into the host nucleus early in the viral lifecycle;product=large T antigen;protein_id=YP_003708382.1;translation=MDKVLNREESLQLMDLLGLERSAWGNIPLMRKAYLKKCKEFHPDKGGDEEKMKKMNTLYKKMEDGVKYAHQPDFGGFWDATEIPTYGTDEWEQWWNAFNEENLFCSEEMPSSDDEATADSQHSTPPKKKRKVEDPKDFPSELLSFLSHAVFSNRTLACFAIYTTKEKAALLYKKIMEKYSVTFISRHNSYNHNILFFLTPHRHRVSAINNYAQKLCTFSFLICKGVNKEYLMYSALTRDPFSVIEESLPGGLKEHDFNPEEAEETKQVSWKLVTEYAMETKCDDVLLLLGMYLEFQYSFEMCLKCIKKEQPSHYKYHEKHYANAAIFADSKNQKTICQQAVDTVLAKKRVDSLQLTREQMLTNRFNDLLDRMDIMFGSTGSADIEEWMAGVAWLHCLLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQGINNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNEYSVPKTLQARFVKQIDFRPKDYLKHCLERSEFLLEKRIIQSGIALLLMLIWYRPVAEFAQSIQSRIVEWKERLDKEFSLSVYQKMKFNVAMGIGVLDWLRNSDDDDEDSQENADKNEDGGEKNMEDSGHETGIDSQSQGSFQAPQSSQSVHDHNQPYHICRGFTCFKKPPTPPPEPET NC_001669.1 feature gene 2842 2907 . - . db_xref=GeneID:29031020;locus_tag=SV40gs1 NC_001669.1 feature misc_RNA 2842 2907 . - . db_xref=GeneID:29031020;locus_tag=SV40gs1;note=SV40-associated small %28SAS%29 RNA%3B 0.21 %5B64%5D NC_001669.1 feature intron 4572 4917 . - . locus_tag=SV40gp6;note=large T antigen %2818s%29 intron %5B32%5D%2C%5B38%5D%3B does not fit consensus NC_001669.1 feature intron 4572 4636 . - . locus_tag=SV40gp6;note=early 19s mRNA %28small t antigen%29 intron %5B32%5D%2C%5B38%5D%3B does not fit consensus NC_001669.1 feature gene 4639 5163 . - . db_xref=GeneID:29031021;locus_tag=SV40gp7 NC_001669.1 feature CDS 4639 5163 . - 0 codon_start=1;db_xref=GI:297591904,GeneID:29031021;locus_tag=SV40gp7;note=small t antigen%3B small T-antigen%3B promotes the efficient replication of genomic DNA%3B binds to and negativley regulates the function of protein phosphotase %28PP2A%29 thereby accelerating the progression to S-phase%3B the small T-antigen shares a region in common with the large T-antigen known as the J-domain%3B the J-domain is required for multiple processes including assembly%2C viral genomic DNA replication and transcription%3B The polyomaviruses are non-enveloped dsDNA viruses%3B the viral genome is organized into two divergent transcriptional units known as early and late regions%3B mRNAs from the early region encode the viral small and large t-antigens%3B the small T antigen and large T antigen are expressed upon entry into the host nucleus early in the viral lifecycle%3B the small T antigen is not essential for replication in all cell lines;product=Small T antigen;protein_id=YP_003708383.1;translation=MDKVLNREESLQLMDLLGLERSAWGNIPLMRKAYLKKCKEFHPDKGGDEEKMKKMNTLYKKMEDGVKYAHQPDFGGFWDATEVFASSLNPGVDAMYCKQWPECAKKMSANCICLLCLLRMKHENRKLYRKDPLVWVDCYCFDCFRMWFGLDLCEGTLLLWCDIIGQTTYRDLKL NC_001669.1 feature protein_bind 5184 5209 . - . bound_moiety=large T-antigen