LOCUS NC_001669 5243 bp DNA circular VRL 22-SEP-2016 DEFINITION Simian virus 40, complete genome. ACCESSION NC_001669 VERSION NC_001669.1 GI:9628421 DBLINK BioProject: PRJNA14024 KEYWORDS RefSeq. SOURCE Macaca mulatta polyomavirus 1 ORGANISM Macaca mulatta polyomavirus 1 Viruses; dsDNA viruses, no RNA stage; Polyomaviridae. REFERENCE 1 (sites) AUTHORS Kube,D. and Milavetz,B. TITLE Generation of a nucleosome-free promoter region in SV40 does not require T-antigen binding to site I JOURNAL Virology 172 (1), 100-105 (1989) PUBMED 2549706 REFERENCE 2 (sites) AUTHORS Behm,M., Lowman,H., Ng,S.C. and Bina,M. TITLE Analysis of temperature-sensitive mutations in the simian virus 40 gene encoding virion protein 1 JOURNAL Proc. Natl. Acad. Sci. U.S.A. 85 (24), 9421-9425 (1988) PUBMED 2849104 REFERENCE 3 (sites) AUTHORS Khalili,K., Brady,J. and Khoury,G. TITLE Translational regulation of SV40 early mRNA defines a new viral protein JOURNAL Cell 48 (4), 639-645 (1987) PUBMED 3028644 REFERENCE 4 (sites) AUTHORS Barrera-Saldana,H., Takahashi,K., Vigneron,M., Wildeman,A., Davidson,I. and Chambon,P. TITLE All six GC-motifs of the SV40 early upstream element contribute to promoter activity in vivo and in vitro JOURNAL EMBO J. 4 (13B), 3839-3849 (1985) PUBMED 3004974 REFERENCE 5 (sites) AUTHORS Stringer,J.R. TITLE Recombination between poly[d(GT).d(CA)] sequences in simian virus 40-infected cultured cells JOURNAL Mol. Cell. Biol. 5 (6), 1247-1259 (1985) PUBMED 2993859 REFERENCE 6 (sites) AUTHORS Scheller,A. and Prives,C. TITLE Simian virus 40 and polyomavirus large tumor antigens have different requirements for high-affinity sequence-specific DNA binding JOURNAL J. Virol. 54 (2), 532-545 (1985) PUBMED 2985816 REFERENCE 7 (sites) AUTHORS Hutchinson,N.I., Chang,L.S., Pater,M.M., Bouck,N., Shenk,T.E. and di Mayorca,G. TITLE Characterization of a new simian virus 40 mutant, tsA3900, isolated from deletion mutant tsA1499 JOURNAL J. Virol. 53 (3), 814-821 (1985) PUBMED 2983092 REFERENCE 8 (sites) AUTHORS Hartzell,S.W., Byrne,B.J. and Subramanian,K.N. TITLE 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 JOURNAL Proc. Natl. Acad. Sci. U.S.A. 81 (20), 6335-6339 (1984) PUBMED 6093097 REFERENCE 9 (sites) AUTHORS Sadofsky,M. and Alwine,J.C. TITLE Sequences on the 3' side of hexanucleotide AAUAAA affect efficiency of cleavage at the polyadenylation site JOURNAL Mol. Cell. Biol. 4 (8), 1460-1468 (1984) PUBMED 6149460 REFERENCE 10 (sites) AUTHORS Hay,R.T., Hendrickson,E.A. and DePamphilis,M.L. TITLE Sequence specificity for the initiation of RNA-primed simian virus 40 DNA synthesis in vivo JOURNAL J. Mol. Biol. 175 (2), 131-157 (1984) PUBMED 6202875 REFERENCE 11 (sites) AUTHORS Lycan,D.E. and Danna,K.J. TITLE S1 mapping of purified nascent transcripts of simian virus 40 JOURNAL Mol. Cell. Biol. 4 (4), 625-633 (1984) PUBMED 6325887 REFERENCE 12 (sites) AUTHORS Pomerantz,B.J. and Hassell,J.A. TITLE Polyomavirus and simian virus 40 large T antigens bind to common DNA sequences JOURNAL J. Virol. 49 (3), 925-937 (1984) PUBMED 6321773 REFERENCE 13 (sites) AUTHORS Hartzell,S.W., Byrne,B.J. and Subramanian,K.N. TITLE Mapping of the late promoter of simian virus 40 JOURNAL Proc. Natl. Acad. Sci. U.S.A. 81 (1), 23-27 (1984) PUBMED 6320166 REFERENCE 14 (sites) AUTHORS Sohn,U., Szyszko,J., Coombs,D. and Krause,M. TITLE 7S-K nuclear RNA from simian virus 40-transformed cells has sequence homology to the viral early promoter JOURNAL Proc. Natl. Acad. Sci. U.S.A. 80 (23), 7090-7094 (1983) PUBMED 6196783 REFERENCE 15 (sites) AUTHORS Mertz,J.E., Murphy,A. and Barkan,A. TITLE Mutants deleted in the agnogene of simian virus 40 define a new complementation group JOURNAL J. Virol. 45 (1), 36-46 (1983) PUBMED 6296443 REFERENCE 16 (sites) AUTHORS Alwine,J.C. TITLE Evidence for simian virus 40 late transcriptional control: mixed infections of wild-type simian virus 40 and a late leader deletion mutant exhibit trans effects on late viral RNA synthesis JOURNAL J. Virol. 42 (3), 798-803 (1982) PUBMED 6284996 REFERENCE 17 (sites) AUTHORS Edwards,K.A., Halligan,B.D., Davis,J.L., Nivera,N.L. and Liu,L.F. TITLE Recognition sites of eukaryotic DNA topoisomerase I: DNA nucleotide sequencing analysis of topo I cleavage sites on SV40 DNA JOURNAL Nucleic Acids Res. 10 (8), 2565-2576 (1982) PUBMED 6281736 REFERENCE 18 (sites) AUTHORS DiMaio,D. and Nathans,D. TITLE Regulatory mutants of simian virus 40. Effect of mutations at a T antigen binding site on DNA replication and expression of viral genes JOURNAL J. Mol. Biol. 156 (3), 531-548 (1982) PUBMED 6288959 REFERENCE 19 (sites) AUTHORS Lebowitz,P. and Ghosh,P.K. TITLE Initiation and regulation of simian virus 40 early transcription in vitro JOURNAL J. Virol. 41 (2), 449-461 (1982) PUBMED 6281460 REFERENCE 20 (sites) AUTHORS Bergsma,D.J., Olive,D.M., Hartzell,S.W. and Subramanian,K.N. TITLE Territorial limits and functional anatomy of the simian virus 40 replication origin JOURNAL Proc. Natl. Acad. Sci. U.S.A. 79 (2), 381-385 (1982) PUBMED 6281769 REFERENCE 21 (sites) AUTHORS Fromm,M. and Berg,P. TITLE Deletion mapping of DNA regions required for SV40 early region promoter function in vivo JOURNAL J. Mol. Appl. Genet. 1 (5), 457-481 (1982) PUBMED 6296253 REFERENCE 22 (sites) AUTHORS Banerji,J., Rusconi,S. and Schaffner,W. TITLE Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences JOURNAL Cell 27 (2 PT 1), 299-308 (1981) PUBMED 6277502 REFERENCE 23 (sites) AUTHORS Hansen,U., Tenen,D.G., Livingston,D.M. and Sharp,P.A. TITLE T antigen repression of SV40 early transcription from two promoters JOURNAL Cell 27 (3 PT 2), 603-613 (1981) PUBMED 6101224 REFERENCE 24 (sites) AUTHORS Moreau,P., Hen,R., Wasylyk,B., Everett,R., Gaub,M.P. and Chambon,P. TITLE The SV40 72 base repair repeat has a striking effect on gene expression both in SV40 and other chimeric recombinants JOURNAL Nucleic Acids Res. 9 (22), 6047-6068 (1981) PUBMED 6273820 REFERENCE 25 (sites) AUTHORS Jackson,V. and Chalkley,R. TITLE Use of whole-cell fixation to visualize replicating and maturing simian virus 40: identification of new viral gene product JOURNAL Proc. Natl. Acad. Sci. U.S.A. 78 (10), 6081-6085 (1981) PUBMED 6273846 REFERENCE 26 (sites) AUTHORS Jay,G., Nomura,S., Anderson,C.W. and Khoury,G. TITLE Identification of the SV40 agnogene product: a DNA binding protein JOURNAL Nature 291 (5813), 346-349 (1981) PUBMED 6262654 REFERENCE 27 (sites) AUTHORS Fitzgerald,M. and Shenk,T. TITLE The sequence 5'-AAUAAA-3'forms parts of the recognition site for polyadenylation of late SV40 mRNAs JOURNAL Cell 24 (1), 251-260 (1981) PUBMED 6113054 REFERENCE 28 (sites) AUTHORS Mathis,D.J. and Chambon,P. TITLE The SV40 early region TATA box is required for accurate in vitro initiation of transcription JOURNAL Nature 290 (5804), 310-315 (1981) PUBMED 6259539 REFERENCE 29 (sites) AUTHORS Buchman,A.R., Burnett,L. and Berg,P. TITLE Appendix A: The SV40 nucleotide sequence JOURNAL (in) Tooze,J. (Ed.); DNA TUMOR VIRUSES - SECOND EDITION REVISED: 799-841; Cold Spring Harbor Laboratory, Cold Spring Harbor (1981) REFERENCE 30 (sites) AUTHORS Shalloway,D., Kleinberger,T. and Livingston,D.M. TITLE Mapping of SV40 DNA replication origin region binding sites for the SV40 T antigen by protection against exonuclease III digestion JOURNAL Cell 20 (2), 411-422 (1980) PUBMED 6248243 REFERENCE 31 (sites) AUTHORS Mark,D.F. and Berg,P. TITLE A third splice site in SV40 early mRNA JOURNAL Cold Spring Harb. Symp. Quant. Biol. 44 (PT 1), 55-62 (1980) PUBMED 6253155 REFERENCE 32 (sites) AUTHORS Haegeman,G., Iserentant,D., Gheysen,D. and Fiers,W. TITLE Characterization of the major altered leader sequence of late mRNA induced by SV40 deletion mutant d1-1811 JOURNAL Nucleic Acids Res. 7 (7), 1799-1814 (1979) PUBMED 231763 REFERENCE 33 (sites) AUTHORS Khoury,G., Gruss,P., Dhar,R. and Lai,C.J. TITLE Processing and expression of early SV40 mRNA: a role for RNA conformation in splicing JOURNAL Cell 18 (1), 85-92 (1979) PUBMED 228860 REFERENCE 34 (sites) AUTHORS Thimmappaya,B. and Shenk,T. TITLE Nucleotide sequence analysis of viable deletion mutants lacking segments of the simian virus 40 genome coding for small t antigen JOURNAL J. Virol. 30 (3), 668-673 (1979) PUBMED 225535 REFERENCE 35 (bases 1 to 5243) AUTHORS Lebowitz,P. and Weissman,S.M. TITLE Organization and transcription of the simian virus 40 genome JOURNAL Curr. Top. Microbiol. Immunol. 87, 43-172 (1979) PUBMED 232871 REFERENCE 36 (sites) AUTHORS Ghosh,P.K., Reddy,V.B., Swinscoe,J., Lebowitz,P. and Weissman,S.M. TITLE Heterogeneity and 5'-terminal structures of the late RNAs of simian virus 40 JOURNAL J. Mol. Biol. 126 (4), 813-846 (1978) PUBMED 218021 REFERENCE 37 (sites) AUTHORS Subramanian,K.N. and Shenk,T. TITLE Definition of the boundaries of the origin of DNA replication in simian virus 40 JOURNAL Nucleic Acids Res. 5 (10), 3635-3642 (1978) PUBMED 214761 REFERENCE 38 (sites) AUTHORS May,E., Kress,M. and May,P. TITLE Characterization of two SV40 early mRNAs and evidence for a nuclear 'prespliced' RNA species JOURNAL Nucleic Acids Res. 5 (9), 3083-3099 (1978) PUBMED 212714 REFERENCE 39 (sites) AUTHORS Lai,C.J., Dhar,R. and Khoury,G. TITLE Mapping the spliced and unspliced late lytic SV40 RNAs JOURNAL Cell 14 (4), 971-982 (1978) PUBMED 210961 REFERENCE 40 (sites) AUTHORS Haegeman,G. and Fiers,W. TITLE Localization of the 5' terminus of late SV40 mRNA JOURNAL Nucleic Acids Res. 5 (7), 2359-2371 (1978) PUBMED 209408 REFERENCE 41 (sites) AUTHORS Ysebaert,M., van Heuverswyn,H., van de Voorde,A. and Fiers,W. TITLE Nucleotide sequence of part of the simian virus 40 Hind-D restriction fragment. The presumed initiation region of the VP2 gene JOURNAL Eur. J. Biochem. 85 (1), 195-204 (1978) PUBMED 205416 REFERENCE 42 (sites) AUTHORS Berk,A.J. and Sharp,P.A. TITLE Spliced early mRNAs of simian virus 40 JOURNAL Proc. Natl. Acad. Sci. U.S.A. 75 (3), 1274-1278 (1978) PUBMED 206891 REFERENCE 43 (sites) AUTHORS Van de Voorde,A., Contreras,R., Rogiers,R. and Fiers,W. TITLE The initiation region of the SV40 VP1 gene JOURNAL Cell 9 (1), 117-120 (1976) PUBMED 184959 REFERENCE 44 (sites) AUTHORS Subramanian,K.N., Ghosh,P.K., Dhar,R., Thimmappaya,B., Zain,S.B., Pan,J. and Weissman,S.M. TITLE The primary structure of regions of SV 40 DNA encoding the ends of mRNA JOURNAL Prog. Nucleic Acid Res. Mol. Biol. 19, 157-164 (1976) PUBMED 190641 REFERENCE 45 (bases 1 to 5243) CONSRTM NCBI Genome Project TITLE Direct Submission JOURNAL Submitted (01-AUG-2000) National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. The reference sequence is identical to J02400. [2] mRNA. [1] mRNA. [3] mRNA. [4] sites; cds start for VP1. [8] direct tandem repeats. [9] mRNA and DNA. [10] overlap between VP1, VP2 and VP3 genes. [11] origin of replication. [15] VP1 gene. [16] mRNA. [13] RNA and DNA. [29] RNA and DNA. [30] sites-late 16S mRNA and RNA splicing. [33] sites-late 16S mRNA and RNA splicing. [40] small t antigen gene. [31] RNA. [18] T antigen binding sites. [32] sites; 5' and 3' termini of 19s late mRNAs. [27] VP2 and VP3 genes. [26] sites-5' termini of late mRNAs. [28] sites-mRNA 3' termini. [38] sites-cDNA, 16S leader segments. [35] sites; cap site for 16s and 19s late mRNAs. [37] sites; mutations in region of origin of replication. [19] sites; splice sites in late mRNAs. [36] sites; early mRNAs. [39] sites; early mRNAs and RNA splicing. [43] review; bases 1 to 163; 181 to 5243. [45] deletion mutant analysis. [53] cDNA. [46] sites-5' termini of early mRNAs. [56] sites; splice sites for large T antigen mRNA. [57] deletion mutant analysis. [49] deletion mutant analysis. [54] deletion mutant analysis. [48] deletion mutant analysis. [51] deletion mutant analysis. [50] cDNA. [47] sites; deletion mutant analysis over bases 4553 to 5172. [52] sites; deletion mutant analysis of major late cap site. [42] sites; splice sites in early mRNAs. [(in) Tooze,J. (Eds.);DNA Tumor Viruses - Second Edition Revised: 799-841;Cold Sp] review; bases 1 to 163; 181 to 5243. [64] deletion mutant analysis. [59] RNA and DNA. [62] deletion and point mutants over the replication origin. [66] deletion mutants over the early promoter. [55] sites; T antigen binding sites. [67] origin-defective deletion mutants. [63] early mRNA initiation sites. [71] sites; early mRNA initiation sites and repression by T antigen. [68] sites; poly-A at 2662; deletion mutants over 2533-2775. [85] deletion mutant analysis. [83] early promoter analysis. [74] deletion mutant analysis. [82] cDNAs over this region. [78] early promoter analysis. [79] sites; promoter for early mRNAs. [69] autoregulation by T antigen. [75] upstream shift of early mRNA initiation site. [76] deletion mutant analysis. [84] sites; cds for agnoprotein. [77] T antigen binding to a deletion mutant. [81] sites; transcriptional enhancement by the 72 bp repeats. [73] cDNAs;. [80] sites; agnoprotein coding sequence. [98] sites; mapping of the origin of replication. [97] sites; topoisomerase cleavage sites. [95] deletion mutant analysis. [99] only joints of deletion mutants. [87] RNA. [94] sites; late mRNA initiation sites. [88] late promoter analysis. [89] mutant analysis over origin of replication. [92] T antigen binding to a deletion mutant. [91] sites; T antigen binding sites. [90] sites; mapping of early region promoter. [70] sites; SV40 enhancement of beta-globin gene expression. [110] mapping of the early promoter. [105] sites; agnogene mutants. [106] mutant analysis. [108] mutant analysis over these regions. [103] topoisomerase II. [111] only joints of deletion mutants. [102] transcription factor binding to early promoter. [112] sites; 7S-K RNA of transformed cells. [101] T antigen binding analysis. [107] cDNA; late mRNA initiation. [100] autoregulation by T antigen. [109] early promoter analysis. [113] T antigen binding sites. [119] sites; sites-5' termini of late mRNAs. [116] T antigen binding analysis. [117] sites; T antigen binding sites. [123] primase initiation sites. [114] transcriptional enhancer analysis. [118] mutant analysis at the replication origin. [120] sites; mRNA polyadenylation signal sequences. [121] chromatin structure at origin of replication; mutational analysis. [122] sites; bidirectional promoter element. [124] sites;. [115] sites; Okazaki fragment sequences. [128] sites; tsA3900 point mutant sequence. [129] sites; large t-antigen binding specificity. [130] temperature-sensitive mutants. [131] sites; recombination in poly(GT. [127] sites; large T-antigen binding sites. [133] sites; SV40 early leader protein (SELP. [93] sites; early SV40 transcription. [134] sites; temperature sensitive mutants in the VP1 gene. [7] sites; ends of 'early' and 'late' mRNA. Kindly reviewed by K. N. Subramanian. Draft entry and computer- readable sequence for [134] kindly submitted by M.Bina, 16-FEB-1989. The E or minus strand of SV40 strain 776 is shown as it is reported by [41] and [34] using the numbering system by [(in) Tooze,J. (Eds.);DNA Tumor Viruses - Second Edition Revised: 799-841;Cold Sp], with exception of of the addition of 17 bases (between nucleotides 164 and 165) to their sequence [44]. Differences between the complete sequences as published by [41] and [34] and this sequence are limited to the 17 bp change, the revision at 328 below, and the numbering. All references tend to agree upon an independent coordinate system, where map units run from 0.00 to 1.00 and the origin is defined by the sole EcoRI site, which is found at base 1782 below. In keeping with [(in) Tooze,J. (Eds.);DNA Tumor Viruses - Second Edition Revised: 799-841;Cold Sp], map units for this entry have been calculated by SV + 3461 mu = ----------- 5243 If the result is > 1, subtract 1 for the value. The origin of this sequence, then, is at 0.66. Identical units are used for Polyoma virus. DNA replication is bidirectional from an origin which has been narrowed by mutational analysis to bases 5193 to 34 [37]. Given that early mRNA transcription also arises from this region, the two processes will be, to some extent, simultaneously regulated. In addition to the 21-bp and 72-bp repeats concerned with early transcription (see below), the origin includes a 17-bp A + T-rich sequence; further demarcation of a 'core' region and an 'auxiliary' region makes the former comprise a 17-bp palindrome (5193-5209), a 15-bp palindrome (5213-5227), a 27-bp palindrome (5230-13) and the A + T-rich region (15-31), and the latter the three 21-bp repeats [89]. Thus the 'core' overlaps the T-antigen binding sites I and II and the 'auxiliary region' (which is said to enhance replication efficiency) overlaps the T-antigen binding site III [89]. Transcription of early mRNAs (18s and 19s) is leftward off the E, or minus, strand and transcription of late mRNAs (16s and 19s) is rightward off the L, or plus, strand. In the former case, the annotation will show the symbols '(c)' and 'comp strand' for the transcripts and products, and for the regulatory elements which govern them. In some references, the E strand has been labeled 'Late' to indicate that it has the polarity of late mRNA, and the L strand 'Early' to indicate that it has the polarity of early mRNA. (Early mRNAs can be produced throughout the lytic cycle.) The characterization of the mRNAs as 18s and 19s early and 16s and 19s late is a simplification: heterogeneity with regard to 5' and 3' termini, splice sites, and abundance as a function of time in the lytic cycle and regulatory events, have all been observed [32] [43],[82],[75]. For the purposes of this entry, only the simplest major mRNA species have been entered in the Sites. The promoter for the early mRNAs is considered to include at least bases 5185 to 250 on the E strand: the T antigen binding sites (for which the minimal spans are given [71]), the 'TATA' box at position 21, the 21-bp repeats, and the 72-bp repeats are all known to play a role in early transcription. One of the effects of regulation at these sites is to shift the cap site to one of at least seven positions between bases 95 and 32 [75]. Bases 55 to 97 are also of interest because they permit base-pairing homology with the small nuclear RNA 7S-K [112] and because they bind the cell factor SP-1 [102]. For late promoter induction to occur at high efficiency two domains are required simultaneously: the minimal replication origin and the 72 bp repeat [124]. The origin-proximal 22 bp portion of the 72-bp repeat is sufficient for induction, while the origin-distal portion is dispensable [124]. If T antigen is present, the 21 bp repeat is dispensable for induction of late promoter activity in vivo [124]. The regulatory elements for early transcription have been annotated for the 'comp strand'. The late region induction signals are to be found in the same region as the early regulatory elements [124]. The efficacy of the 72-bp repeat in promoting transcription has been demonstrated for both orientations [81]. The SAS-RNA is a small viral associated RNA whose function is unknown. It appears to arise through processing from some of the longer early transcripts; mutants in the SAS-RNA coding region remain viable [64]. Seven proteins -- the small t antigen, the large T antigen, the three structural proteins, the early leader protein [133], and the agnoprotein (which is thought to be involved with structural development [106])-- are known to be translated from the multiplicity of mRNAs. The existence of a middle T antigen, known to exist in Polyoma, has been suggested [56]. For a summary of other possible coding sequences, see [(in) Tooze,J. (Eds.);DNA Tumor Viruses - Second Edition Revised: 799-841;Cold Sp]. Missing data project [124-129], [7]. EMBL features not translated to GenBank features: key from to description PRM 21 15 (C) TATA-box [3] MSG 120 2674 major 16S RNA. COMPLETENESS: full length. FEATURES Location/Qualifiers source 1..5243 /organism="Macaca mulatta polyomavirus 1" /mol_type="genomic DNA" /db_xref="taxon:1891767" gene complement(join(5188..5243,1..16)) /locus_tag="SV40gp1" /db_xref="GeneID:29031022" CDS complement(join(5188..5243,1..16)) /locus_tag="SV40gp1" /note="early leader protein (SELP; [133])" /codon_start=1 /product="hypothetical protein" /protein_id="YP_003708377.1" /db_xref="GI:297591898" /db_xref="GeneID:29031022" /translation="MQRPRPPRPLSYSRSSEEAFLEA" rep_origin join(5191..5243,1..31) /note="replication origin core region; 0.67 [89]" protein_bind complement(13..52) /bound_moiety="large T-antigen" regulatory complement(21..27) /regulatory_class="other" /note="early mRNA promoter element; 0.66 [66],[78],[79]" prim_transcript complement(31..2599) /note="early mRNA (alt.) [23],[71],[75]" prim_transcript complement(31..2587) /note="early mRNA (alt.) [3],[39],[46],[71],[75]" rep_origin 32..83 /note="replication origin auxiliary region; 0.67 [89]" protein_bind complement(36..61) /bound_moiety="large T-antigen" repeat_region complement(40..60) /note="21 bp non-tandem repeat I [110],[102],[112]" repeat_region complement(62..82) /note="21 bp tandem repeat II [110],[102],[112]" repeat_region complement(83..103) /note="21 bp tandem repeat III [110],[102],[112]" repeat_region complement(107..178) /note="72 bp tandem repeat enhancer sequence A [83],[78], [81],[110]" variation 164..182 /note="gggactttccacacctggt in strain 776 [44]; gt in strain 777; 0.69 [41],[34]" /replace="gt" repeat_region complement(179..250) /note="72 bp tandem repeat enhancer sequence B [83],[78], [81],[110]" prim_transcript 264..2676 /note="minor late 19s mRNA [38],[71],[75]" intron 295..434 /note="late 19s intron [32],[38]" prim_transcript 325..2676 /note="major late 19s mRNA [17],[30],[38],[35],[Proc. Natl. Acad. Sci. U.S.A. 76, 731-735 (1979" gene 335..523 /locus_tag="SV40gp2" /db_xref="GeneID:29031015" CDS 335..523 /locus_tag="SV40gp2" /note="agnoprotein (lp-1, VCP); agnoprotein; involved in the localization of VP1 to the peri-nuclear region of host cells; involved in the release of progeny virions from the host cell; The polyomaviruses are non-enveloped dsDNA viruses; the viral genome is organized into two divergent transcriptional units known as early and late regions; mRNAs transcribed from the 5' proximal portion of the late region encode the agnoprotein; there is a high degree of sequence conservation between polyomaviral agnoproteins in the N-terminal and central domains" /codon_start=1 /product="agnoprotein" /protein_id="YP_003708378.1" /db_xref="GI:297591899" /db_xref="GeneID:29031015" /translation="MVLRRLSRQASVKVRRSWTESKKTAQRLFVFVLELLLQFCEGED TVDGKRKKPERLTEKPES" intron 527..1462 /note="late 16s intron [30],[38],[19]" gene 562..1620 /locus_tag="SV40gp3" /db_xref="GeneID:29031016" CDS 562..1620 /locus_tag="SV40gp3" /note="VP2 minor structural protein; VP2, VP3; 72 pentamers of VP1 comprise the outer capsid and form a T = 7 icosahedral lattice; a single copy of either VP2 or VP3 interact with each VP1 pentamer; VP2 is an N-terminally extended and myristoylated isoform of VP3; hetero-oligomers of VP2 and VP3 intergrate into the endoplasmic reticulum to facilitate transport of the genomic DNA into the nucleus; The polyomaviruses are non-enveloped dsDNA viruses; the viral genome is organized into two divergent transcriptional units known as early and late regions; mRNAs from the early region encode the viral small and large t-antigens; mRNAs from the late region encode the structural proteins, VP1, VP2 and VP3; the promoters of the early and late regions closely resemble host promoters and replication is therefore facilitated by host-cell machinery" /codon_start=1 /product="VP2" /protein_id="YP_003708379.1" /db_xref="GI:297591900" /db_xref="GeneID:29031016" /translation="MGAALTLLGDLIATVSEAAAATGFSVAEIAAGEAAAAIEVQLAS VATVEGLTTSEAIAAIGLTPQAYAVISGAPAAIAGFAALLQTVTGVSAVAQVGYRFFS DWDHKVSTVGLYQQPGMAVDLYRPDDYYDILFPGVQTFVHSVQYLDPRHWGPTLFNAI SQAFWRVIQNDIPRLTSQELERRTQRYLRDSLARFLEETTWTVINAPVNWYNSLQDYY STLSPIRPTMVRQVANREGLQISFGHTYDNIDEADSIQQVTERWEAQSQSPNVQSGEF IEKFEAPGGANQRTAPQWMLPLLLGLYGSVTSALKAYEDGPNKKKRKLSRGSSQKTKG TSASAKARHKRRNRSSRS" gene 916..1620 /locus_tag="SV40gp4" /db_xref="GeneID:29031017" CDS 916..1620 /locus_tag="SV40gp4" /note="VP3 minor structural protein" /codon_start=1 /product="hypothetical protein" /protein_id="YP_003708380.1" /db_xref="GI:297591901" /db_xref="GeneID:29031017" /translation="MAVDLYRPDDYYDILFPGVQTFVHSVQYLDPRHWGPTLFNAISQ AFWRVIQNDIPRLTSQELERRTQRYLRDSLARFLEETTWTVINAPVNWYNSLQDYYST LSPIRPTMVRQVANREGLQISFGHTYDNIDEADSIQQVTERWEAQSQSPNVQSGEFIE KFEAPGGANQRTAPQWMLPLLLGLYGSVTSALKAYEDGPNKKKRKLSRGSSQKTKGTS ASAKARHKRRNRSSRS" gene 1499..2593 /locus_tag="SV40gp5" /db_xref="GeneID:29031018" CDS 1499..2593 /locus_tag="SV40gp5" /note="VP1 major structural protein; VP1; major capsid protein of polyomavirus; 72 pentamers of VP1 comprise the outer capsid and form a T = 7 icosahedral lattice; VP1 contains an amino-terminal bipartite nuclear targeting signal that overlaps its DNA-binding-domain; The polyomaviruses are non-enveloped dsDNA viruses with a major capsid protein, VP1, that facilitates binding of genomic DNA and entry into target cells; the viral genome is organized into two divergent transcriptional units known as early and late regions; mRNAs from the early region encode the viral small and large t-antigens; mRNAs from the late region encode the structural proteins, VP1, VP2 and VP3" /codon_start=1 /product="Major capsid protein VP1" /protein_id="YP_003708381.1" /db_xref="GI:297591902" /db_xref="GeneID:29031018" /translation="MKMAPTKRKGSCPGAAPKKPKEPVQVPKLVIKGGIEVLGVKTGV DSFTEVECFLNPQMGNPDEHQKGLSKSLAAEKQFTDDSPDKEQLPCYSVARIPLPNLN EDLTCGNILMWEAVTVKTEVIGVTAMLNLHSGTQKTHENGAGKPIQGSNFHFFAVGGE PLELQGVLANYRTKYPAQTVTPKNATVDSQQMNTDHKAVLDKDNAYPVECWVPDPSKN ENTRYFGTYTGGENVPPVLHITNTATTVLLDEQGVGPLCKADSLYVSAVDICGLFTNT SGTQQWKGLPRYFKITLRKRSVKNPYPISFLLSDLINRRTQRVDGQPMIGMSSQVEEV RVYEDTEELPGDPDMIRYIDEFGQTTTRMQ" variation 1626 /locus_tag="SV40gp5" /note="g in wild-type; a in temperature-sensitive mutant tsC260" variation 1667 /locus_tag="SV40gp5" /note="c in wild-type; a in temperature-sensitive mutant tsB228" variation 1680 /locus_tag="SV40gp5" /note="c in wild-type; g in temperature-sensitive mutant tsB218" variation 1718 /locus_tag="SV40gp5" /note="g in wild-type; a in temperature-sensitive mutant tsB[204,211,265]" variation 1719 /locus_tag="SV40gp5" /note="c in wild-type; t in temperature-sensitive mutant tsB8" variation 1756 /locus_tag="SV40gp5" /note="a in wild-type; c in temperature-sensitive mutant tsB8" variation 1995 /locus_tag="SV40gp5" /note="g in wild-type; c in temperature-sensitive mutant tsB221" variation 2003 /locus_tag="SV40gp5" /note="g in wild-type; a in temperature-sensitive mutant tsB201" variation 2084 /locus_tag="SV40gp5" /note="c in wild-type; t in temperature-sensitive mutant tsBC223" variation 2091 /locus_tag="SV40gp5" /note="c in wild-type; c in temperature-sensitive mutant tsB4" variation 2141 /locus_tag="SV40gp5" /note="c in wild-type; t in temperature-sensitive mutant tsC219" variation 2237 /locus_tag="SV40gp5" /note="c in wild-type; a in temperature-sensitive mutant tsC240" variation 2262 /locus_tag="SV40gp5" /note="c in wild-type; t in temperature-sensitive mutant tsC260" variation 2354 /locus_tag="SV40gp5" /note="c in wild-type; t in temperature-sensitive mutant tsBC[208,214,216,217,248,274]" variation 2367 /locus_tag="SV40gp5" /note="a in wild-type; c in temperature-sensitive mutant tsBC11" prim_transcript complement(2587..5236) /note="early mRNA (alt.) [3],[8],[39],[46],[63]" prim_transcript complement(2587..5230) /note="early mRNA (alt.) [3],[39],[46],[78]" prim_transcript complement(2587..5225) /note="early mRNA (alt.) [3],[39],[46],[50],[63]" prim_transcript complement(2599..5236) /note="early mRNA (alt.) [8],[23],[46],[63]" prim_transcript complement(2599..5230) /note="early mRNA (alt.) [23],[78]" prim_transcript complement(2599..5225) /note="early mRNA (alt.) [23],[50],[63]" regulatory complement(2608..2613) /regulatory_class="polyA_signal_sequence" /note="early mRNA polyadenyation signal on the comp strand; 0.16 [23],[120]" regulatory complement(2637..2642) /regulatory_class="polyA_signal_sequence" /note="early mRNA polyadenyation signal on the comp strand; 0.16 [23],[120]" regulatory 2657..2662 /regulatory_class="polyA_signal_sequence" /note="late mRNA polyadenyation signal; 0.17 [23],[68], [120]" gene complement(2691..5163) /locus_tag="SV40gp6" /db_xref="GeneID:29031019" CDS complement(join(2691..4571,4918..5163)) /locus_tag="SV40gp6" /note="large T antigen; binds to the viral origin of replication; regulates the transcription of early region mRNA; helicase activity facilitates movement of the virion DNA replication fork; the small T antigen shares a region in common with the large T antigen known as the J-domain; the J-domain is required for multiple processes including assembly, viral genomic DNA replication and transcription; The polyomaviruses are non-enveloped dsDNA viruses; the viral genome is organized into two divergent transcriptional units known as early and late regions; mRNAs from the early region encode the viral small and large t-antigens; the small T antigen and large T antigen are expressed upon entry into the host nucleus early in the viral lifecycle" /codon_start=1 /product="large T antigen" /protein_id="YP_003708382.1" /db_xref="GI:297591903" /db_xref="GeneID:29031019" /translation="MDKVLNREESLQLMDLLGLERSAWGNIPLMRKAYLKKCKEFHPD KGGDEEKMKKMNTLYKKMEDGVKYAHQPDFGGFWDATEIPTYGTDEWEQWWNAFNEEN LFCSEEMPSSDDEATADSQHSTPPKKKRKVEDPKDFPSELLSFLSHAVFSNRTLACFA IYTTKEKAALLYKKIMEKYSVTFISRHNSYNHNILFFLTPHRHRVSAINNYAQKLCTF SFLICKGVNKEYLMYSALTRDPFSVIEESLPGGLKEHDFNPEEAEETKQVSWKLVTEY AMETKCDDVLLLLGMYLEFQYSFEMCLKCIKKEQPSHYKYHEKHYANAAIFADSKNQK TICQQAVDTVLAKKRVDSLQLTREQMLTNRFNDLLDRMDIMFGSTGSADIEEWMAGVA WLHCLLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNV NLPLDRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQGINNLDNLRDYLDGSVKVN LEKKHLNKRTQIFPPGIVTMNEYSVPKTLQARFVKQIDFRPKDYLKHCLERSEFLLEK RIIQSGIALLLMLIWYRPVAEFAQSIQSRIVEWKERLDKEFSLSVYQKMKFNVAMGIG VLDWLRNSDDDDEDSQENADKNEDGGEKNMEDSGHETGIDSQSQGSFQAPQSSQSVHD HNQPYHICRGFTCFKKPPTPPPEPET" gene complement(2842..2907) /locus_tag="SV40gs1" /db_xref="GeneID:29031020" misc_RNA complement(2842..2907) /locus_tag="SV40gs1" /note="SV40-associated small (SAS) RNA; 0.21 [64]" /db_xref="GeneID:29031020" intron complement(4572..4917) /locus_tag="SV40gp6" /note="large T antigen (18s) intron [32],[38]; does not fit consensus" intron complement(4572..4636) /locus_tag="SV40gp6" /note="early 19s mRNA (small t antigen) intron [32],[38]; does not fit consensus" gene complement(4639..5163) /locus_tag="SV40gp7" /db_xref="GeneID:29031021" CDS complement(4639..5163) /locus_tag="SV40gp7" /note="small t antigen; small T-antigen; promotes the efficient replication of genomic DNA; binds to and negativley regulates the function of protein phosphotase (PP2A) thereby accelerating the progression to S-phase; the small T-antigen shares a region in common with the large T-antigen known as the J-domain; the J-domain is required for multiple processes including assembly, viral genomic DNA replication and transcription; The polyomaviruses are non-enveloped dsDNA viruses; the viral genome is organized into two divergent transcriptional units known as early and late regions; mRNAs from the early region encode the viral small and large t-antigens; the small T antigen and large T antigen are expressed upon entry into the host nucleus early in the viral lifecycle; the small T antigen is not essential for replication in all cell lines" /codon_start=1 /product="Small T antigen" /protein_id="YP_003708383.1" /db_xref="GI:297591904" /db_xref="GeneID:29031021" /translation="MDKVLNREESLQLMDLLGLERSAWGNIPLMRKAYLKKCKEFHPD KGGDEEKMKKMNTLYKKMEDGVKYAHQPDFGGFWDATEVFASSLNPGVDAMYCKQWPE CAKKMSANCICLLCLLRMKHENRKLYRKDPLVWVDCYCFDCFRMWFGLDLCEGTLLLW CDIIGQTTYRDLKL" protein_bind complement(5184..5209) /bound_moiety="large T-antigen" ORIGIN 1 gcctcggcct ctgcataaat aaaaaaaatt agtcagccat ggggcggaga atgggcggaa 61 ctgggcggag ttaggggcgg gatgggcgga gttaggggcg ggactatggt tgctgactaa 121 ttgagatgca tgctttgcat acttctgcct gctggggagc ctggggactt tccacacctg 181 gttgctgact aattgagatg catgctttgc atacttctgc ctgctgggga gcctggggac 241 tttccacacc ctaactgaca cacattccac agctggttct ttccgcctca gaaggtacct 301 aaccaagttc ctctttcaga ggttatttca ggccatggtg ctgcgccggc tgtcacgcca 361 ggcctccgtt aaggttcgta ggtcatggac tgaaagtaaa aaaacagctc aacgcctttt 421 tgtgtttgtt ttagagcttt tgctgcaatt ttgtgaaggg gaagatactg ttgacgggaa 481 acgcaaaaaa ccagaaaggt taactgaaaa accagaaagt taactggtaa gtttagtctt 541 tttgtctttt atttcaggtc catgggtgct gctttaacac tgttggggga cctaattgct 601 actgtgtctg aagctgctgc tgctactgga ttttcagtag ctgaaattgc tgctggagag 661 gccgctgctg caattgaagt gcaacttgca tctgttgcta ctgttgaagg cctaacaacc 721 tctgaggcaa ttgctgctat aggcctcact ccacaggcct atgctgtgat atctggggct 781 cctgctgcta tagctggatt tgcagcttta ctgcaaactg tgactggtgt gagcgctgtt 841 gctcaagtgg ggtatagatt ttttagtgac tgggatcaca aagtttctac tgttggttta 901 tatcaacaac caggaatggc tgtagatttg tataggccag atgattacta tgatatttta 961 tttcctggag tacaaacctt tgttcacagt gttcagtatc ttgaccccag acattggggt 1021 ccaacacttt ttaatgccat ttctcaagct ttttggcgtg taatacaaaa tgacattcct 1081 aggctcacct cacaggagct tgaaagaaga acccaaagat atttaaggga cagtttggca 1141 aggtttttag aggaaactac ttggacagta attaatgctc ctgttaattg gtataactct 1201 ttacaagatt actactctac tttgtctccc attaggccta caatggtgag acaagtagcc 1261 aacagggaag ggttgcaaat atcatttggg cacacctatg ataatattga tgaagcagac 1321 agtattcagc aagtaactga gaggtgggaa gctcaaagcc aaagtcctaa tgtgcagtca 1381 ggtgaattta ttgaaaaatt tgaggctcct ggtggtgcaa atcaaagaac tgctcctcag 1441 tggatgttgc ctttacttct aggcctgtac ggaagtgtta cttctgctct aaaagcttat 1501 gaagatggcc ccaacaaaaa gaaaaggaag ttgtccaggg gcagctccca aaaaaccaaa 1561 ggaaccagtg caagtgccaa agctcgtcat aaaaggagga atagaagttc taggagttaa 1621 aactggagta gacagcttca ctgaggtgga gtgcttttta aatcctcaaa tgggcaatcc 1681 tgatgaacat caaaaaggct taagtaaaag cttagcagct gaaaaacagt ttacagatga 1741 ctctccagac aaagaacaac tgccttgcta cagtgtggct agaattcctt tgcctaattt 1801 aaatgaggac ttaacctgtg gaaatatttt gatgtgggaa gctgttactg ttaaaactga 1861 ggttattggg gtaactgcta tgttaaactt gcattcaggg acacaaaaaa ctcatgaaaa 1921 tggtgctgga aaacccattc aagggtcaaa ttttcatttt tttgctgttg gtggggaacc 1981 tttggagctg cagggtgtgt tagcaaacta caggaccaaa tatcctgctc aaactgtaac 2041 cccaaaaaat gctacagttg acagtcagca gatgaacact gaccacaagg ctgttttgga 2101 taaggataat gcttatccag tggagtgctg ggttcctgat ccaagtaaaa atgaaaacac 2161 tagatatttt ggaacctaca caggtgggga aaatgtgcct cctgttttgc acattactaa 2221 cacagcaacc acagtgcttc ttgatgagca gggtgttggg cccttgtgca aagctgacag 2281 cttgtatgtt tctgctgttg acatttgtgg gctgtttacc aacacttctg gaacacagca 2341 gtggaaggga cttcccagat attttaaaat tacccttaga aagcggtctg tgaaaaaccc 2401 ctacccaatt tcctttttgt taagtgacct aattaacagg aggacacaga gggtggatgg 2461 gcagcctatg attggaatgt cctctcaagt agaggaggtt agggtttatg aggacacaga 2521 ggagcttcct ggggatccag acatgataag atacattgat gagtttggac aaaccacaac 2581 tagaatgcag tgaaaaaaat gctttatttg tgaaatttgt gatgctattg ctttatttgt 2641 aaccattata agctgcaata aacaagttaa caacaacaat tgcattcatt ttatgtttca 2701 ggttcagggg gaggtgtggg aggtttttta aagcaagtaa aacctctaca aatgtggtat 2761 ggctgattat gatcatgaac agactgtgag gactgagggg cctgaaatga gccttgggac 2821 tgtgaatcaa tgcctgtttc atgccctgag tcttccatgt tcttctcccc accatcttca 2881 tttttatcag cattttcctg gctgtcttca tcatcatcat cactgtttct tagccaatct 2941 aaaactccaa ttcccatagc cacattaaac ttcatttttt gatacactga caaactaaac 3001 tctttgtcca atctctcttt ccactccaca attctgctct gaatactttg agcaaactca 3061 gccacaggtc tgtaccaaat taacataaga agcaaagcaa tgccactttg aattattctc 3121 ttttctaaca aaaactcact gcgttccagg caatgcttta aataatcttt gggcctaaaa 3181 tctatttgtt ttacaaatct ggcctgcagt gttttaggca cactgtactc attcatggtg 3241 actattccag ggggaaatat ttgagttctt ttatttaggt gtttcttttc taagtttacc 3301 ttaacactgc catccaaata atcccttaaa ttgtccaggt tattaattcc ctgacctgaa 3361 ggcaaatctc tggactcccc tccagtgccc tttacatcct caaaaactac taaaaactgg 3421 tcaatagcta ctcctagctc aaagttcagc ctgtccaagg gcaaattaac atttaaagct 3481 ttccccccac ataattcaag caaagcagct gctaatgtag ttttaccact atcaattggt 3541 cctttaaaca gccagtatct ttttttagga atgttgtaca ccatgcattt taaaaagtca 3601 tacaccactg aatccatttt gggcaacaaa cagtgtagcc aagcaactcc agccatccat 3661 tcttctatgt cagcagagcc tgtagaacca aacattatat ccatcctatc caaaagatca 3721 ttaaatctgt ttgttaacat ttgttctcta gttaattgta ggctatcaac ccgcttttta 3781 gctaaaacag tatcaacagc ctgttggcat atggtttttt ggtttttgct gtcagcaaat 3841 atagcagcat ttgcataatg cttttcatgg tacttatagt ggctgggctg ttctttttta 3901 atacatttta aacacatttc aaaactgtac tgaaattcca agtacatccc aagcaataac 3961 aacacatcat cacattttgt ttccattgca tactctgtta caagcttcca ggacacttgt 4021 ttagtttcct ctgcttcttc tggattaaaa tcatgctcct ttaacccacc tggcaaactt 4081 tcctcaataa cagaaaatgg atctctagtc aaggcactat acatcaaata ttccttatta 4141 acccctttac aaattaaaaa gctaaaggta cacaattttt gagcatagtt attaatagca 4201 gacactctat gcctgtgtgg agtaagaaaa aacagtatgt tatgattata actgttatgc 4261 ctacttataa aggttacaga atatttttcc ataattttct tgtatagcag tgcagctttt 4321 tcctttgtgg tgtaaatagc aaagcaagca agagttctat tactaaacac agcatgactc 4381 aaaaaactta gcaattctga aggaaagtcc ttggggtctt ctacctttct cttctttttt 4441 ggaggagtag aatgttgaga gtcagcagta gcctcatcat cactagatgg catttcttct 4501 gagcaaaaca ggttttcctc attaaaggca ttccaccact gctcccattc atcagttcca 4561 taggttggaa tctaaaatac acaaacaatt agaatcagta gtttaacaca ttatacactt 4621 aaaaatttta tatttacctt agagctttaa atctctgtag gtagtttgtc caattatgtc 4681 acaccacaga agtaaggttc cttcacaaag atcaagtcca aaccacattc taaagcaatc 4741 gaagcagtag caatcaaccc acacaagtgg atctttcctg tataattttc tattttcatg 4801 cttcatcctc agtaagcaca gcaagcatat gcagttagca gacattttct ttgcacactc 4861 aggccattgt ttgcagtaca ttgcatcaac accaggattt aaggaagaag caaatacctc 4921 agttgcatcc cagaagcctc caaagtcagg ttgatgagca tattttactc catcttccat 4981 tttcttgtac agagtattca ttttcttcat tttttcttca tctcctcctt tatcaggatg 5041 aaactccttg cattttttta aatatgcctt tctcatcaga ggaatattcc cccaggcact 5101 cctttcaaga cctagaaggt ccattagctg caaagattcc tctctgttta aaactttatc 5161 catctttgca aagctttttg caaaagccta ggcctccaaa aaagcctcct cactacttct 5221 ggaatagctc agaggccgag gcg //