Database: RefSeq
Entry: NC_001422
LinkDB: NC_001422
Original site: NC_001422 
LOCUS       NC_001422               5386 bp ss-DNA     circular PHG 06-JUL-2018
DEFINITION  Coliphage phi-X174, complete genome.
VERSION     NC_001422.1
DBLINK      BioProject: PRJNA14015
SOURCE      Escherichia virus phiX174
  ORGANISM  Escherichia virus phiX174
            Viruses; ssDNA viruses; Microviridae; Bullavirinae;
REFERENCE   1  (bases 2380 to 2512; 2593 to 2786; 2788 to 2947)
  AUTHORS   Air,G.M., Els,M.C., Brown,L.E., Laver,W.G. and Webster,R.G.
  TITLE     Location of antigenic sites on the three-dimensional structure of
            the influenza N2 virus neuraminidase
  JOURNAL   Virology 145 (2), 237-248 (1985)
   PUBMED   2411049
REFERENCE   2  (bases 1064 to 1757)
  AUTHORS   Merville,M.P., Piette,J., Lopez,M., Decuyper,J. and van de Vorst,A.
  TITLE     Termination sites of the in vitro DNA synthesis on single-stranded
            DNA photosensitized by promazines
  JOURNAL   J. Biol. Chem. 259 (24), 15069-15077 (1984)
   PUBMED   6239864
REFERENCE   3  (bases 449 to 482; 504 to 598; 1047 to 1111)
  AUTHORS   Ueda,K., Morita,J. and Komano,T.
  TITLE     Sequence specificity of heat-labile sites in DNA induced by
            mitomycin C
  JOURNAL   Biochemistry 23 (8), 1634-1640 (1984)
   PUBMED   6232949
REFERENCE   4  (bases 436 to 490; 630 to 669; 930 to 979)
  AUTHORS   Takeshita,M., Kappen,L.S., Grollman,A.P., Eisenberg,M. and
  TITLE     Strand scission of deoxyribonucleic acid by neocarzinostatin,
            auromomycin, and bleomycin: studies on base release and nucleotide
            sequence specificity
  JOURNAL   Biochemistry 20 (26), 7599-7606 (1981)
   PUBMED   6173064
REFERENCE   5  (bases 4248 to 4332)
  AUTHORS   Heidekamp,F., Langeveld,S.A., Baas,P.D. and Jansz,H.S.
  TITLE     Studies of the recognition sequence of phi X174 gene A protein.
            Cleavage site of phi X gene A protein in St-1 RFI DNA
  JOURNAL   Nucleic Acids Res. 8 (9), 2009-2021 (1980)
   PUBMED   6253953
REFERENCE   6  (bases 4256 to 4317)
  AUTHORS   Langeveld,S.A., van Mansfeld,A.D., de Winter,J.M. and Weisbeek,P.J.
  TITLE     Cleavage of single-stranded DNA by the A and A* proteins of
            bacteriophage phi X174
  JOURNAL   Nucleic Acids Res. 7 (8), 2177-2188 (1979)
   PUBMED   160544
REFERENCE   7  (bases 1290 to 1302; 1340 to 1430; 1510 to 1570; 1600 to 1750)
  AUTHORS   Air,G.M., Coulson,A.R., Fiddes,J.C., Friedmann,T., Hutchison,C.A.
            III, Sanger,F., Slocombe,P.M. and Smith,A.J.
  TITLE     Nucleotide sequence of the F protein coding region of bacteriophage
            phiX174 and the amino acid sequence of its product
  JOURNAL   J. Mol. Biol. 125 (2), 247-254 (1978)
   PUBMED   731694
REFERENCE   8  (bases 1 to 5386)
  AUTHORS   Sanger,F., Coulson,A.R., Friedmann,T., Air,G.M., Barrell,B.G.,
            Brown,N.L., Fiddes,J.C., Hutchison,C.A. III, Slocombe,P.M. and
  TITLE     The nucleotide sequence of bacteriophage phiX174
  JOURNAL   J. Mol. Biol. 125 (2), 225-246 (1978)
   PUBMED   731693
REFERENCE   9  (sites)
  AUTHORS   Fiddes,J.C.
  TITLE     The nucleotide sequence of a viral DNA
  JOURNAL   Sci. Am. 237 (6), 54-67 (1977)
   PUBMED   929160
REFERENCE   10 (bases 4505 to 5374)
  AUTHORS   Brown,N.L. and Smith,M.
  TITLE     The sequence of a region of bacteriophage phiX174 DNA coding for
            parts of genes A and B
  JOURNAL   J. Mol. Biol. 116 (1), 1-28 (1977)
   PUBMED   592379
REFERENCE   11 (bases 1 to 5375)
  AUTHORS   Sanger,F., Air,G.M., Barrell,B.G., Brown,N.L., Coulson,A.R.,
            Fiddes,C.A., Hutchison,C.A., Slocombe,P.M. and Smith,M.
  TITLE     Nucleotide sequence of bacteriophage phi X174 DNA
  JOURNAL   Nature 265 (5596), 687-695 (1977)
   PUBMED   870828
REFERENCE   12 (bases 5346 to 5386; 1 to 159)
  AUTHORS   Smith,M., Brown,N.L., Air,G.M., Barrell,B.G., Coulson,A.R.,
            Hutchison,C.A. III and Sanger,F.
  TITLE     DNA sequence at the C termini of the overlapping genes A and B in
            bacteriophage phi X174
  JOURNAL   Nature 265 (5596), 702-705 (1977)
   PUBMED   859575
REFERENCE   13 (bases 5022 to 5132)
  AUTHORS   Brown,N.L. and Smith,M.
  TITLE     DNA sequence of a region of the phi X174 genome coding for a
            ribosome binding site
  JOURNAL   Nature 265 (5596), 695-698 (1977)
   PUBMED   859573
REFERENCE   14 (bases 2395 to 2922)
  AUTHORS   Air,G.M., Sanger,F. and Coulson,A.R.
  TITLE     Nucleotide and amino acid sequences of gene G of omegaX174
  JOURNAL   J. Mol. Biol. 108 (3), 519-533 (1976)
   PUBMED   1088827
REFERENCE   15 (bases 1017 to 1762)
  AUTHORS   Air,G.M., Blackburn,E.H., Coulson,A.R., Galibert,F., Sanger,F.,
            Sedat,J.W. and Ziff,E.B.
  TITLE     Gene F of bacteriophage phiX174. Correlation of nucleotide
            sequences from the DNA and amino acid sequences from the gene
  JOURNAL   J. Mol. Biol. 107 (4), 445-458 (1976)
   PUBMED   1088826
REFERENCE   16 (bases 1017 to 1081)
  AUTHORS   Sedat,J., Ziff,E. and Galibert,F.
  TITLE     Direct determination of DNA nucleotide sequences. Structure of
            large specific fragments of bacteriophage phiX174 DNA
  JOURNAL   J. Mol. Biol. 107 (4), 391-416 (1976)
   PUBMED   1003475
REFERENCE   17 (bases 730 to 903)
  AUTHORS   Blackburn,E.H.
  TITLE     Transcription and sequence analysis of a fragment of bacteriophage
            phiX174 DNA
  JOURNAL   J. Mol. Biol. 107 (4), 417-431 (1976)
   PUBMED   826641
REFERENCE   18 (bases 2263 to 2421)
  AUTHORS   Fiddes,J.C.
  TITLE     Nucleotide sequence of the intercistronic region between genes G
            and F in bacteriophage phiX174 DNA
  JOURNAL   J. Mol. Biol. 107 (1), 1-24 (1976)
   PUBMED   826639
REFERENCE   19 (bases 4137 to 4207)
  AUTHORS   Mansfeld,A.D., Vereijken,J.M. and Jansz,H.S.
  TITLE     The nucleotide sequence of a DNA fragment, 71 base pairs in length,
            near the origin of DNA replication of bacteriophage 0X174
  JOURNAL   Nucleic Acids Res. 3 (10), 2827-2844 (1976)
   PUBMED   995652
REFERENCE   20 (bases 2365 to 2591)
  AUTHORS   Air,G.M., Blackburn,E.H., Sanger,F. and Coulson,A.R.
  TITLE     The nucleotide and amino acid sequences of the N (5') terminal
            region of gene G of bacteriophage phiphiX 174
  JOURNAL   J. Mol. Biol. 96 (4), 703-719 (1975)
   PUBMED   1081600
REFERENCE   21 (bases 2370 to 2420)
  AUTHORS   Barrell,B.G., Weith,H.L., Donelson,J.E. and Robertson,H.D.
  TITLE     Sequence analysis of the ribosome-protected bacteriophase phiX174
            DNA fragment containing the gene G initiation site
  JOURNAL   J. Mol. Biol. 92 (3), 377-393 (1975)
   PUBMED   1095758
REFERENCE   22 (bases 2370 to 2421)
  AUTHORS   Robertson,H.D., Barrell,B.G., Weith,H.L. and Donelson,J.E.
  TITLE     Isolation and sequence analysis of a ribosome-protected fragment
            from bacteriophage phiX 174 DNA
  JOURNAL   Nature New Biol. 241 (106), 38-40 (1973)
   PUBMED   4572838
REFERENCE   23 (bases 1047 to 1094)
  AUTHORS   Ziff,E.B., Sedat,J.W. and Galibert,F.
  TITLE     Determination of the nucleotide sequence of a fragment of
            bacteriophage phiX 174 DNA
  JOURNAL   Nature New Biol. 241 (106), 34-37 (1973)
   PUBMED   4349156
REFERENCE   24 (bases 1 to 5386)
  CONSRTM   NCBI Genome Project
  TITLE     Direct Submission
  JOURNAL   Submitted (06-JUL-2018) 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 J02482.
            [8]  intermittent sequences.
            [15]  review; discussion of complete genome.
            Double checked with sumex tape.
            Single-stranded circular DNA which codes for eleven proteins.
            Replicative form is duplex, icosahedron, related to s13 & g4. [21]
            indicates that mitomycin C reduced with sodium borohydride induced
            heat-labile sites in DNA most preferentially at dinucleotide
            sequence 'gt' (especially 'Pu-g-t').
            Bacteriophage phi-X174 single stranded DNA molecules were
            irradiated with near UV light in the presence of promazine
            derivatives, after priming with restriction fragments or synthetic
            primers [22].  The resulting DNA fragments were used as templates
            for in vitro complementary chain synthesis by E.coli DNA polymerase
            I [22].  More than 90% of the observed chain terminations were
            mapped one nucleotide before a guanine residue [22].  Photoreaction
            occurred more predominantly with guanine residues localized in
            single-stranded parts of the genome [22].  These same guanine
            residues could also be damaged when the reaction was performed in
            the dark, in the presence of promazine cation radicals [22].
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..5386
                     /organism="Escherichia virus phiX174"
                     /mol_type="genomic DNA"
     gene            join(3981..5386,1..136)
     CDS             join(3981..5386,1..136)
                     /function="viral strand synthesis"
                     /note="rf replication"
     misc_feature    join(4002..5386,1..133)
                     /note="DNA replication initiation protein gpA; Region: A;
     gene            join(4497..5386,1..136)
     CDS             join(4497..5386,1..136)
                     /function="shut off host DNA synthesis"
     misc_feature    join(<4497..5386,1..133)
                     /note="Bacteriophage replication gene A protein (GPA);
                     Region: Phage_GPA; cl15276"
     gene            join(5075..5386,1..51)
     CDS             join(5075..5386,1..51)
                     /function="capsid morphogenesis"
     misc_feature    join(5084..5386,1..48)
                     /note="Scaffold protein B; Region: Phage_B; pfam02304"
     variation       23
                     /note="in am18 and am35 [14]"
     variation       25
                     /note="ts116 [14]"
     gene            51..221
     CDS             51..221
     misc_feature    51..218
                     /note="Bacteriophage protein K; Region: Protein_K;
     variation       57
                     /note="am6 [14]"
     variation       117
                     /note="am6 [14]"
     gene            133..393
     CDS             133..393
                     /note="DNA maturation"
     misc_feature    145..348
                     /note="Phage protein C; Region: Phage_C; pfam12025"
     gene            358..3975
     mRNA            358..3975
                     /product="major transcript"
     gene            358..991
     mRNA            358..991
                     /product="minor transcript"
     CDS             390..848
                     /function="capsid morphogenesis"
     misc_feature    393..845
                     /note="external scaffolding protein; Region: D; PHA00006"
     gene            568..843
     CDS             568..843
                     /function="cell lysis"
     misc_feature    568..840
                     /note="cell lysis protein; Region: E; PHA00007"
     gene            848..964
     CDS             848..964
                     /note="core protein; DNA condensation"
     misc_feature    851..961
                     /note="Microvirus J protein; Region: Microvir_J;
     CDS             1001..2284
                     /note="major coat protein"
     misc_feature    1001..2281
                     /note="capsid protein; Region: F; PHA00009"
     gene            2395..2922
     CDS             2395..2922
                     /note="major spike protein"
     misc_feature    2395..2919
                     /note="Major spike protein (G protein); Region: Phage_G;
     gene            2931..3917
     CDS             2931..3917
                     /note="minor spike protein"
     misc_feature    2982..3911
                     /note="Microvirus H protein (pilot protein); Region:
                     Microvir_H; cl27995"
     misc_feature    3962
                     /note="transcription start site"
     rep_origin      4306
                     /note="origin of viral strand synthesis"
     misc_feature    4899
                     /note="transcription start site"
        1 gagttttatc gcttccatga cgcagaagtt aacactttcg gatatttctg atgagtcgaa
       61 aaattatctt gataaagcag gaattactac tgcttgttta cgaattaaat cgaagtggac
      121 tgctggcgga aaatgagaaa attcgaccta tccttgcgca gctcgagaag ctcttacttt
      181 gcgacctttc gccatcaact aacgattctg tcaaaaactg acgcgttgga tgaggagaag
      241 tggcttaata tgcttggcac gttcgtcaag gactggttta gatatgagtc acattttgtt
      301 catggtagag attctcttgt tgacatttta aaagagcgtg gattactatc tgagtccgat
      361 gctgttcaac cactaatagg taagaaatca tgagtcaagt tactgaacaa tccgtacgtt
      421 tccagaccgc tttggcctct attaagctca ttcaggcttc tgccgttttg gatttaaccg
      481 aagatgattt cgattttctg acgagtaaca aagtttggat tgctactgac cgctctcgtg
      541 ctcgtcgctg cgttgaggct tgcgtttatg gtacgctgga ctttgtggga taccctcgct
      601 ttcctgctcc tgttgagttt attgctgccg tcattgctta ttatgttcat cccgtcaaca
      661 ttcaaacggc ctgtctcatc atggaaggcg ctgaatttac ggaaaacatt attaatggcg
      721 tcgagcgtcc ggttaaagcc gctgaattgt tcgcgtttac cttgcgtgta cgcgcaggaa
      781 acactgacgt tcttactgac gcagaagaaa acgtgcgtca aaaattacgt gcggaaggag
      841 tgatgtaatg tctaaaggta aaaaacgttc tggcgctcgc cctggtcgtc cgcagccgtt
      901 gcgaggtact aaaggcaagc gtaaaggcgc tcgtctttgg tatgtaggtg gtcaacaatt
      961 ttaattgcag gggcttcggc cccttacttg aggataaatt atgtctaata ttcaaactgg
     1021 cgccgagcgt atgccgcatg acctttccca tcttggcttc cttgctggtc agattggtcg
     1081 tcttattacc atttcaacta ctccggttat cgctggcgac tccttcgaga tggacgccgt
     1141 tggcgctctc cgtctttctc cattgcgtcg tggccttgct attgactcta ctgtagacat
     1201 ttttactttt tatgtccctc atcgtcacgt ttatggtgaa cagtggatta agttcatgaa
     1261 ggatggtgtt aatgccactc ctctcccgac tgttaacact actggttata ttgaccatgc
     1321 cgcttttctt ggcacgatta accctgatac caataaaatc cctaagcatt tgtttcaggg
     1381 ttatttgaat atctataaca actattttaa agcgccgtgg atgcctgacc gtaccgaggc
     1441 taaccctaat gagcttaatc aagatgatgc tcgttatggt ttccgttgct gccatctcaa
     1501 aaacatttgg actgctccgc ttcctcctga gactgagctt tctcgccaaa tgacgacttc
     1561 taccacatct attgacatta tgggtctgca agctgcttat gctaatttgc atactgacca
     1621 agaacgtgat tacttcatgc agcgttacca tgatgttatt tcttcatttg gaggtaaaac
     1681 ctcttatgac gctgacaacc gtcctttact tgtcatgcgc tctaatctct gggcatctgg
     1741 ctatgatgtt gatggaactg accaaacgtc gttaggccag ttttctggtc gtgttcaaca
     1801 gacctataaa cattctgtgc cgcgtttctt tgttcctgag catggcacta tgtttactct
     1861 tgcgcttgtt cgttttccgc ctactgcgac taaagagatt cagtacctta acgctaaagg
     1921 tgctttgact tataccgata ttgctggcga ccctgttttg tatggcaact tgccgccgcg
     1981 tgaaatttct atgaaggatg ttttccgttc tggtgattcg tctaagaagt ttaagattgc
     2041 tgagggtcag tggtatcgtt atgcgccttc gtatgtttct cctgcttatc accttcttga
     2101 aggcttccca ttcattcagg aaccgccttc tggtgatttg caagaacgcg tacttattcg
     2161 ccaccatgat tatgaccagt gtttccagtc cgttcagttg ttgcagtgga atagtcaggt
     2221 taaatttaat gtgaccgttt atcgcaatct gccgaccact cgcgattcaa tcatgacttc
     2281 gtgataaaag attgagtgtg aggttataac gccgaagcgg taaaaatttt aatttttgcc
     2341 gctgaggggt tgaccaagcg aagcgcggta ggttttctgc ttaggagttt aatcatgttt
     2401 cagactttta tttctcgcca taattcaaac tttttttctg ataagctggt tctcacttct
     2461 gttactccag cttcttcggc acctgtttta cagacaccta aagctacatc gtcaacgtta
     2521 tattttgata gtttgacggt taatgctggt aatggtggtt ttcttcattg cattcagatg
     2581 gatacatctg tcaacgccgc taatcaggtt gtttctgttg gtgctgatat tgcttttgat
     2641 gccgacccta aattttttgc ctgtttggtt cgctttgagt cttcttcggt tccgactacc
     2701 ctcccgactg cctatgatgt ttatcctttg aatggtcgcc atgatggtgg ttattatacc
     2761 gtcaaggact gtgtgactat tgacgtcctt ccccgtacgc cgggcaataa cgtttatgtt
     2821 ggtttcatgg tttggtctaa ctttaccgct actaaatgcc gcggattggt ttcgctgaat
     2881 caggttatta aagagattat ttgtctccag ccacttaagt gaggtgattt atgtttggtg
     2941 ctattgctgg cggtattgct tctgctcttg ctggtggcgc catgtctaaa ttgtttggag
     3001 gcggtcaaaa agccgcctcc ggtggcattc aaggtgatgt gcttgctacc gataacaata
     3061 ctgtaggcat gggtgatgct ggtattaaat ctgccattca aggctctaat gttcctaacc
     3121 ctgatgaggc cgcccctagt tttgtttctg gtgctatggc taaagctggt aaaggacttc
     3181 ttgaaggtac gttgcaggct ggcacttctg ccgtttctga taagttgctt gatttggttg
     3241 gacttggtgg caagtctgcc gctgataaag gaaaggatac tcgtgattat cttgctgctg
     3301 catttcctga gcttaatgct tgggagcgtg ctggtgctga tgcttcctct gctggtatgg
     3361 ttgacgccgg atttgagaat caaaaagagc ttactaaaat gcaactggac aatcagaaag
     3421 agattgccga gatgcaaaat gagactcaaa aagagattgc tggcattcag tcggcgactt
     3481 cacgccagaa tacgaaagac caggtatatg cacaaaatga gatgcttgct tatcaacaga
     3541 aggagtctac tgctcgcgtt gcgtctatta tggaaaacac caatctttcc aagcaacagc
     3601 aggtttccga gattatgcgc caaatgctta ctcaagctca aacggctggt cagtatttta
     3661 ccaatgacca aatcaaagaa atgactcgca aggttagtgc tgaggttgac ttagttcatc
     3721 agcaaacgca gaatcagcgg tatggctctt ctcatattgg cgctactgca aaggatattt
     3781 ctaatgtcgt cactgatgct gcttctggtg tggttgatat ttttcatggt attgataaag
     3841 ctgttgccga tacttggaac aatttctgga aagacggtaa agctgatggt attggctcta
     3901 atttgtctag gaaataaccg tcaggattga caccctccca attgtatgtt ttcatgcctc
     3961 caaatcttgg aggctttttt atggttcgtt cttattaccc ttctgaatgt cacgctgatt
     4021 attttgactt tgagcgtatc gaggctctta aacctgctat tgaggcttgt ggcatttcta
     4081 ctctttctca atccccaatg cttggcttcc ataagcagat ggataaccgc atcaagctct
     4141 tggaagagat tctgtctttt cgtatgcagg gcgttgagtt cgataatggt gatatgtatg
     4201 ttgacggcca taaggctgct tctgacgttc gtgatgagtt tgtatctgtt actgagaagt
     4261 taatggatga attggcacaa tgctacaatg tgctccccca acttgatatt aataacacta
     4321 tagaccaccg ccccgaaggg gacgaaaaat ggtttttaga gaacgagaag acggttacgc
     4381 agttttgccg caagctggct gctgaacgcc ctcttaagga tattcgcgat gagtataatt
     4441 accccaaaaa gaaaggtatt aaggatgagt gttcaagatt gctggaggcc tccactatga
     4501 aatcgcgtag aggctttgct attcagcgtt tgatgaatgc aatgcgacag gctcatgctg
     4561 atggttggtt tatcgttttt gacactctca cgttggctga cgaccgatta gaggcgtttt
     4621 atgataatcc caatgctttg cgtgactatt ttcgtgatat tggtcgtatg gttcttgctg
     4681 ccgagggtcg caaggctaat gattcacacg ccgactgcta tcagtatttt tgtgtgcctg
     4741 agtatggtac agctaatggc cgtcttcatt tccatgcggt gcactttatg cggacacttc
     4801 ctacaggtag cgttgaccct aattttggtc gtcgggtacg caatcgccgc cagttaaata
     4861 gcttgcaaaa tacgtggcct tatggttaca gtatgcccat cgcagttcgc tacacgcagg
     4921 acgctttttc acgttctggt tggttgtggc ctgttgatgc taaaggtgag ccgcttaaag
     4981 ctaccagtta tatggctgtt ggtttctatg tggctaaata cgttaacaaa aagtcagata
     5041 tggaccttgc tgctaaaggt ctaggagcta aagaatggaa caactcacta aaaaccaagc
     5101 tgtcgctact tcccaagaag ctgttcagaa tcagaatgag ccgcaacttc gggatgaaaa
     5161 tgctcacaat gacaaatctg tccacggagt gcttaatcca acttaccaag ctgggttacg
     5221 acgcgacgcc gttcaaccag atattgaagc agaacgcaaa aagagagatg agattgaggc
     5281 tgggaaaagt tactgtagcc gacgttttgg cggcgcaacc tgtgacgaca aatctgctca
     5341 aatttatgcg cgcttcgata aaaatgattg gcgtatccaa cctgca
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