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LOCUS NC_001422 5386 bp ss-DNA circular PHG 09-JUL-2002
DEFINITION Coliphage phiX174, complete genome.
VERSION NC_001422.1 GI:9626372
SOURCE coliphage phiX174.
ORGANISM coliphage phiX174
Viruses; ssDNA viruses; Microviridae; Microvirus.
REFERENCE 1 (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)
MEDLINE 73161741
PUBMED 4349156
REFERENCE 2 (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)
MEDLINE 73161742
PUBMED 4572838
REFERENCE 3 (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)
MEDLINE 75192039
PUBMED 1095758
REFERENCE 4 (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)
MEDLINE 76072037
PUBMED 1081600
REFERENCE 5 (bases 2263 to 2421)
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)
MEDLINE 77074135
PUBMED 826639
REFERENCE 6 (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)
MEDLINE 77057432
PUBMED 995652
REFERENCE 7 (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)
MEDLINE 77074161
PUBMED 826641
REFERENCE 8 (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)
MEDLINE 77074160
PUBMED 1003475
REFERENCE 9 (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)
MEDLINE 77074163
PUBMED 1088826
REFERENCE 10 (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)
MEDLINE 77121207
PUBMED 1088827
REFERENCE 11 (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)
MEDLINE 77171176
PUBMED 859573
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)
MEDLINE 77171178
PUBMED 859575
REFERENCE 13 (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 Nucliotide sequence of bacteriophage phi X174 DNA
JOURNAL Nature 265 (5596), 687-695 (1977)
MEDLINE 77171175
PUBMED 870828
REFERENCE 14 (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)
MEDLINE 78069208
PUBMED 592379
REFERENCE 15 (sites)
TITLE The nucleotide sequence of a viral DNA
JOURNAL Sci. Am. 237 (6), 54-67 (1977)
MEDLINE 78054683
PUBMED 929160
REFERENCE 16 (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)
MEDLINE 79091185
PUBMED 731693
REFERENCE 17 (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)
MEDLINE 79091186
PUBMED 731694
REFERENCE 18 (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)
MEDLINE 80101074
PUBMED 160544
REFERENCE 19 (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)
MEDLINE 81053861
PUBMED 6253953
REFERENCE 20 (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 (N.Y.) 20 (26), 7599-7606 (1981)
MEDLINE 82113627
PUBMED 6173064
REFERENCE 21 (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 (N.Y.) 23 (8), 1634-1640 (1984)
MEDLINE 84203526
PUBMED 6232949
REFERENCE 22 (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)
MEDLINE 85079985
PUBMED 6239864
REFERENCE 23 (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)
MEDLINE 85274373
PUBMED 2411049
COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The
reference sequence was derived from 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].
FEATURES Location/Qualifiers
source 1..5386
/organism="coliphage phiX174"
/specific_host="Escherichia coli"
CDS join(3981..5386,1..136)
/product="rf replication, viral strand synthesis protein"
CDS join(4497..5386,1..136)
/product="shut off host DNA synthesis protein"
CDS join(5075..5386,1..51)
/product="capsid morphogenesis protein"
variation 23
/note="c in wt; t in am18 and am35 [14]"
variation 25
/note="g in wt; c in ts116 [14]"
CDS 51..221
/product="gene K protein"
variation 57
/note="c in wt; t in am6 [14]"
variation 117
/note="g in wt; a in am6 [14]"
CDS 133..393
/product="DNA maturation protein"
mRNA 358..3975
/note="mRNA (major alt.)"
mRNA 358..991
/note="mRNA (minor alt.)"
CDS 390..848
/product="capsid morphogenesis protein"
CDS 568..843
/product="cell lysis protein"
CDS 848..964
/product="core protein, DNA condensation protein"
CDS 1001..2284
/product="major coat protein"
CDS 2395..2922
/product="major spike protein"
CDS 2931..3917
/product="minor spike protein, adsorption"
misc_feature 3962
/note="transcription start site"
rep_origin 4306
/note="origin of viral strand synthesis"
misc_feature 4899
/note="transcription start site"
BASE COUNT 1291 a 1157 c 1254 g 1684 t
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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