Sequence Extractor

Sequence Extractor generates a clickable restriction map and PCR primer map of a DNA sequence. Protein translations and intron/exon boundaries are also shown. Use Sequence Extractor to build DNA constructs in silico. Please read the list of program features to learn more.

Paste a sequence into the text area below. Accepted formats are: raw, GenBank, EMBL, and FASTA.

LOCUS       U01668       4133 bp    DNA   circular  SYN       01-JUL-1997
DEFINITION  Phagemid cloning vector pKSS, complete sequence.
ACCESSION   U01668
VERSION     U01668.1  GI:405986
KEYWORDS    direct-selection cloning vehicle; positive-selection; pheS.
SOURCE      unidentified cloning vector.
  ORGANISM  unidentified cloning vector
            artificial sequence; vectors.
REFERENCE   1  (bases 3084 to 3868)
  AUTHORS   Selzer,G., Som,T., Itoh,T. and Tomizawa,J.
  TITLE     The origin of replication of plasmid p15A and comparative studies
            on the nucleotide sequences around the origin of related plasmids
  JOURNAL   Cell 32, 119-129 (1983)
  MEDLINE   83129391
REFERENCE   2  (bases 59 to 1239)
  AUTHORS   Fayat,G., Mayaux,J., Sacerdot,C., Fromant,M., Springer,M.,
            Grunberg-Manago,M. and Blanquet,S.
  TITLE     Escherichia coli phenylalanyl-tRNA synthetase operon region.
            Evidence for an attenuation mechanism. Identification of the gene
            for the ribosomal protein L20
  JOURNAL   J. Mol. Biol. 171, 239-261 (1983)
  MEDLINE   84090239
REFERENCE   3  (bases 1313 to 1474; 1932 to 4100)
  AUTHORS   Yanisch-Perron,C., Vieira,J. and Messing,J.
  TITLE     Improved M13 phage cloning vectors and host strains: nucleotide
            sequences of the M13mp18 and pUC19 vectors
  JOURNAL   Gene 33, 103-119 (1985)
  MEDLINE   85180545
REFERENCE   4  (bases 1932 to 3868)
  AUTHORS   Balbas,P., Soberon,X., Merino,E., Zurita,M., Lomeli,H., Valle,F.,
            Flores,N. and Bolivar,F.
  TITLE     Plasmid vector pBR322 and its special-purpose derivatives - A
            review
  JOURNAL   Gene 50, 3-40 (1986)
  MEDLINE   87219889
REFERENCE   5  (bases 1476 to 1931)
  AUTHORS   Short,J.M., Fernandez,J.M., Sorge,J.A. and Huse,W.D.
  TITLE     Lambda ZAP: A bacteriophage lambda expression vector with in vivo
            excision properties
  JOURNAL   Nucleic Acids Res. 16, 7583-7600 (1988)
  MEDLINE   88319944
REFERENCE   6  (bases 365 to 366; 1026 to 1026)
  AUTHORS   Kast,P. and Hennecke,H.
  TITLE     Amino acid substrate specificity of Escherichia coli
            phenylalanyl-tRNA synthetase altered by distinct mutations
  JOURNAL   J. Mol. Biol. 222, 99-124 (1991)
  MEDLINE   92046090
REFERENCE   7  (bases 3220 to 3255)
  AUTHORS   Lin-Chao,S., Chen,W.-T. and Wong,T.-T.
  TITLE     High copy number of the pUC plasmid results from a
            Rom/Rop-suppressible point mutation in RNA II
  JOURNAL   Mol. Microbiol. 6, 3385-3393 (1992)
  MEDLINE   93133118
REFERENCE   8  (bases 1 to 55; 1316 to 4099)
  AUTHORS   Alting-Mees,M.A., Sorge,J.A. and Short,J.M.
  TITLE     pBluescriptII: Multifunctional cloning and mapping vectors
  JOURNAL   Meth. Enzymol. 216, 483-495 (1992)
  MEDLINE   93125166
REFERENCE   9  (bases 4091 to 4133; 1 to 61; 1237 to 1336)
  AUTHORS   Kast,P.
  TITLE     pKSS - A second-generation general purpose cloning vector for
            efficient positive selection of recombinant clones
  JOURNAL   Gene 138, 109-114 (1994)
  MEDLINE   94171019
REFERENCE   10 (bases 1 to 4133)
  AUTHORS   Kast,P.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-SEP-1993) Dept. of Chemistry and Molecular Biology,
            The Scripps Research Institute, 10550 North Torrey Pines Road, La
            Jolla, CA 92037, USA
COMMENT     On Oct 6, 1993 this sequence version replaced gi:403935.
FEATURES             Location/Qualifiers
     source          1..4133
                     /organism="unidentified cloning vector"
                     /db_xref="taxon:45196"
                     /lab_host="Escherichia coli"
     misc_feature    1..61
                     /note="multiple cloning site I:
                     KpnI-EcoO109I-ApaI-AvaI-XhoI-SalI-AccI-HincII-ClaI-H
                     indIII-EcoRV-EcoRI-AvaI-SmaI"
                     /citation=[9]
     misc_feature    join(1..55,1240..4133)
                     /note="derived from GenBank accession X52331"
     gene            146..1129
                     /gene="pheS"
                     /note="Gly294 mutant"
     CDS             146..1129
                     /gene="pheS (Gly294 mutant)"
                     /EC_number="6.1.1.20"
                     /function="confers p-Cl-phenylalanine sensitivity"
                     /citation=[2]
                     /codon_start=1
                     /transl_table=11
                     /product="phenylalanyl-tRNA synthetase alpha subunit
                     (Gly294 variant)"
                     /protein_id="AAB61946.1"
                     /db_xref="GI:403936"
                     /translation="MSHLAELVASAKAAISQASDVAALDNVRVEYLGKKGHLTLQMTT
                     LRELPPEERPAAGAVINEAKEQVQQALNARKAELESAALNARLAAETIDVSLPGRRIE
                     NGGLHPVTRTIDRIESFFGELGFTVATGPEIEDDYHNFDALNIPGHHPARADHDTFWF
                     DTTRLLRTQTSGVQIRTMKAQQPPIRIIAPGRVYRNDYDQTHTPMFHQMEGLIVDTNI
                     SFTNLKGTLHDFLRNFFEEDLQIRFRPSYFPFTEPSAEVDVMGKNGKWLEVLGCGMVH
                     PNVLRNVGIDPEVYSGFGFGMGMERLTMLRYGVTDLRSFFENDLRFLKQFK"
     old_sequence    365..366
                     /gene="pheS"
                     /citation=[2]
                     /replace="GC"
     gene            1026
                     /gene="pheS (wild type)"
     variation       1026
                     /gene="pheS (wild type)"
                     /note="the exchange of codon GCC (Ala294, wild type) with
                     GGC (Gly294, mutant pheS, as present on pKSS) yielded the
                     phenotypic change from p-Cl-phenylalanine resistance to
                     sensitivity"
                     /citation=[6]
                     /replace="C"
     misc_feature    1243..1284
                     /note="multiple cloning site II:
                     BamHI-SpeI-XbaI-EagI-NotI-DsaI-SacII(KspI)-SacI(SstI )"
                     /citation=[9]
     promoter        complement(1292..1311)
                     /standard_name="T7 promoter"
                     /citation=[5]
     gene            1314..>1474
                     /gene="'lacZ'"
     CDS             1314..>1474
                     /gene="lacZ"
                     /EC_number="3.2.1.23"
                     /note="N-truncated alpha-fragment of beta-galactosidase;
                     blue/white screening with the lacZ system is irrelevant in
                     pKSS"
                     /citation=[5]
                     /codon_start=3
                     /transl_table=11
                     /product="beta-galactosidase fragment"
                     /protein_id="AAB61947.1"
                     /db_xref="GI:403937"
                     /translation="SLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQ
                     QLRSLNGEW"
     primer_bind     complement(1318..1334)
                     /note="annealing site for universal M13(-20) sequencing
                     primer"
                     /citation=[5]
     rep_origin      1476..1931
                     /standard_name="f1 phage origin region for single strand
                     DNA replication"
                     /note="nicking site of gene II protein is between pos.
                     1768 and 1769"
                     /citation=[5]
                     /direction=right
     old_sequence    1922
                     /citation=[5]
                     /replace="T"
     gene            2062..2922
                     /gene="bla"
     CDS             2062..2922
                     /gene="bla"
                     /EC_number="3.5.2.6"
                     /function="provides resistance to ampicillin"
                     /citation=[3]
                     /codon_start=1
                     /transl_table=11
                     /product="pre-beta-lactamase"
                     /protein_id="AAB61948.1"
                     /db_xref="GI:403938"
                     /translation="MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGY
                     IELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVE
                     YSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRL
                     DRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPL
                     LRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIA
                     EIGASLIKHW"
     sig_peptide     2062..2130
                     /gene="bla"
     mat_peptide     2131..2919
                     /gene="bla"
                     /EC_number="3.5.2.6"
                     /product="beta-lactamase"
     variation       2305
                     /gene="bla"
                     /note="mutation of HincII site of pBR322 [3]"
                     /citation=[3]
                     /replace="G"
     variation       2606
                     /gene="bla"
                     /note="mutation of PstI site of pBR322 [3]"
                     /citation=[3]
                     /replace="C"
     rep_origin      3082..3696
                     /standard_name="pMB1 (ColE1-like) plasmid origin of
                     replication, as in pBR322 [4]"
                     /note="the DNA region indicated is sufficient for a
                     functional replication origin [1]; DNA replication
                     initiates at pos. 3681 to 3683 [4]"
                     /citation=[1]
                     /direction=right
     old_sequence    3240
                     /note="according to [7], the T at position 3240 is
                     responsible for the higher copy number of pUC derivatives
                     [3,8], including pKSS, compared to their parent pBR322
                     [1,4]"
                     /citation=[1]
                     /replace="C"
     gene            3864..3956
                     /gene="'lacI"
     CDS             3864..3956
                     /gene="'lacI"
                     /note="vestigal C-terminal portion of lac repressor; this
                     3' portion of lacI is not functional"
                     /citation=[3]
                     /codon_start=1
                     /transl_table=11
                     /product="lac repressor fragment"
                     /protein_id="AAB61949.1"
                     /db_xref="GI:403939"
                     /translation="APNTQTASPRALADSLMQLARQVSRLESGQ"
     protein_bind    3957..3994
                     /standard_name="CAP binding site (wild-type sequence)"
                     /citation=[5]
                     /bound_moiety="catabolite activator protein (CAP)"
     promoter        3957..4061
                     /standard_name="lac promoter-operator region (wild type)"
                     /note="for details and references to the lac
                     promoter-operator region see [(in) Miller,J.H. and
                     Reznikoff,W.S. (eds); The Operon; 2nd ed (1980); Cold
                     Spring Harbor; pp.177-243.]"
                     /citation=[5]
     -35_signal      4005..4010
                     /gene="lacZ'"
     gene            4005..4093
                     /gene="lacZ'"
     -10_signal      4029..4034
                     /gene="lacZ'"
     protein_bind    4041..4061
                     /gene="lacZ'"
                     /standard_name="lacO; lac operator"
                     /bound_moiety="lac repressor protein"
     CDS             4079..>4093
                     /gene="lacZ'"
                     /note="N-terminal 5 residues of beta-galactosidase"
                     /citation=[5]
                     /codon_start=1
                     /transl_table=11
                     /product="beta-galactosidase fragment"
                     /protein_id="AAB61950.1"
                     /db_xref="GI:2213571"
                     /translation="MTMIT"
     promoter        4104..4123
                     /standard_name="T3 promoter"
                     /citation=[5]
     old_sequence    4133
                     /note="all pBluescript I KS (+/-) vectors (and pKSS)
                     exhibit the deletion of the G nucleotide 5' to the KpnI
                     site [8,9]"
                     /citation=[5]
                     /replace="TG"
BASE COUNT     1010 a   1052 c   1053 g   1018 t
ORIGIN      
        1 ggtaccgggc cccccctcga ggtcgacggt atcgataagc ttgatatcga attcccccgg
       61 gaccaaaatg gcaagtaaaa tagcctgatg ggataggctc taagtccaac gaaccagtgt
      121 caccactgac acaatgagga aaaccatgtc acatctcgca gaactggttg ccagtgcgaa
      181 ggcggccatt agccaggcgt cagatgttgc cgcgttagat aatgtgcgcg tcgaatattt
      241 gggtaaaaaa gggcacttaa cccttcagat gacgaccctg cgtgagctgc cgccagaaga
      301 gcgtccggca gctggtgcgg ttatcaacga agcgaaagag caggttcagc aggcgctgaa
      361 tgcgcgtaaa gcggaactgg aaagcgctgc actgaatgcg cgtctggcgg cggaaacgat
      421 tgatgtctct ctgccaggtc gtcgcattga aaacggcggt ctgcatccgg ttacccgtac
      481 catcgaccgt atcgaaagtt tcttcggtga gcttggcttt accgtggcaa ccgggccgga
      541 aatcgaagac gattatcata acttcgatgc tctgaacatt cctggtcacc acccggcgcg
      601 cgctgaccac gacactttct ggtttgacac tacccgcctg ctgcgtaccc agacctctgg
      661 cgtacagatc cgcaccatga aagcccagca gccaccgatt cgtatcatcg cgcctggccg
      721 tgtttatcgt aacgactacg accagactca cacgccgatg ttccatcaga tggaaggtct
      781 gattgttgat accaacatca gctttaccaa cctgaaaggc acgctgcacg acttcctgcg
      841 taacttcttt gaggaagatt tgcagattcg cttccgtcct tcctacttcc cgtttaccga
      901 accttctgca gaagtggacg tcatgggtaa aaacggtaaa tggctggaag tgctgggctg
      961 cgggatggtg catccgaacg tgttgcgtaa cgttggcatc gacccggaag tttactctgg
     1021 tttcggcttc gggatgggga tggagcgtct gactatgttg cgttacggcg tcaccgacct
     1081 gcgttcattc ttcgaaaacg atctgcgttt cctcaaacag tttaaataag gcaggaatag
     1141 attatgaaat tcagtgaact gtggttacgc gaatgggtga acccggcgat tgatagcgat
     1201 gcgctggcaa atcaaatcac tatggcgggc ctggaagttg ggggatccac tagttctaga
     1261 gcggccgcca ccgcggtgga gctccaattc gccctatagt gagtcgtatt acaattcact
     1321 ggccgtcgtt ttacaacgtc gtgactggga aaaccctggc gttacccaac ttaatcgcct
     1381 tgcagcacat ccccctttcg ccagctggcg taatagcgaa gaggcccgca ccgatcgccc
     1441 ttcccaacag ttgcgcagcc tgaatggcga atgggacgcg ccctgtagcg gcgcattaag
     1501 cgcggcgggt gtggtggtta cgcgcagcgt gaccgctaca cttgccagcg ccctagcgcc
     1561 cgctcctttc gctttcttcc cttcctttct cgccacgttc gccggctttc cccgtcaagc
     1621 tctaaatcgg gggctccctt tagggttccg atttagtgct ttacggcacc tcgaccccaa
     1681 aaaacttgat tagggtgatg gttcacgtag tgggccatcg ccctgataga cggtttttcg
     1741 ccctttgacg ttggagtcca cgttctttaa tagtggactc ttgttccaaa ctggaacaac
     1801 actcaaccct atctcggtct attcttttga tttataaggg attttgccga tttcggccta
     1861 ttggttaaaa aatgagctga tttaacaaaa atttaacgcg aattttaaca aaatattaac
     1921 gcttacaatt taggtggcac ttttcgggga aatgtgcgcg gaacccctat ttgtttattt
     1981 ttctaaatac attcaaatat gtatccgctc atgagacaat aaccctgata aatgcttcaa
     2041 taatattgaa aaaggaagag tatgagtatt caacatttcc gtgtcgccct tattcccttt
     2101 tttgcggcat tttgccttcc tgtttttgct cacccagaaa cgctggtgaa agtaaaagat
     2161 gctgaagatc agttgggtgc acgagtgggt tacatcgaac tggatctcaa cagcggtaag
     2221 atccttgaga gttttcgccc cgaagaacgt tttccaatga tgagcacttt taaagttctg
     2281 ctatgtggcg cggtattatc ccgtattgac gccgggcaag agcaactcgg tcgccgcata
     2341 cactattctc agaatgactt ggttgagtac tcaccagtca cagaaaagca tcttacggat
     2401 ggcatgacag taagagaatt atgcagtgct gccataacca tgagtgataa cactgcggcc
     2461 aacttacttc tgacaacgat cggaggaccg aaggagctaa ccgctttttt gcacaacatg
     2521 ggggatcatg taactcgcct tgatcgttgg gaaccggagc tgaatgaagc cataccaaac
     2581 gacgagcgtg acaccacgat gcctgtagca atggcaacaa cgttgcgcaa actattaact
     2641 ggcgaactac ttactctagc ttcccggcaa caattaatag actggatgga ggcggataaa
     2701 gttgcaggac cacttctgcg ctcggccctt ccggctggct ggtttattgc tgataaatct
     2761 ggagccggtg agcgtgggtc tcgcggtatc attgcagcac tggggccaga tggtaagccc
     2821 tcccgtatcg tagttatcta cacgacgggg agtcaggcaa ctatggatga acgaaataga
     2881 cagatcgctg agataggtgc ctcactgatt aagcattggt aactgtcaga ccaagtttac
     2941 tcatatatac tttagattga tttaaaactt catttttaat ttaaaaggat ctaggtgaag
     3001 atcctttttg ataatctcat gaccaaaatc ccttaacgtg agttttcgtt ccactgagcg
     3061 tcagaccccg tagaaaagat caaaggatct tcttgagatc ctttttttct gcgcgtaatc
     3121 tgctgcttgc aaacaaaaaa accaccgcta ccagcggtgg tttgtttgcc ggatcaagag
     3181 ctaccaactc tttttccgaa ggtaactggc ttcagcagag cgcagatacc aaatactgtt
     3241 cttctagtgt agccgtagtt aggccaccac ttcaagaact ctgtagcacc gcctacatac
     3301 ctcgctctgc taatcctgtt accagtggct gctgccagtg gcgataagtc gtgtcttacc
     3361 gggttggact caagacgata gttaccggat aaggcgcagc ggtcgggctg aacggggggt
     3421 tcgtgcacac agcccagctt ggagcgaacg acctacaccg aactgagata cctacagcgt
     3481 gagctatgag aaagcgccac gcttcccgaa gggagaaagg cggacaggta tccggtaagc
     3541 ggcagggtcg gaacaggaga gcgcacgagg gagcttccag ggggaaacgc ctggtatctt
     3601 tatagtcctg tcgggtttcg ccacctctga cttgagcgtc gatttttgtg atgctcgtca
     3661 ggggggcgga gcctatggaa aaacgccagc aacgcggcct ttttacggtt cctggccttt
     3721 tgctggcctt ttgctcacat gttctttcct gcgttatccc ctgattctgt ggataaccgt
     3781 attaccgcct ttgagtgagc tgataccgct cgccgcagcc gaacgaccga gcgcagcgag
     3841 tcagtgagcg aggaagcgga agagcgccca atacgcaaac cgcctctccc cgcgcgttgg
     3901 ccgattcatt aatgcagctg gcacgacagg tttcccgact ggaaagcggg cagtgagcgc
     3961 aacgcaatta atgtgagtta gctcactcat taggcacccc aggctttaca ctttatgctt
     4021 ccggctcgta tgttgtgtgg aattgtgagc ggataacaat ttcacacagg aaacagctat
     4081 gaccatgatt acgccaagct cgaaattaac cctcactaaa gggaacaaaa gct
//

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