Import from Notes

*** you can now paste a genbank record directly into an empty main window, where you would usually paste DNA sequence. The record is automatically saved in the sequences 'notes' and features can be imported ***

DNA sequence can be imported from the notes section of a DNADynamo file containing a Genbank mRNA file entry. The advantage of using this import facility is that DNA sequence is automatically loaded, translation start and stop points are set according to the CDS and misellaneous features such as protein motifs are entered as annotations in the annotation box, saving you time. Details of the format are described at the bottom of this page. The NCBI entrez nucleotide viewer entry can be placed in the notes section via the System-ClipBoard (use your web-browsers 'Select All' function or use the mouse to drag and select the relevant text in your web-browser, select the browsers 'Copy to ClipBoard' function, and finally select DNADynamos 'Paste-from-ClipBoard' function while the Notes section is open).

DNADynamo requires the following format elements

LOCUS ... mRNA - identifies the file as mRNA data

ORIGIN ... "DNA Sequence to be imported" ... \\ - the DNA Sequence to be imported

CDS start..end - where start and end represent an open reading frame within the sequence

Misc_feature start..end /note "description" - where start and end represent the beginning and end of a feature within the Protein, and "description" a text description of this feature.

Support for importing large Genbank DNA records (GENOME ANNOTATION REFSEQ) is in development and will be available in future versions of DNADynamo

The following is an example record that may be imported... you can test it out by selecting it with the mouse (press and drag) copying (Ctrl-c) and pasting (Edit/Paste or Ctrl-V) this example into the Notes and then selecting "Import DNA from Notes"


LOCUS       NM_030640               3566 bp    mRNA    linear   PRI 23-JAN-2004
DEFINITION  Homo sapiens dual specificity phosphatase 16 (DUSP16), mRNA.
ACCESSION   NM_030640 XM_039106
VERSION     NM_030640.1  GI:38372910
KEYWORDS    .
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 3566)
  AUTHORS   Hoornaert,I., Marynen,P., Goris,J., Sciot,R. and Baens,M.
  TITLE     MAPK phosphatase DUSP16/MKP-7, a candidate tumor suppressor for
            chromosome region 12p12-13, reduces BCR-ABL-induced transformation
  JOURNAL   Oncogene 22 (49), 7728-7736 (2003)
   PUBMED   14586399
  REMARK    GeneRIF: context-dependent role for DUSP16 on cell transformation
            and apoptosis.
REFERENCE   2  (bases 1 to 3566)
  AUTHORS   Masuda,K., Shima,H., Watanabe,M. and Kikuchi,K.
  TITLE     MKP-7, a novel mitogen-activated protein kinase phosphatase,
            functions as a shuttle protein
  JOURNAL   J. Biol. Chem. 276 (42), 39002-39011 (2001)
   PUBMED   11489891
REFERENCE   3  (bases 1 to 3566)
  AUTHORS   Tanoue,T., Yamamoto,T., Maeda,R. and Nishida,E.
  TITLE     A Novel MAPK phosphatase MKP-7 acts preferentially on JNK/SAPK and
            p38 alpha and beta MAPKs
  JOURNAL   J. Biol. Chem. 276 (28), 26629-26639 (2001)
   PUBMED   11359773
COMMENT     VALIDATED REFSEQ: This record has undergone preliminary review of
            the sequence, but has not yet been subject to final review. The
            reference sequence was derived from AF506796.1.
FEATURES             Location/Qualifiers
     source          1..3566
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="12"
                     /map="12p13"
     gene            1..3566
                     /gene="DUSP16"
                     /note="synonyms: MKP7, MKP-7, KIAA1700"
                     /db_xref="GeneID:80824"
                     /db_xref="LocusID:80824"
                     /db_xref="MIM:607175"
     CDS             633..2630
                     /gene="DUSP16"
                     /EC_number="3.1.3.48"
                     /EC_number="3.1.3.16"
                     /note="MAPK phosphatase-7"
                     /codon_start=1
                     /product="dual specificity phosphatase 16"
                     /protein_id="NP_085143.1"
                     /db_xref="GI:38372911"
                     /db_xref="GeneID:80824"
                     /db_xref="LocusID:80824"
                     /db_xref="MIM:607175"
                     /translation="MAHEMIGTQIVTERLVALLESGTEKVLLIDSRPFVEYNTSHILE
                     AININCSKLMKRRLQQDKVLITELIQHSAKHKVDIDCSQKVVVYDQSSQDVASLSSDC
                     FLTVLLGKLEKSFNSVHLLAGGFAEFSRCFPGLCEGKSTLVPTCISQPCLPVANIGPT
                     RILPNLYLGCQRDVLNKELMQQNGIGYVLNASNTCPKPDFIPESHFLRVPVNDSFCEK
                     ILPWLDKSVDFIEKAKASNGCVLVHCLAGISRSATIAIAYIMKRMDMSLDEAYRFVKE
                     KRPTISPNFNFLGQLLDYEKKIKNQTGASGPKSKLKLLHLEKPNEPVPAVSEGGQKSE
                     TPLSPPCADSATSEAAGQRPVHPASVPSVPSVQPSLLEDSPLVQALSGLHLSADRLED
                     SNKLKRSFSLDIKSVSYSASMAASLHGFSSSEDALEYYKPSTTLDGTNKLCQFSPVQE
                     LSEQTPETSPDKEEASIPKKLQTARPSDSQSKRLHSVRTSSSGTAQRSLLSPLHRSGS
                     VEDNYHTSFLFGLSTSQQHLTKSAGLGLKGWHSDILAPQTSTPSLTSSWYFATESSHF
                     YSASAIYGGSASYSAYSCSQLPTCGDQVYSVRRRQKPSDRADSRRSWHEESPFEKQFK
                     RRSCQMEFGESIMSENRSREELGKVGSQSSFSGSMEIIEVS"
     misc_feature    681..1031
                     /gene="DUSP16"
                     /note="RHOD; Region: Rhodanese Homology Domain"
                     /db_xref="CDD:24284"
     misc_feature    897..1691
                     /gene="DUSP16"
                     /note="KOG1716; Region: Dual specificity phosphatase
                     [Defense mechanisms]"
                     /db_xref="CDD:19503"
     misc_feature    1104..1523
                     /gene="DUSP16"
                     /note="DSPc; Region: Dual specificity phosphatase,
                     catalytic domain"
                     /db_xref="CDD:24472"
ORIGIN      
        1 ggaagagaaa gagtgaagaa aagttgcgag cgtctcctct cttcctaagc ctcccgcccc
       61 aacccacccc tcagagaagg agaagataat atactgaaaa gaagaggagg aggagagcga
      121 cgggacggga cgcgagcggg agcgcagccg ccctctcggc tccgcggcgg cgcctcgcaa
      181 gtccgggagg cgaggggggc ccgaggggag acgccgtgac aactttcgtt tccctctgag
      241 ggaattggga ggtcggcggc cccaaaagct ttcagtccag tgtaaagctg ttggagcgcg
      301 ggagcaaagg taaagaatga tgtaatgcgc tggctgctcc aaagcatctt ttgttgtgga
      361 atggttattc cagtcatctc tttatgaatc aaatgtgagg ggctgctttg tggacggagt
      421 cctttgcaag agcacatcaa cgggaaagag aaagagacat tcacttggag ggctcttgct
      481 gaaaatgggt ttaactctcc ttttgccagt caccaccagc ctgacctcat acacttttag
      541 tacaatggag tggctgagcc tttgagcaca ccaccattac atcatcgtgg caaattaaag
      601 aaggaggtgg gaaaagagga cttattgttg tcatggccca tgagatgatt ggaactcaaa
      661 ttgttactga gaggttggtg gctctgctgg aaagtggaac ggaaaaagtg ctgctaattg
      721 atagccggcc atttgtggaa tacaatacat cccacatttt ggaagccatt aatatcaact
      781 gctccaagct tatgaagcga aggttgcaac aggacaaagt gttaattaca gagctcatcc
      841 agcattcagc gaaacataag gttgacattg attgcagtca gaaggttgta gtttacgatc
      901 aaagctccca agatgttgcc tctctctctt cagactgttt tctcactgta cttctgggta
      961 aactggagaa gagcttcaac tctgttcacc tgcttgcagg tgggtttgct gagttctctc
     1021 gttgtttccc tggcctctgt gaaggaaaat ccactctagt ccctacctgc atttctcagc
     1081 cttgcttacc tgttgccaac attgggccaa cccgaattct tcccaatctt tatcttggct
     1141 gccagcgaga tgtcctcaac aaggagctga tgcagcagaa tgggattggt tatgtgttaa
     1201 atgccagcaa tacctgtcca aagcctgact ttatccccga gtctcatttc ctgcgtgtgc
     1261 ctgtgaatga cagcttttgt gagaaaattt tgccgtggtt ggacaaatca gtagatttca
     1321 ttgagaaagc aaaagcctcc aatggatgtg ttctagtgca ctgtttagct gggatctccc
     1381 gctccgccac catcgctatc gcctacatca tgaagaggat ggacatgtct ttagatgaag
     1441 cttacagatt tgtgaaagaa aaaagaccta ctatatctcc aaacttcaat tttctgggcc
     1501 aactcctgga ctatgagaag aagattaaga accagactgg agcatcaggg ccaaagagca
     1561 aactcaagct gctgcacctg gagaagccaa atgaacctgt ccctgctgtc tcagagggtg
     1621 gacagaaaag cgagacgccc ctcagtccac cctgtgccga ctctgctacc tcagaggcag
     1681 caggacaaag gcccgtgcat cccgccagcg tgcccagcgt gcccagcgtg cagccgtcgc
     1741 tgttagagga cagcccgctg gtacaggcgc tcagtgggct gcacctgtcc gcagacaggc
     1801 tggaagacag caataagctc aagcgttcct tctctctgga tatcaaatca gtttcatatt
     1861 cagccagcat ggcagcatcc ttacatggct tctcctcatc agaagatgct ttggaatact
     1921 acaaaccttc cactactctg gatgggacca acaagctatg ccagttctcc cctgttcagg
     1981 aactatcgga gcagactccc gaaaccagtc ctgataagga ggaagccagc atccccaaga
     2041 agctgcagac cgccaggcct tcagacagcc agagcaagcg attgcattcg gtcagaacca
     2101 gcagcagtgg caccgcccag aggtcccttt tatctccact gcatcgaagt gggagcgtgg
     2161 aggacaatta ccacaccagc ttccttttcg gcctttccac cagccagcag cacctcacga
     2221 agtctgctgg cctgggcctt aagggctggc actcggatat cttggccccc cagacctcta
     2281 ccccttccct gaccagcagc tggtattttg ccacagagtc ctcacacttc tactctgcct
     2341 cagccatcta cggaggcagt gccagttact ctgcctacag ctgcagccag ctgcccactt
     2401 gcggagacca agtctattct gtgcgcaggc ggcagaagcc aagtgacaga gctgactcgc
     2461 ggcggagctg gcatgaagag agcccctttg aaaagcagtt taaacgcaga agctgccaaa
     2521 tggaatttgg agagagcatc atgtcagaga acaggtcacg ggaagagctg gggaaagtgg
     2581 gcagtcagtc tagcttttcg ggcagcatgg aaatcattga ggtctcctga gaagaaagac
     2641 acttgtgact tctatagaca attttttttt cttgttcaca aaaaaattcc ctgtaaatct
     2701 gaaatatata tatgtacata catatatatt tttggaaaat ggagctatgg tgtaaaagca
     2761 acaggtggat caacccagtt gttactctct taacatctgc atttgagaga tcagctaata
     2821 cttctctcaa caaaaatgga agggcagatg ctagaatccc ccctagacgg aggaaaacca
     2881 ttttattcag tgaattacac atcctcttgt tcttaaaaaa gcaagtgtct ttggtgttgg
     2941 aggacaaaat cccctaccat tttcacgttg tgctactaag agatctcaaa tattagtctt
     3001 tgtccggacc cttccatagt acaccttagc gctgagactg agccagcttg ggggtcaggt
     3061 aggtagaccc tgttagggac agagcctagt ggtaaatcca agagaaatga tcctatccaa
     3121 agctgattca caaacccacg ctcacctgac agccgaggga cacgagcatc actctgctgg
     3181 acggaccatt aggggccttg ccaaggtcta ccttagagca aacccagtac ctcagacagg
     3241 aaagtcgggg ctttgaccac taccatatct ggtagcccat tttctaggca ttgtgaatag
     3301 gtaggtagct agtcacactt ttcagaccaa ttcaaactgt ctatgcacaa aattcccgtg
     3361 ggcctagatg gagataattt ttttttcttc tcagctttat gaagagaagg gaaactgtct
     3421 aggattcagc tgaaccacca ggaacctggc aacatcacga tttaagctaa ggttgggagg
     3481 ctaacgagtc tacctccctc tttgtaaatc aaagaattgt ttaaaatggg attgtcaatc
     3541 ctttaaataa agatgaactt ggtttc
//