*** 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
//