Difference between revisions of "Part:BBa K801999:Design"

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<partinfo>BBa_K801999 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K801999 SequenceAndFeatures</partinfo>
  
 +
<br>'''Keywords:'''
 +
<!--These keywords are necessary to find your part using a fulltext sarch.-->
 +
<!--keyword_1, keyword_2, keyword_3, keyword_4, keyword_5-->
 +
 +
<br>'''Abbreviations:'''
 +
<!--*used_abbreviation_1 = full_name_of_used_abbreviations_1-->
 +
<!--*used_abbreviation_2 = full_name_of_used_abbreviations_2-->
  
 
===Design Notes===
 
===Design Notes===
  
 +
'''Related BioBrick:'''
 +
<!--*Other versions:[https://parts.igem.org/wiki/index.php?title=Part:BBa_?????? BBa_??????: Name_of_part] -->
 +
<!--*Related BioBricks:[https://parts.igem.org/wiki/index.php?title=Part:BBa_?????? BBa_??????: Name_of_part]
  
−
Cloning Detaills:
+
'''Cloning details:'''<br>
−
<!--Part was designed in RFC10/RFC23/RFC25</br>-->
+
<!--*Designed in RFC10/RFC23/RFC25-->
−
<!--Mutation C889G to delete XbaI restriction site</br>-->
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<!--*Mutation C889G to delete XbaI restriction site-->
−
<!--Part was truncated upstream/downstram compared to template because ???</br>-->
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<!--*Truncation upstream/downstream compared to template, ?explanation?-->
  
 +
'''Quality control measures:'''<br>
 +
<!--*Test digestion using ?enzyme1? & ?enzyme2?/Not yet performed-->
 +
<!--*Sequencing using primer ?primer_name?/Not yet sequenced-->
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<!--*Part was partly sequenced/Part was totally sequenced-->
 +
 +
'''Backbone:'''<br>
 +
<!--*Backbone name: pSB1C3'/?backbone_name?-->
 +
<!--*Resistance: Amp/Cp/Kan/-->
 +
<!--*Copynumber: low/medium/high-->
 +
 +
'''Protein coding:'''<br>
 +
<!--*Protein: ?Name_of_gene_product? [Nucleotide 1 to ???]-->
 +
<!--*The protein has the amino acid replacements ???99??? to ???99???.-->
 +
<!--*The protein encoded is posttranslationally modified by ???.-->
 +
<!--*Tag: n-terminally fused/c-terminally fused His5/His6/Strep/Flag/other-->
 +
 +
'''Enzymatic activity:'''
 +
<!--none/EC-number ?.?.?.?-->
 +
 +
'''Cytotoxicity:'''<br>
 +
<!--none/not known/cytotoxic for ''organism name''-->
 +
 +
'''Safety notes:'''<br>
 +
<!--Known and anticipated sefety issues: none/health_risk/environmental_risk/other_risk-->
 +
<!--Known and anticipated security issues: none/other.-->
 +
 +
'''Intellectual property:'''
 +
<!--Information on patent situation.-->
 +
<!--Intellectual property claims made by the authors.-->
 +
 +
'''Corresponding part author/authors:'''
 +
<!--https://igem.org/User_Information.cgi?user_id=????/email-->
  
 
===Source===
 
===Source===
−
Source:
 
−
<!--Preexisting BioBrick [Bba_???]</br>-->
 
−
<!--cDNA Clone [???Clonename???]</br>-->
 
−
<!--Synthesized</br>-->
 
  
−
Organism:
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'''Source:'''<br>
−
<!--Genesequence derived from ''???Aequorea victoria???''</br>-->
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<!--*Commercial system: plasmid name, system name, company name-->
−
<!--Codonoptimized for ''???Aequorea victoria???''</br>-->
+
<!--*Plasmid: p???, provided by ?name_of_person?, ?institute/university?, ?country?-->
 +
<!--*Preexisting BioBrick ?Bba_number?-->
 +
<!--*cDNA Clone: ?clone_name?, ?company_name?-->
 +
<!--*Synthesized by ?company_name?.-->
 +
 
 +
<!--'''Forward Primer:'''<br><code>5'- ??? - 3'</code><br>-->
 +
<!--'''Reverse Primer:'''<br><code>5'- ??? - 3'</code><br>-->
 +
 
 +
'''Organism:'''<br>
 +
<!--*Genesequence derived from ''?organism_name?''-->
 +
<!--*Codonoptimized for ''?organism_name?''-->
 +
<!--*Designed for the following Chassis: ''?organism-name?''-->
 +
<!--*Statement about functionality in other chassis.-->
 +
 
 +
<!--Thank you very much for using BBF RFC 82 to describe the present BioBrick. If you have any remarks or recommendations concerning this RFC we would highly appreciate to get your feedback on: []-->
 +
 
  
 
===References===
 
===References===
−
<!--[http://www.ncbi.nlm.nih.gov/pubmed/????20010584???|Pubmed: ???xx et al., 20012???]-->
+
<!-- Here you find templates to insert references to literature and different databases-->
−
<!--[http://www.rcsb.org/pdb/explore/explore.do?structureId=???1EMA???|PDB: ???Structure of GFP???]-->
+
  
−
==XML==
+
'''Literature references:'''<br>
−
<html>
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<!--*[http://www.ncbi.nlm.nih.gov/pubmed/?PMID? '''Pubmed:''' ?Author(s)?, ?year?: ?title?]-->
−
<?xml version="1.0"?>
+
−
<style>
+
  
−
BBa_K801999 {
+
'''Database references:'''<br>
−
}
+
<!--*[http://www.ncbi.nlm.nih.gov/nuccore/?accessNr? '''GenBank''': ?title?]-->
 +
<!--*[http://www.ebi.ac.uk/interpro/IEntry?ac=?accessNr? '''Interpro''': ?title?]-->
 +
<!--*[http://www.uniprot.org/uniprot/?accessNr? '''Uniprot''': ?title?]-->
 +
<!--*[http://pfam.sanger.ac.uk/family/?accessNr? '''Pfam:''' ?title?]-->
 +
<!--*[http://www.rcsb.org/pdb/explore/explore.do?structureId=?accessNR? '''PDB:''' ?tile?]-->
 +
<!--*[http://www.brenda-enzymes.info/php/result_flat.php4?ecno=?accessNr? '''Branda:''' ?title?]-->
 +
 
 +
 
 +
 
 +
[[Image:TUM12-Test_page1.png]]
 +
 
 +
 
 +
<partinfo>BBa_K801999 short</partinfo>
 +
 
 +
<br>'''Keywords:'''
 +
fluorescent, reporter, chromophore, luminescence, bioluminescence, photoprotein
 +
 
 +
<br>'''Used abbreviations:'''
 +
*GFP = Green Fluorescent Protein
 +
 
 +
===Design Notes===
 +
 
 +
'''Other versions of this BioBrick:'''
 +
*The BioBrick BBa_I757008 encodes a yellow fluorescent protein (mVenus) derived from GFP
 +
*The BioBrick BBa_I757008 encodes GFP in RFC25 for protein fusions
 +
 
 +
'''Cloning details:'''<br>
 +
*Part was designed in RFC10
 +
*Mutation G381A to delete XbaI restriction site
 +
*The correctness of the part was checked by sequencing
 +
 
 +
'''Protein coding:'''<br>
 +
*Green Fluorescent Protein [Nucleotide 1 to 714]
 +
*The protein has the amino acid replacements Ser65Thr in order to increase fluorescence, photostability and to shift the major excitation peak to 488 nm. (see Heim et al., 1995)
 +
*The protein encoded is posttranslationally modified by a cross-link between Ser65 and Gly67 to form the chromophore.
 +
 
 +
'''Enzymatic activity:'''
 +
none
 +
 
 +
'''Cytotoxicity:'''
 +
none
 +
 
 +
===Source===
 +
'''Source:'''
 +
*Amplified from plasmid: pSB1C3-GFP-generator, provided by Osamu Shimomura, Boston University School of Medicine, USA
 +
 
 +
'''Forward Primer:'''<br>
 +
<code>5'- ATGATGATGATG - 3'</code><br>
 +
'''Reverse Primer:'''<br>
 +
<code>5'- ATGATGATGATG - 3'</code><br>
 +
 
 +
'''Organism:'''
 +
*Sequence derived from ''Aequorea victoria''
 +
*Codon optimized for ''Escherichia coli''
 +
 
 +
===References===
 +
<!-- Here you find templates to insert references to important publications, GenBank entries, PDB structures and so on-->
  
−
.nodel1 {
+
'''Literature references:'''<br>
−
  position:relative;
+
*[http://www.ncbi.nlm.nih.gov/pubmed/20010584 '''Pubmed:''' Prasher, 1995: Using GFP to see the light.(Review)]
−
  top:5px;
+
*[http://www.ncbi.nlm.nih.gov/pubmed/7854443 '''Pubmed''': Heim, 1995: Improved green fluorescence.(Reference for Chromophore)]
−
  left:10px;
+
−
  padding:5px;
+
−
  display: block;
+
−
}
+
−
.nodel2 {
+
−
  position:relative;
+
−
  top:10px;
+
−
  left:5px;
+
−
  padding:5px;
+
−
  display: block;
+
−
}
+
−
.nodel2 {
+
−
  position:relative;
+
−
  top:10px;
+
−
  left:5px;
+
−
  padding:5px;
+
−
  display: block;
+
−
}
+
  
−
</style>
+
'''Sequence references:'''<br>
 +
*[http://www.ncbi.nlm.nih.gov/nuccore/X83959.1 '''GenBank''': A.victoria mRNA for green fluorescent protein (ID:gfp1)]
 +
*[http://www.ebi.ac.uk/interpro/IEntry?ac=IPR011584 '''Interpro''': Green fluorescent protein-related ]
 +
*[http://www.uniprot.org/uniprot/P42212 '''Uniprot''': Green fluorescent protein]
 +
*[http://pfam.sanger.ac.uk/family/PF01353 '''Pfam:''' Green fluorescent protein]
  
−
<BBa_K801999>
+
'''Structure reference:'''<br>
−
        <Name class="nodel1">K801999</Name
+
*[http://www.rcsb.org/pdb/explore/explore.do?structureId=1EMA '''PDB:''' Green Fluorescent Protein from Aequorea victoria]<br>
−
        <Source class="nodel1">
+
−
    <Biobrick attribute="nodel2">BBa_???</Biobrick>
+
−
    <cDNA class="nodel2">???Clonename???</cDNA>
+
−
    <Synthesized class="nodel2">true</Synthesized>
+
−
</Source>
+
−
<Organism class="nodel1">
+
−
<Origin class="nodel2">(???Species e.g. Homo sapiens???)</Origin>
+
−
<Optimized class="nodel2">(???Species e.g. Homo sapiens???)</Optimized>
+
−
</Organisms>
+
−
<References class="nodel1">
+
−
<Pubmed class="nodel2">
+
−
<ID class="nodel3">20010584</ID>
+
−
<Year class="nodel3">2012</Year>
+
−
<Author  class="nodel3">Vogt et al.</Author>
+
−
</Pubmed>
+
−
</References>
+
−
</BBa_K801999>
+
−
</html>
+

Latest revision as of 13:11, 22 September 2012

Test page for standardized BioBrick part descriptions


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Keywords:


Abbreviations:

Design Notes

Related BioBrick:

Quality control measures:

Backbone:

Protein coding:

Enzymatic activity:

Cytotoxicity:

Safety notes:

Intellectual property:

Corresponding part author/authors:

Source

Source:


Organism:


References

Literature references:

Database references:


TUM12-Test page1.png


Test page for standardized BioBrick part descriptions


Keywords: fluorescent, reporter, chromophore, luminescence, bioluminescence, photoprotein


Used abbreviations:

  • GFP = Green Fluorescent Protein

Design Notes

Other versions of this BioBrick:

  • The BioBrick BBa_I757008 encodes a yellow fluorescent protein (mVenus) derived from GFP
  • The BioBrick BBa_I757008 encodes GFP in RFC25 for protein fusions

Cloning details:

  • Part was designed in RFC10
  • Mutation G381A to delete XbaI restriction site
  • The correctness of the part was checked by sequencing

Protein coding:

  • Green Fluorescent Protein [Nucleotide 1 to 714]
  • The protein has the amino acid replacements Ser65Thr in order to increase fluorescence, photostability and to shift the major excitation peak to 488 nm. (see Heim et al., 1995)
  • The protein encoded is posttranslationally modified by a cross-link between Ser65 and Gly67 to form the chromophore.

Enzymatic activity: none

Cytotoxicity: none

Source

Source:

  • Amplified from plasmid: pSB1C3-GFP-generator, provided by Osamu Shimomura, Boston University School of Medicine, USA

Forward Primer:
5'- ATGATGATGATG - 3'
Reverse Primer:
5'- ATGATGATGATG - 3'

Organism:

  • Sequence derived from Aequorea victoria
  • Codon optimized for Escherichia coli

References

Literature references:

  • [http://www.ncbi.nlm.nih.gov/pubmed/20010584 Pubmed: Prasher, 1995: Using GFP to see the light.(Review)]
  • [http://www.ncbi.nlm.nih.gov/pubmed/7854443 Pubmed: Heim, 1995: Improved green fluorescence.(Reference for Chromophore)]

Sequence references:

  • [http://www.ncbi.nlm.nih.gov/nuccore/X83959.1 GenBank: A.victoria mRNA for green fluorescent protein (ID:gfp1)]
  • [http://www.ebi.ac.uk/interpro/IEntry?ac=IPR011584 Interpro: Green fluorescent protein-related ]
  • [http://www.uniprot.org/uniprot/P42212 Uniprot: Green fluorescent protein]
  • [http://pfam.sanger.ac.uk/family/PF01353 Pfam: Green fluorescent protein]

Structure reference:

  • [http://www.rcsb.org/pdb/explore/explore.do?structureId=1EMA PDB: Green Fluorescent Protein from Aequorea victoria]