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

(→‎References)
 
(42 intermediate revisions by 2 users not shown)
Line 3: Line 3:
  
 
<partinfo>BBa_K801999 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K801999 SequenceAndFeatures</partinfo>
−
'''Keywords:'''<br>
+
 
−
<!--keyword 1, keyword 2, keyword 3, keyword 4, keyword 5-->
+
<br>'''Keywords:'''
−
'''Abbreviations:'''
+
<!--These keywords are necessary to find your part using a fulltext sarch.-->
−
<!--used abbreviation 1 = provide full name of used abbreviations 1-->
+
<!--keyword_1, keyword_2, keyword_3, keyword_4, keyword_5-->
−
<!--used abbreviation 2 = provide full name of used abbreviations 2-->
+
 
 +
<br>'''Abbreviations:'''
 +
<!--*used_abbreviation_1 = full_name_of_used_abbreviations_1-->
 +
<!--*used_abbreviation_2 = full_name_of_used_abbreviations_2-->
  
 
===Design Notes===
 
===Design Notes===
−
'''Other versions of this BioBrick:'''<br>
+
 
−
<!--The BioBrick Bba_??? encodes the the same functionality but instead...<br>-->
+
'''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 details:'''<br>
 
'''Cloning details:'''<br>
−
<!--Part was designed in RFC10/RFC23/RFC25<br>-->
+
<!--*Designed in RFC10/RFC23/RFC25-->
−
<!--Mutation C889G to delete XbaI restriction site<br>-->
+
<!--*Mutation C889G to delete XbaI restriction site-->
−
<!--Part was truncated upstream/downstream compared to template in order to ???<br>-->
+
<!--*Truncation upstream/downstream compared to template, ?explanation?-->
−
<!--The correctness of part was checked by sequencing" or "... was not yet checked by sequencing<br>-->
+
 
 +
'''Quality control measures:'''<br>
 +
<!--*Test digestion using ?enzyme1? & ?enzyme2?/Not yet performed-->
 +
<!--*Sequencing using primer ?primer_name?/Not yet sequenced-->
 +
<!--*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 coding:'''<br>
−
<!--The BioBrick does not encode a protein" or "Name of gene product [Nucleotide 1 to ???]<br>-->
+
<!--*Protein: ?Name_of_gene_product? [Nucleotide 1 to ???]-->
−
<!--The protein has the amino acid replacements Cys59Tyr in order to...<br>-->
+
<!--*The protein has the amino acid replacements ???99??? to ???99???.-->
−
<!--The protein encoded is posttranslationally modified...<br>-->
+
<!--*The protein encoded is posttranslationally modified by ???.-->
 +
<!--*Tag: n-terminally fused/c-terminally fused His5/His6/Strep/Flag/other-->
  
−
'''Enzymatic activity:'''<br>
+
'''Enzymatic activity:'''
−
<!--none/EC-number ?.?.?.?<br>-->
+
<!--none/EC-number ?.?.?.?-->
  
 
'''Cytotoxicity:'''<br>
 
'''Cytotoxicity:'''<br>
−
<!--none/not known/cytotoxic for ''organim name''<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:'''<br>
 
'''Source:'''<br>
−
<!--Adapted from commercial system: plasmid name, system name, company name<br>-->
+
<!--*Commercial system: plasmid name, system name, company name-->
−
<!--Preexisting BioBrick Bba_number<br>-->
+
<!--*Plasmid: p???, provided by ?name_of_person?, ?institute/university?, ?country?-->
−
<!--cDNA Clone: clone name, company name <br>-->
+
<!--*Preexisting BioBrick ?Bba_number?-->
−
<!--Synthesized<br>-->
+
<!--*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>
 
'''Organism:'''<br>
−
<!--Genesequence derived from ''organism name''<br>-->
+
<!--*Genesequence derived from ''?organism_name?''-->
−
<!--Codonoptimized for ''organism name''<br>-->
+
<!--*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===
−
<!-- Here you find templates to insert references to important publications, genebank entries, PDB structures and so on-->
+
<!-- Here you find templates to insert references to literature and different databases-->
  
 
'''Literature references:'''<br>
 
'''Literature references:'''<br>
−
<!--[http://www.ncbi.nlm.nih.gov/pubmed/20010584 Pubmed: name et al., year: title of the publication]<br>-->
+
<!--*[http://www.ncbi.nlm.nih.gov/pubmed/?PMID? '''Pubmed:''' ?Author(s)?, ?year?: ?title?]-->
  
−
'''Seqeuence references:'''<br>
+
'''Database references:'''<br>
−
<!--[http://www.ncbi.nlm.nih.gov/nuccore/???] -->
+
<!--*[http://www.ncbi.nlm.nih.gov/nuccore/?accessNr? '''GenBank''': ?title?]-->
−
<!--[[http://www.uniprot.org/uniprot/???]-->
+
<!--*[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?]-->
  
−
'''Structure reference:'''<br>
 
−
<!--[http://www.rcsb.org/pdb/explore/explore.do?structureId=1EMA PDB: tile of the structure]<br>-->
 
  
  
Line 60: Line 98:
 
<partinfo>BBa_K801999 short</partinfo>
 
<partinfo>BBa_K801999 short</partinfo>
  
 +
<br>'''Keywords:'''
 +
fluorescent, reporter, chromophore, luminescence, bioluminescence, photoprotein
  
−
'''Keywords:'''<br>
+
<br>'''Used abbreviations:'''
−
fluorescent, reporter
+
−
'''Abbreviations:'''
+
 
*GFP = Green Fluorescent Protein
 
*GFP = Green Fluorescent Protein
−
 
  
 
===Design Notes===
 
===Design Notes===
−
'''Other versions of this BioBrick:'''<br>
+
 
−
<!--"The BioBrick Bba_??? encodes the the same functionality but instead..."<br>-->
+
'''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>
 
'''Cloning details:'''<br>
−
<!--"Part was designed in RFC10/RFC23/RFC25"<br>-->
+
*Part was designed in RFC10
−
<!--"Mutation C889G to delete XbaI restriction site"<br>-->
+
*Mutation G381A to delete XbaI restriction site
−
<!--"Part was truncated upstream/downstream compared to template in order to ???"<br>-->
+
*The correctness of the part was checked by sequencing
−
<!--"The correctness of part was checked by sequencing" or "... was not yet checked by sequencing"<br>-->
+
  
 
'''Protein coding:'''<br>
 
'''Protein coding:'''<br>
−
<!--"The BioBrick does not encode a protein" or "Name of gene product [Nucleotide 1 to ???]"<br>-->
+
*Green Fluorescent Protein [Nucleotide 1 to 714]
−
<!--"The protein has the amino acid replacements Cys59Tyr in order to..."<br>-->
+
*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..."<br>-->
+
*The protein encoded is posttranslationally modified by a cross-link between Ser65 and Gly67 to form the chromophore.
  
−
'''Enzymatic activity:'''<br>
+
'''Enzymatic activity:'''
−
<!--none/EC-number ?.?.?.?<br>-->
+
none
  
−
'''Cytotoxicity:'''<br>
+
'''Cytotoxicity:'''
−
<!--none/not known/cytotoxic for ''organim name''<br>-->
+
none
  
 
===Source===
 
===Source===
−
'''Source:'''<br>
+
'''Source:'''
−
<!--Adapted from commercial system: plasmid name, system name, company name<br>-->
+
*Amplified from plasmid: pSB1C3-GFP-generator, provided by Osamu Shimomura, Boston University School of Medicine, USA
−
<!--Preexisting BioBrick Bba_number<br>-->
+
−
<!--cDNA Clone: clone name, company name <br>-->
+
−
<!--Synthesized<br>-->
+
  
−
'''Organism:'''<br>
+
'''Forward Primer:'''<br>
−
<!--Genesequence derived from ''organism name''<br>-->
+
<code>5'- ATGATGATGATG - 3'</code><br>
−
<!--Codonoptimized for ''organism name''<br>-->
+
'''Reverse Primer:'''<br>
 +
<code>5'- ATGATGATGATG - 3'</code><br>
 +
 
 +
'''Organism:'''
 +
*Sequence derived from ''Aequorea victoria''
 +
*Codon optimized for ''Escherichia coli''
  
 
===References===
 
===References===
−
<!-- Here you find templates to insert references to important publications, genebank entries, PDB structures and so on-->
+
<!-- Here you find templates to insert references to important publications, GenBank entries, PDB structures and so on-->
  
 
'''Literature references:'''<br>
 
'''Literature references:'''<br>
−
*[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/20010584 '''Pubmed:''' Prasher, 1995: Using GFP to see the light.(Review)]
−
*[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)]
  
−
'''Seqeuence references:'''<br>
+
'''Sequence references:'''<br>
−
*[http://www.ncbi.nlm.nih.gov/nuccore/X83959.1: A.victoria mRNA for green fluorescent protein (ID:gfp1)]
+
*[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.ebi.ac.uk/interpro/IEntry?ac=IPR011584 '''Interpro''': Green fluorescent protein-related ]
−
*[http://www.uniprot.org/uniprot/P42212 Uniprot: Green fluorescent protein]
+
*[http://www.uniprot.org/uniprot/P42212 '''Uniprot''': Green fluorescent protein]
−
*[http://pfam.sanger.ac.uk/family/PF01353 Pfam: Green fluorescent protein]
+
*[http://pfam.sanger.ac.uk/family/PF01353 '''Pfam:''' Green fluorescent protein]
  
 
'''Structure reference:'''<br>
 
'''Structure reference:'''<br>
−
*[http://www.rcsb.org/pdb/explore/explore.do?structureId=1EMA PDB: Green Fluorescent Protein from Aequorea victoria]<br>
+
*[http://www.rcsb.org/pdb/explore/explore.do?structureId=1EMA '''PDB:''' Green Fluorescent Protein from Aequorea victoria]<br>

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]