Difference between revisions of "Part:BBa K801999:Design"
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<br>'''Keywords:''' | <br>'''Keywords:''' | ||
+ | <!--These keywords are necessary to find your part using a fulltext sarch.--> | ||
<!--keyword_1, keyword_2, keyword_3, keyword_4, keyword_5--> | <!--keyword_1, keyword_2, keyword_3, keyword_4, keyword_5--> | ||
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===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 details:'''<br> | '''Cloning details:'''<br> | ||
− | <!--* | + | <!--*Designed in RFC10/RFC23/RFC25--> |
<!--*Mutation C889G to delete XbaI restriction site--> | <!--*Mutation C889G to delete XbaI restriction site--> | ||
− | <!--* | + | <!--*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--> | ||
+ | <!--*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> | ||
− | <!--* | + | <!--*Protein: ?Name_of_gene_product? [Nucleotide 1 to ???]--> |
− | <!--*The protein has the amino acid replacements ???99??? to ???.--> | + | <!--*The protein has the amino acid replacements ???99??? to ???99???.--> |
<!--*The protein encoded is posttranslationally modified by ???.--> | <!--*The protein encoded is posttranslationally modified by ???.--> | ||
+ | <!--*Tag: n-terminally fused/c-terminally fused His5/His6/Strep/Flag/other--> | ||
'''Enzymatic activity:''' | '''Enzymatic activity:''' | ||
<!--none/EC-number ?.?.?.?--> | <!--none/EC-number ?.?.?.?--> | ||
− | '''Cytotoxicity:''' | + | '''Cytotoxicity:'''<br> |
− | <!--none/not known/cytotoxic for '' | + | <!--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> | ||
− | <!--* | + | <!--*Commercial system: plasmid name, system name, company name--> |
− | <!--* | + | <!--*Plasmid: p???, provided by ?name_of_person?, ?institute/university?, ?country?--> |
<!--*Preexisting BioBrick ?Bba_number?--> | <!--*Preexisting BioBrick ?Bba_number?--> | ||
<!--*cDNA Clone: ?clone_name?, ?company_name?--> | <!--*cDNA Clone: ?clone_name?, ?company_name?--> | ||
Line 42: | Line 66: | ||
<!--'''Forward Primer:'''<br><code>5'- ??? - 3'</code><br>--> | <!--'''Forward Primer:'''<br><code>5'- ??? - 3'</code><br>--> | ||
− | |||
<!--'''Reverse Primer:'''<br><code>5'- ??? - 3'</code><br>--> | <!--'''Reverse Primer:'''<br><code>5'- ??? - 3'</code><br>--> | ||
Line 48: | Line 71: | ||
<!--*Genesequence derived from ''?organism_name?''--> | <!--*Genesequence derived from ''?organism_name?''--> | ||
<!--*Codonoptimized for ''?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=== | ||
− | <!-- Here you find templates to insert references to | + | <!-- 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/ | + | <!--*[http://www.ncbi.nlm.nih.gov/pubmed/?PMID? '''Pubmed:''' ?Author(s)?, ?year?: ?title?]--> |
− | ''' | + | '''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?]--> | ||
− | |||
− | |||
Line 69: | Line 99: | ||
<br>'''Keywords:''' | <br>'''Keywords:''' | ||
− | fluorescent, reporter, chromophore, luminescence, bioluminescence, photoprotein | + | fluorescent, reporter, chromophore, luminescence, bioluminescence, photoprotein |
<br>'''Used abbreviations:''' | <br>'''Used abbreviations:''' | ||
Line 77: | Line 107: | ||
'''Other versions of this BioBrick:''' | '''Other versions of this BioBrick:''' | ||
− | *The BioBrick BBa_I757008 encodes a yellow fluorescent protein (mVenus) derived from GFP | + | *The BioBrick BBa_I757008 encodes a yellow fluorescent protein (mVenus) derived from GFP |
− | *The BioBrick BBa_I757008 encodes GFP in RFC25 for protein fusions | + | *The BioBrick BBa_I757008 encodes GFP in RFC25 for protein fusions |
'''Cloning details:'''<br> | '''Cloning details:'''<br> | ||
− | *Part was designed in RFC10 | + | *Part was designed in RFC10 |
*Mutation G381A to delete XbaI restriction site | *Mutation G381A to delete XbaI restriction site | ||
− | *The correctness of the part was checked by sequencing | + | *The correctness of the part was checked by sequencing |
'''Protein coding:'''<br> | '''Protein coding:'''<br> | ||
− | *Green Fluorescent | + | *Green Fluorescent Protein [Nucleotide 1 to 714] |
− | *The protein has the amino acid replacements Ser65Thr in order to | + | *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 | + | *The protein encoded is posttranslationally modified by a cross-link between Ser65 and Gly67 to form the chromophore. |
'''Enzymatic activity:''' | '''Enzymatic activity:''' | ||
Line 98: | Line 128: | ||
===Source=== | ===Source=== | ||
'''Source:''' | '''Source:''' | ||
− | *Amplified from plasmid: pSB1C3-GFP-generator, provided by | + | *Amplified from plasmid: pSB1C3-GFP-generator, provided by Osamu Shimomura, Boston University School of Medicine, USA |
'''Forward Primer:'''<br> | '''Forward Primer:'''<br> | ||
− | <code>5'- | + | <code>5'- ATGATGATGATG - 3'</code><br> |
'''Reverse Primer:'''<br> | '''Reverse Primer:'''<br> | ||
− | <code>5'- | + | <code>5'- ATGATGATGATG - 3'</code><br> |
− | + | ||
'''Organism:''' | '''Organism:''' | ||
− | * | + | *Sequence derived from ''Aequorea victoria'' |
− | * | + | *Codon optimized for ''Escherichia coli'' |
===References=== | ===References=== | ||
− | <!-- Here you find templates to insert references to important publications, | + | <!-- 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/7854443 ''Pubmed'': Heim, 1995: Improved green fluorescence.(Reference for | + | *[http://www.ncbi.nlm.nih.gov/pubmed/7854443 '''Pubmed''': Heim, 1995: Improved green fluorescence.(Reference for Chromophore)] |
− | ''' | + | '''Sequence references:'''<br> |
− | *[http://www.ncbi.nlm.nih.gov/nuccore/X83959.1 '' | + | *[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
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE 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:
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]