Difference between revisions of "User:Scmohr/Gray box"
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===Box Content=== | ===Box Content=== | ||
| − | <SPAN style= 'color:blue'>'''Source of DNA sequence:'''</span> | + | <SPAN style= 'color:blue'>'''Source of ''original'' DNA sequence:'''</span> |
*<SPAN style= 'color:blue'>'''GenBank GI: ___________''' </span> <SPAN style= 'color:red'>''There are two different kinds of GenBank numbers, "GI" numbers and "Accession/Version" numbers. It will be important to have that clarified in the part-deposit instructions. (Maybe it doesn't matter as long as they are clickable links...) The GI numbers are less ambiguous.''</span> | *<SPAN style= 'color:blue'>'''GenBank GI: ___________''' </span> <SPAN style= 'color:red'>''There are two different kinds of GenBank numbers, "GI" numbers and "Accession/Version" numbers. It will be important to have that clarified in the part-deposit instructions. (Maybe it doesn't matter as long as they are clickable links...) The GI numbers are less ambiguous.''</span> | ||
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===Box Content=== | ===Box Content=== | ||
| − | <SPAN style= 'color:blue'>'''Source of DNA sequence:'''</span> | + | <SPAN style= 'color:blue'>'''Source of ''original'' DNA sequence:'''</span> |
*<SPAN style= 'color:blue'>'''GenBank GI: ___________''' </span> | *<SPAN style= 'color:blue'>'''GenBank GI: ___________''' </span> | ||
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<SPAN style= 'color:blue'>'''Designer homepage: ___________''' | <SPAN style= 'color:blue'>'''Designer homepage: ___________''' | ||
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=='''For Protein Coding Sequences - Enzyme Example:'''== | =='''For Protein Coding Sequences - Enzyme Example:'''== | ||
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'''Nickname: AAT 1 ''[[or]] ATF1''''' | '''Nickname: AAT 1 ''[[or]] ATF1''''' | ||
| − | '''Source of DNA sequence:'''<SPAN style= 'color:blue'> </span> | + | '''Source of ''original'' DNA sequence:'''<SPAN style= 'color:blue'> </span> |
*'''GenBank <SPAN style= 'color:blue'>[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=Nucleotide&dopt=GenBank&val=1420813 GI: 1420813'''] </span> | *'''GenBank <SPAN style= 'color:blue'>[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=Nucleotide&dopt=GenBank&val=1420813 GI: 1420813'''] </span> | ||
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'''Designer: <SPAN style= 'color:blue'>[http://parts2.mit.edu/wiki/index.php/MIT_2006 Andre Green''']</span> | '''Designer: <SPAN style= 'color:blue'>[http://parts2.mit.edu/wiki/index.php/MIT_2006 Andre Green''']</span> | ||
| − | + | =='''For Protein Coding Sequences - Repressors and Activators:'''== | |
| − | =='''For Protein Coding Sequences - | + | |
===Box Heading:=== | ===Box Heading:=== | ||
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===Box Content=== | ===Box Content=== | ||
| − | <SPAN style= 'color:blue'>'''Source of DNA sequence:'''</span> | + | <SPAN style= 'color:blue'>'''Source of ''original'' DNA sequence:'''</span> |
*<SPAN style= 'color:blue'>'''GenBank GI: ___________''' </span> | *<SPAN style= 'color:blue'>'''GenBank GI: ___________''' </span> | ||
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<SPAN style= 'color:blue'>'''Designer homepage: ___________''' | <SPAN style= 'color:blue'>'''Designer homepage: ___________''' | ||
| − | |||
=='''For Protein Coding Sequences - Repressors and Activators - Example:'''== | =='''For Protein Coding Sequences - Repressors and Activators - Example:'''== | ||
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'''Nickname: tetR ''' | '''Nickname: tetR ''' | ||
| − | '''Source of DNA sequence:'''<SPAN style= 'color:blue'> </span> | + | '''Source of ''original'' DNA sequence:'''<SPAN style= 'color:blue'> </span> |
*'''GenBank <SPAN style= 'color:blue'>[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=Nucleotide&dopt=GenBank&val=42494906 GI: 42494906'''] </span> | *'''GenBank <SPAN style= 'color:blue'>[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=Nucleotide&dopt=GenBank&val=42494906 GI: 42494906'''] </span> | ||
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'''Literature references (PubMed IDs): | '''Literature references (PubMed IDs): | ||
| − | <SPAN style= 'color:blue'>[http://www.ncbi.nlm.nih.gov/pubmed/ | + | <SPAN style= 'color:blue'>[http://www.ncbi.nlm.nih.gov/pubmed/9092630?dopt=Abstract '''PM 9092630'''] </span> |
| − | '''Designer: <SPAN style= 'color:blue'> | + | '''Designer: <SPAN style= 'color:blue'> June Rhee, Connie Tao, Ty Thomson, Louis Waldman'''</span> |
| + | |||
| + | =='''For Terminators:'''== | ||
===Box Heading:=== | ===Box Heading:=== | ||
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===Box Content=== | ===Box Content=== | ||
| − | <SPAN style= 'color:blue'>'''Source of DNA sequence:'''</span> | + | <SPAN style= 'color:blue'>'''Source of ''original'' DNA sequence:'''</span> |
*<SPAN style= 'color:blue'>'''GenBank GI: ___________''' </span> | *<SPAN style= 'color:blue'>'''GenBank GI: ___________''' </span> | ||
*<SPAN style= 'color:blue'>'''Other: ___________''' | *<SPAN style= 'color:blue'>'''Other: ___________''' | ||
| − | <SPAN style= 'color:blue'>'''Structure ( | + | <SPAN style= 'color:blue'>'''3D-Structure (NDB_ID): ___________''' </span> |
| − | <SPAN style= 'color:blue'>''' | + | <SPAN style= 'color:blue'>'''Rfam entry: ___________''' |
| + | <SPAN style= 'color:blue'>'''Secondary-Structure Prediction Tools: ___________''' | ||
| + | |||
<SPAN style= 'color:blue'>'''Biological Origin: ___________''' | <SPAN style= 'color:blue'>'''Biological Origin: ___________''' | ||
<SPAN style= 'color:blue'>'''Literature references: ___________''' </span> (Up to three PubMed IDs) | <SPAN style= 'color:blue'>'''Literature references: ___________''' </span> (Up to three PubMed IDs) | ||
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<SPAN style= 'color:blue'>'''Designer homepage: ___________''' | <SPAN style= 'color:blue'>'''Designer homepage: ___________''' | ||
Latest revision as of 21:25, 17 July 2008
This page will contain drafts of potential "Gray Boxes" for different categories of basic parts.
Contents
For all basic parts:
Comments are given in red italics.. Words to appear in the "gray box" are in bold blue. Simple explanatory notes are in plain black text. The intent is for each item in the gray box to have a descriptive, clickable link.
DISCLAIMER
Note: The database links in this box refer to reference information that may not exactly correspond to a given part, since by definition the parts have been engineered.
This statement needs to appear in every box, perhaps on the side or at the bottom.
Box Heading:
INFORMATION LINKS FOR ___________ (part number inserted automatically)
Box Content
Source of original DNA sequence:
- GenBank GI: ___________ There are two different kinds of GenBank numbers, "GI" numbers and "Accession/Version" numbers. It will be important to have that clarified in the part-deposit instructions. (Maybe it doesn't matter as long as they are clickable links...) The GI numbers are less ambiguous.
- Other: ___________ Possible "other" links include other databases (for example, RNA databases) or a laboratory webpage.
Structure (PDB_ID): ___________
UniProt (Accession no.): ___________ Like GenBank, UniProt also uses two different kinds of identifier, "Accession number" and "Entry name." Only Accession numbers work as links. When users search UniProt, however, the hit lists come back with entry names displayed and a naive user might try to put that in as a link. A specific instruction (such as: For links to UniProt, always use the "Accession number," not the "Entry name") should be provided
Biological origin: ___________The link can go to one of the NCBI Taxonomy pages -- see, for example, http://www.ncbi.nlm.nih.gov/sites/entrez?db=taxonomy.
Literature references: ___________ (Up to three PubMed IDs)
Designer homepage: ___________This link could be to an individual, an iGEM team or a laboratory.
For Protein Coding Sequences - Enzymes:
Box Heading:
REFERENCE INFORMATION LINKS FOR ___________ (part number inserted automatically)
Box Content
Source of original DNA sequence:
- GenBank GI: ___________
- Other: ___________
Structure (PDB_ID): ___________
UniProt (Accession No.): ___________
Reaction (EC No.): ___________
Biological Origin: ___________
Literature references: ___________ (Up to three PubMed IDs)
Designer homepage: ___________
For Protein Coding Sequences - Enzyme Example:
Box Heading:
INFORMATION LINKS FOR BBa_J45014
Box Content:
NAME: [http://www.expasy.org/enzyme/2.3.1.84 Alcohol O-acetyltransferase 1]
Nickname: AAT 1 or ATF1
Source of original DNA sequence:
- GenBank [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=Nucleotide&dopt=GenBank&val=1420813 GI: 1420813]
- Other: n/a
Structure (PDB_ID): n/a
UniProt (Accession No.): [http://www.uniprot.org/uniprot/P40353 P40353]
Reaction (EC No.): [http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/3/1/84.html EC 2.3.1.84]
Biological Origin: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=4932&lvl=3&lin=f&keep=1&srchmode=1&unlock Saccharomyces cerevisiae]
Literature references (PubMed IDs): [http://www.ncbi.nlm.nih.gov/pubmed/8085822?dopt=Abstract PM 8085822,] [http://www.ncbi.nlm.nih.gov/pubmed/12937998?dopt=Abstract PM 12937998,] [http://www.ncbi.nlm.nih.gov/pubmed/17891501?dopt=Abstract PM 17891501]
Designer: [http://parts2.mit.edu/wiki/index.php/MIT_2006 Andre Green]
For Protein Coding Sequences - Repressors and Activators:
Box Heading:
REFERENCE INFORMATION LINKS FOR ___________ (part number inserted automatically)
Box Content
Source of original DNA sequence:
- GenBank GI: ___________
- Other: ___________
Structure (PDB_ID): ___________
UniProt (Accession No.): ___________
Biological Origin: ___________
Literature references: ___________ (Up to three PubMed IDs)
Designer homepage: ___________
For Protein Coding Sequences - Repressors and Activators - Example:
Box Heading:
INFORMATION LINKS FOR BBa_C0040
Box Content:
NAME: Tetracycline repressor from transposon Tn10]
Nickname: tetR
Source of original DNA sequence:
- GenBank [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=Nucleotide&dopt=GenBank&val=42494906 GI: 42494906]
Other: n/a
Structure (PDB_ID): [http://www.pdb.org/pdb/cgi/explore.cgi?pdbId=2NS7 2NS7]
UniProt (Accession No.): [http://www.uniprot.org/uniprot/Q6QR72 Q6QR72]
Biological Origin: [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=562 Escherichia coli]
Literature references (PubMed IDs): [http://www.ncbi.nlm.nih.gov/pubmed/9092630?dopt=Abstract PM 9092630]
Designer: June Rhee, Connie Tao, Ty Thomson, Louis Waldman
For Terminators:
Box Heading:
REFERENCE INFORMATION LINKS FOR ___________ (part number inserted automatically)
Box Content
Source of original DNA sequence:
- GenBank GI: ___________
- Other: ___________
3D-Structure (NDB_ID): ___________
Rfam entry: ___________
Secondary-Structure Prediction Tools: ___________
Biological Origin: ___________
Literature references: ___________ (Up to three PubMed IDs)
Designer homepage: ___________