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root/owl/trunk/src/owl/core/sequence/geneticCode.dat
Revision: 1114
Committed: Wed Jun 16 10:26:22 2010 UTC (12 years, 3 months ago) by jmduarteg
File size: 10644 byte(s)
Log Message:
New feature: code for dna to protein translation
Line User Rev File contents
1 jmduarteg 1114 --**************************************************************************
2     -- This is the NCBI genetic code table
3     -- Initial base data set from Andrzej Elzanowski while at PIR International
4     -- Addition of Eubacterial and Alternative Yeast by J.Ostell at NCBI
5     -- Base 1-3 of each codon have been added as comments to facilitate
6     -- readability at the suggestion of Peter Rice, EMBL
7     -- Later additions by Taxonomy Group staff at NCBI
8     --
9     -- Version 3.9
10     -- Code 14 differs from code 9 only by translating UAA to Tyr rather than
11     -- STOP. A recent study (Telford et al, 2000) has found no evidence that
12     -- the codon UAA codes for Tyr in the flatworms, but other opinions exist.
13     -- There are very few GenBank records that are translated with code 14,
14     -- but a test translation shows that retranslating these records with code
15     -- 9 can cause premature terminations. Therefore, GenBank will maintain
16     -- code 14 until further information becomes available.
17     --
18     -- Version 3.8
19     -- Added GTG start to Echinoderm mitochondrial code, code 9
20     --
21     -- Version 3.7
22     -- Added code 23 Thraustochytrium mitochondrial code
23     -- formerly OGMP code 93
24     -- submitted by Gertraude Berger, Ph.D.
25     --
26     -- Version 3.6
27     -- Added code 22 TAG-Leu, TCA-stop
28     -- found in mitochondrial DNA of Scenedesmus obliquus
29     -- submitted by Gertraude Berger, Ph.D.
30     -- Organelle Genome Megasequencing Program, Univ Montreal
31     --
32     -- Version 3.5
33     -- Added code 21, Trematode Mitochondrial
34     -- (as deduced from: Garey & Wolstenholme,1989; Ohama et al, 1990)
35     -- Added code 16, Chlorophycean Mitochondrial
36     -- (TAG can translated to Leucine instaed to STOP in chlorophyceans
37     -- and fungi)
38     --
39     -- Version 3.4
40     -- Added CTG,TTG as allowed alternate start codons in Standard code.
41     -- Prats et al. 1989, Hann et al. 1992
42     --
43     -- Version 3.3 - 10/13/95
44     -- Added alternate intiation codon ATC to code 5
45     -- based on complete mitochondrial genome of honeybee
46     -- Crozier and Crozier (1993)
47     --
48     -- Version 3.2 - 6/24/95
49     -- Code Comments
50     -- 10 Alternative Ciliate Macronuclear renamed to Euplotid Macro...
51     -- 15 Bleharisma Macro.. code added
52     -- 5 Invertebrate Mito.. GTG allowed as alternate initiator
53     -- 11 Eubacterial renamed to Bacterial as most alternate starts
54     -- have been found in Achea
55     --
56     --
57     -- Version 3.1 - 1995
58     -- Updated as per Andrzej Elzanowski at NCBI
59     -- Complete documentation in NCBI toolkit documentation
60     -- Note: 2 genetic codes have been deleted
61     --
62     -- Old id Use id - Notes
63     --
64     -- id 7 id 4 - Kinetoplast code now merged in code id 4
65     -- id 8 id 1 - all plant chloroplast differences due to RNA edit
66     --
67     --*************************************************************************
68    
69     Genetic-code-table ::= {
70     {
71     name "Standard" ,
72     name "SGC0" ,
73     id 1 ,
74     ncbieaa "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
75     sncbieaa "---M---------------M---------------M----------------------------"
76     -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
77     -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
78     -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
79     },
80     {
81     name "Vertebrate Mitochondrial" ,
82     name "SGC1" ,
83     id 2 ,
84     ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG",
85     sncbieaa "--------------------------------MMMM---------------M------------"
86     -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
87     -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
88     -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
89     },
90     {
91     name "Yeast Mitochondrial" ,
92     name "SGC2" ,
93     id 3 ,
94     ncbieaa "FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
95     sncbieaa "----------------------------------MM----------------------------"
96     -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
97     -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
98     -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
99     },
100     {
101     name "Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate
102     Mitochondrial; Mycoplasma; Spiroplasma" ,
103     name "SGC3" ,
104     id 4 ,
105     ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
106     sncbieaa "--MM---------------M------------MMMM---------------M------------"
107     -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
108     -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
109     -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
110     },
111     {
112     name "Invertebrate Mitochondrial" ,
113     name "SGC4" ,
114     id 5 ,
115     ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG",
116     sncbieaa "---M----------------------------MMMM---------------M------------"
117     -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
118     -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
119     -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
120     },
121     {
122     name "Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear" ,
123     name "SGC5" ,
124     id 6 ,
125     ncbieaa "FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
126     sncbieaa "-----------------------------------M----------------------------"
127     -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
128     -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
129     -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
130     },
131     {
132     name "Echinoderm Mitochondrial; Flatworm Mitochondrial" ,
133     name "SGC8" ,
134     id 9 ,
135     ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
136     sncbieaa "-----------------------------------M---------------M------------"
137     -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
138     -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
139     -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
140     },
141     {
142     name "Euplotid Nuclear" ,
143     name "SGC9" ,
144     id 10 ,
145     ncbieaa "FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
146     sncbieaa "-----------------------------------M----------------------------"
147     -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
148     -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
149     -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
150     },
151     {
152     name "Bacterial and Plant Plastid" ,
153     id 11 ,
154     ncbieaa "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
155     sncbieaa "---M---------------M------------MMMM---------------M------------"
156     -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
157     -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
158     -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
159     },
160     {
161     name "Alternative Yeast Nuclear" ,
162     id 12 ,
163     ncbieaa "FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
164     sncbieaa "-------------------M---------------M----------------------------"
165     -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
166     -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
167     -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
168     },
169     {
170     name "Ascidian Mitochondrial" ,
171     id 13 ,
172     ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG",
173     sncbieaa "---M------------------------------MM---------------M------------"
174     -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
175     -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
176     -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
177     },
178     {
179     name "Alternative Flatworm Mitochondrial" ,
180     id 14 ,
181     ncbieaa "FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
182     sncbieaa "-----------------------------------M----------------------------"
183     -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
184     -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
185     -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
186     } ,
187     {
188     name "Blepharisma Macronuclear" ,
189     id 15 ,
190     ncbieaa "FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
191     sncbieaa "-----------------------------------M----------------------------"
192     -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
193     -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
194     -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
195     } ,
196     {
197     name "Chlorophycean Mitochondrial" ,
198     id 16 ,
199     ncbieaa "FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
200     sncbieaa "-----------------------------------M----------------------------"
201     -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
202     -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
203     -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
204     } ,
205     {
206     name "Trematode Mitochondrial" ,
207     id 21 ,
208     ncbieaa "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG",
209     sncbieaa "-----------------------------------M---------------M------------"
210     -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
211     -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
212     -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
213     } ,
214     {
215     name "Scenedesmus obliquus Mitochondrial" ,
216     id 22 ,
217     ncbieaa "FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
218     sncbieaa "-----------------------------------M----------------------------"
219     -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
220     -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
221     -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
222     } ,
223     {
224     name "Thraustochytrium Mitochondrial" ,
225     id 23 ,
226     ncbieaa "FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG",
227     sncbieaa "--------------------------------M--M---------------M------------"
228     -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
229     -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
230     -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
231     }
232     }