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root/owl/trunk/src/owl/core/sequence/geneticCode.dat
Revision: 1114
Committed: Wed Jun 16 10:26:22 2010 UTC (9 years, 3 months ago) by jmduarteg
File size: 10644 byte(s)
Log Message:
New feature: code for dna to protein translation
Line File contents
1 --**************************************************************************
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 }