1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
|
<!-- ============================================
::DATATOOL:: Generated from "seqfeat.asn"
::DATATOOL:: by application DATATOOL version 1.9.0
::DATATOOL:: on 09/15/2008 23:08:25
============================================ -->
<!-- ============================================ -->
<!-- This section is mapped from module "NCBI-RNA"
================================================= -->
<!--
**********************************************************************
NCBI RNAs
by James Ostell, 1990
version 0.8
**********************************************************************
-->
<!-- Elements used by other modules:
RNA-ref,
Trna-ext,
RNA-gen,
RNA-qual,
RNA-qual-set -->
<!-- Elements referenced from other modules:
Seq-loc FROM NCBI-Seqloc -->
<!-- ============================================ -->
<!--
*** rnas ***********************************************
*
* various rnas
*
minimal RNA sequence
-->
<!ELEMENT RNA-ref (
RNA-ref_type,
RNA-ref_pseudo?,
RNA-ref_ext?)>
<!-- type of RNA feature -->
<!ELEMENT RNA-ref_type %ENUM;>
<!--
snRNA - will become ncRNA, with RNA-gen.class = snRNA
scRNA - will become ncRNA, with RNA-gen.class = scRNA
snoRNA - will become ncRNA, with RNA-gen.class = snoRNA
ncRNA - non-coding RNA; subsumes snRNA, scRNA, snoRNA
-->
<!ATTLIST RNA-ref_type value (
unknown |
premsg |
mRNA |
tRNA |
rRNA |
snRNA |
scRNA |
snoRNA |
ncRNA |
tmRNA |
miscRNA |
other
) #REQUIRED >
<!ELEMENT RNA-ref_pseudo EMPTY>
<!ATTLIST RNA-ref_pseudo value ( true | false ) #REQUIRED >
<!-- generic fields for ncRNA, tmRNA, miscRNA -->
<!ELEMENT RNA-ref_ext (
RNA-ref_ext_name |
RNA-ref_ext_tRNA |
RNA-ref_ext_gen)>
<!-- for naming "other" type -->
<!ELEMENT RNA-ref_ext_name (#PCDATA)>
<!-- for tRNAs -->
<!ELEMENT RNA-ref_ext_tRNA (Trna-ext)>
<!ELEMENT RNA-ref_ext_gen (RNA-gen)>
<!-- tRNA feature extensions -->
<!ELEMENT Trna-ext (
Trna-ext_aa?,
Trna-ext_codon?,
Trna-ext_anticodon?)>
<!-- aa this carries -->
<!ELEMENT Trna-ext_aa (
Trna-ext_aa_iupacaa |
Trna-ext_aa_ncbieaa |
Trna-ext_aa_ncbi8aa |
Trna-ext_aa_ncbistdaa)>
<!ELEMENT Trna-ext_aa_iupacaa (%INTEGER;)>
<!ELEMENT Trna-ext_aa_ncbieaa (%INTEGER;)>
<!ELEMENT Trna-ext_aa_ncbi8aa (%INTEGER;)>
<!ELEMENT Trna-ext_aa_ncbistdaa (%INTEGER;)>
<!-- codon(s) as in Genetic-code -->
<!ELEMENT Trna-ext_codon (Trna-ext_codon_E*)>
<!ELEMENT Trna-ext_codon_E (%INTEGER;)>
<!-- location of anticodon -->
<!ELEMENT Trna-ext_anticodon (Seq-loc)>
<!ELEMENT RNA-gen (
RNA-gen_class?,
RNA-gen_product?,
RNA-gen_quals?)>
<!--
for ncRNAs, the class of non-coding RNA:
examples: antisense_RNA, guide_RNA, snRNA
-->
<!ELEMENT RNA-gen_class (#PCDATA)>
<!ELEMENT RNA-gen_product (#PCDATA)>
<!-- e.g., tag_peptide qualifier for tmRNAs -->
<!ELEMENT RNA-gen_quals (RNA-qual-set)>
<!-- Additional data values for RNA-gen, -->
<!ELEMENT RNA-qual (
RNA-qual_qual,
RNA-qual_val)>
<!-- in a tag (qual), value (val) format -->
<!ELEMENT RNA-qual_qual (#PCDATA)>
<!ELEMENT RNA-qual_val (#PCDATA)>
<!ELEMENT RNA-qual-set (RNA-qual*)>
|
