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1 --$Revision: 6.27 $
2 --**********************************************************************
3 --
4 -- NCBI Sequence Feature elements
5 -- by James Ostell, 1990
6 -- Version 3.0 - June 1994
7 --
8 --**********************************************************************
9
10 NCBI-Seqfeat DEFINITIONS ::=
11 BEGIN
12
13 EXPORTS Seq-feat, Feat-id, Genetic-code;
14
15 IMPORTS Gene-ref FROM NCBI-Gene
16 Prot-ref FROM NCBI-Protein
17 Org-ref FROM NCBI-Organism
18 BioSource FROM NCBI-BioSource
19 RNA-ref FROM NCBI-RNA
20 Seq-loc, Giimport-id FROM NCBI-Seqloc
21 Pubdesc, Numbering, Heterogen FROM NCBI-Sequence
22 Rsite-ref FROM NCBI-Rsite
23 Txinit FROM NCBI-TxInit
24 Pub-set FROM NCBI-Pub
25 Object-id, Dbtag, User-object FROM NCBI-General;
26
27 --*** Feature identifiers ********************************
28 --*
29
30 Feat-id ::= CHOICE {
31 gibb INTEGER , -- geninfo backbone
32 giim Giimport-id , -- geninfo import
33 local Object-id , -- for local software use
34 general Dbtag } -- for use by various databases
35
36 --*** Seq-feat *******************************************
37 --* sequence feature generalization
38
39 Seq-feat ::= SEQUENCE {
40 id Feat-id OPTIONAL ,
41 data SeqFeatData , -- the specific data
42 partial BOOLEAN OPTIONAL , -- incomplete in some way?
43 except BOOLEAN OPTIONAL , -- something funny about this?
44 comment VisibleString OPTIONAL ,
45 product Seq-loc OPTIONAL , -- product of process
46 location Seq-loc , -- feature made from
47 qual SEQUENCE OF Gb-qual OPTIONAL , -- qualifiers
48 title VisibleString OPTIONAL , -- for user defined label
49 ext User-object OPTIONAL , -- user defined structure extension
50 cit Pub-set OPTIONAL , -- citations for this feature
51 exp-ev ENUMERATED { -- evidence for existence of feature
52 experimental (1) , -- any reasonable experimental check
53 not-experimental (2) } OPTIONAL , -- similarity, pattern, etc
54 xref SET OF SeqFeatXref OPTIONAL , -- cite other relevant features
55 dbxref SET OF Dbtag OPTIONAL , -- support for xref to other databases
56 pseudo BOOLEAN OPTIONAL , -- annotated on pseudogene?
57 except-text VisibleString OPTIONAL , -- explain if except=TRUE
58 ids SET OF Feat-id OPTIONAL , -- set of Ids; will replace 'id' field
59 exts SET OF User-object OPTIONAL } -- set of extensions; will replace 'ext' field
60
61 SeqFeatData ::= CHOICE {
62 gene Gene-ref ,
63 org Org-ref ,
64 cdregion Cdregion ,
65 prot Prot-ref ,
66 rna RNA-ref ,
67 pub Pubdesc , -- publication applies to this seq
68 seq Seq-loc , -- to annotate origin from another seq
69 imp Imp-feat ,
70 region VisibleString, -- named region (globin locus)
71 comment NULL , -- just a comment
72 bond ENUMERATED {
73 disulfide (1) ,
74 thiolester (2) ,
75 xlink (3) ,
76 thioether (4) ,
77 other (255) } ,
78 site ENUMERATED {
79 active (1) ,
80 binding (2) ,
81 cleavage (3) ,
82 inhibit (4) ,
83 modified (5),
84 glycosylation (6) ,
85 myristoylation (7) ,
86 mutagenized (8) ,
87 metal-binding (9) ,
88 phosphorylation (10) ,
89 acetylation (11) ,
90 amidation (12) ,
91 methylation (13) ,
92 hydroxylation (14) ,
93 sulfatation (15) ,
94 oxidative-deamination (16) ,
95 pyrrolidone-carboxylic-acid (17) ,
96 gamma-carboxyglutamic-acid (18) ,
97 blocked (19) ,
98 lipid-binding (20) ,
99 np-binding (21) ,
100 dna-binding (22) ,
101 signal-peptide (23) ,
102 transit-peptide (24) ,
103 transmembrane-region (25) ,
104 nitrosylation (26) ,
105 other (255) } ,
106 rsite Rsite-ref , -- restriction site (for maps really)
107 user User-object , -- user defined structure
108 txinit Txinit , -- transcription initiation
109 num Numbering , -- a numbering system
110 psec-str ENUMERATED { -- protein secondary structure
111 helix (1) , -- any helix
112 sheet (2) , -- beta sheet
113 turn (3) } , -- beta or gamma turn
114 non-std-residue VisibleString , -- non-standard residue here in seq
115 het Heterogen , -- cofactor, prosthetic grp, etc, bound to seq
116 biosrc BioSource,
117 clone Clone-ref
118 }
119
120 SeqFeatXref ::= SEQUENCE { -- both optional because can have one or both
121 id Feat-id OPTIONAL , -- the feature copied
122 data SeqFeatData OPTIONAL } -- the specific data
123
124 --*** CdRegion ***********************************************
125 --*
126 --* Instructions to translate from a nucleic acid to a peptide
127 --* conflict means it's supposed to translate but doesn't
128 --*
129
130
131 Cdregion ::= SEQUENCE {
132 orf BOOLEAN OPTIONAL , -- just an ORF ?
133 frame ENUMERATED {
134 not-set (0) , -- not set, code uses one
135 one (1) ,
136 two (2) ,
137 three (3) } DEFAULT not-set , -- reading frame
138 conflict BOOLEAN OPTIONAL , -- conflict
139 gaps INTEGER OPTIONAL , -- number of gaps on conflict/except
140 mismatch INTEGER OPTIONAL , -- number of mismatches on above
141 code Genetic-code OPTIONAL , -- genetic code used
142 code-break SEQUENCE OF Code-break OPTIONAL , -- individual exceptions
143 stops INTEGER OPTIONAL } -- number of stop codons on above
144
145 -- each code is 64 cells long, in the order where
146 -- T=0,C=1,A=2,G=3, TTT=0, TTC=1, TCA=4, etc
147 -- NOTE: this order does NOT correspond to a Seq-data
148 -- encoding. It is "natural" to codon usage instead.
149 -- the value in each cell is the AA coded for
150 -- start= AA coded only if first in peptide
151 -- in start array, if codon is not a legitimate start
152 -- codon, that cell will have the "gap" symbol for
153 -- that alphabet. Otherwise it will have the AA
154 -- encoded when that codon is used at the start.
155
156 Genetic-code ::= SET OF CHOICE {
157 name VisibleString , -- name of a code
158 id INTEGER , -- id in dbase
159 ncbieaa VisibleString , -- indexed to IUPAC extended
160 ncbi8aa OCTET STRING , -- indexed to NCBI8aa
161 ncbistdaa OCTET STRING , -- indexed to NCBIstdaa
162 sncbieaa VisibleString , -- start, indexed to IUPAC extended
163 sncbi8aa OCTET STRING , -- start, indexed to NCBI8aa
164 sncbistdaa OCTET STRING } -- start, indexed to NCBIstdaa
165
166 Code-break ::= SEQUENCE { -- specific codon exceptions
167 loc Seq-loc , -- location of exception
168 aa CHOICE { -- the amino acid
169 ncbieaa INTEGER , -- ASCII value of NCBIeaa code
170 ncbi8aa INTEGER , -- NCBI8aa code
171 ncbistdaa INTEGER } } -- NCBIstdaa code
172
173 Genetic-code-table ::= SET OF Genetic-code -- table of genetic codes
174
175 --*** Import ***********************************************
176 --*
177 --* Features imported from other databases
178 --*
179
180 Imp-feat ::= SEQUENCE {
181 key VisibleString ,
182 loc VisibleString OPTIONAL , -- original location string
183 descr VisibleString OPTIONAL } -- text description
184
185 Gb-qual ::= SEQUENCE {
186 qual VisibleString ,
187 val VisibleString }
188
189
190 --*** Clone-ref ***********************************************
191 --*
192 --* Specification of clone features
193 --*
194
195 Clone-ref ::= SEQUENCE {
196 name VisibleString, -- Official clone symbol
197 library VisibleString OPTIONAL, -- Library name
198
199 concordant BOOLEAN DEFAULT FALSE, -- OPTIONAL?
200 unique BOOLEAN DEFAULT FALSE, -- OPTIONAL?
201 placement-method INTEGER {
202 end-seq (0), -- Clone placed by end sequence
203 insert-alignment (1), -- Clone placed by insert alignment
204 sts (2), -- Clone placed by STS
205 fish (3),
206 fingerprint (4),
207 other (255)
208 } OPTIONAL,
209 clone-seq Clone-seq-set OPTIONAL
210 }
211
212 Clone-seq-set ::= SET OF Clone-seq
213
214
215 Clone-seq ::= SEQUENCE {
216 type INTEGER {
217 insert (0),
218 end (1),
219 other (255)
220 },
221 confidence INTEGER {
222 multiple (0), -- Multiple hits
223 na (1), -- Unspecified
224 nohit-rep (2), -- No hits, repetitive
225 nohitnorep (3), -- No hits, not repetitive
226 other-chrm (4), -- Hit on different chromosome
227 unique (5),
228 virtual (6), -- Virtual (hasn't been sequenced)
229 other (255)
230 } OPTIONAL,
231 location Seq-loc, -- location on sequence
232 seq Seq-loc OPTIONAL, -- clone sequence location
233 align-id Dbtag OPTIONAL
234 }
235
236
237 END
238
239 --**********************************************************************
240 --
241 -- NCBI Restriction Sites
242 -- by James Ostell, 1990
243 -- version 0.8
244 --
245 --**********************************************************************
246
247 NCBI-Rsite DEFINITIONS ::=
248 BEGIN
249
250 EXPORTS Rsite-ref;
251
252 IMPORTS Dbtag FROM NCBI-General;
253
254 Rsite-ref ::= CHOICE {
255 str VisibleString , -- may be unparsable
256 db Dbtag } -- pointer to a restriction site database
257
258 END
259
260 --**********************************************************************
261 --
262 -- NCBI RNAs
263 -- by James Ostell, 1990
264 -- version 0.8
265 --
266 --**********************************************************************
267
268 NCBI-RNA DEFINITIONS ::=
269 BEGIN
270
271 EXPORTS RNA-ref, Trna-ext, RNA-gen, RNA-qual, RNA-qual-set;
272
273 IMPORTS Seq-loc FROM NCBI-Seqloc;
274
275 --*** rnas ***********************************************
276 --*
277 --* various rnas
278 --*
279 -- minimal RNA sequence
280 RNA-ref ::= SEQUENCE {
281 type ENUMERATED { -- type of RNA feature
282 unknown (0) ,
283 premsg (1) ,
284 mRNA (2) ,
285 tRNA (3) ,
286 rRNA (4) ,
287 snRNA (5) , -- will become ncRNA, with RNA-gen.class = snRNA
288 scRNA (6) , -- will become ncRNA, with RNA-gen.class = scRNA
289 snoRNA (7) , -- will become ncRNA, with RNA-gen.class = snoRNA
290 ncRNA (8) , -- non-coding RNA; subsumes snRNA, scRNA, snoRNA
291 tmRNA (9) ,
292 miscRNA (10) ,
293 other (255) } ,
294 pseudo BOOLEAN OPTIONAL ,
295 ext CHOICE {
296 name VisibleString , -- for naming "other" type
297 tRNA Trna-ext , -- for tRNAs
298 gen RNA-gen } OPTIONAL -- generic fields for ncRNA, tmRNA, miscRNA
299 }
300
301 Trna-ext ::= SEQUENCE { -- tRNA feature extensions
302 aa CHOICE { -- aa this carries
303 iupacaa INTEGER ,
304 ncbieaa INTEGER ,
305 ncbi8aa INTEGER ,
306 ncbistdaa INTEGER } OPTIONAL ,
307 codon SET OF INTEGER OPTIONAL , -- codon(s) as in Genetic-code
308 anticodon Seq-loc OPTIONAL } -- location of anticodon
309
310 RNA-gen ::= SEQUENCE {
311 class VisibleString OPTIONAL , -- for ncRNAs, the class of non-coding RNA:
312 -- examples: antisense_RNA, guide_RNA, snRNA
313 product VisibleString OPTIONAL ,
314 quals RNA-qual-set OPTIONAL -- e.g., tag_peptide qualifier for tmRNAs
315 }
316
317 RNA-qual ::= SEQUENCE { -- Additional data values for RNA-gen,
318 qual VisibleString , -- in a tag (qual), value (val) format
319 val VisibleString }
320
321 RNA-qual-set ::= SEQUENCE OF RNA-qual
322
323 END
324
325 --**********************************************************************
326 --
327 -- NCBI Genes
328 -- by James Ostell, 1990
329 -- version 0.8
330 --
331 --**********************************************************************
332
333 NCBI-Gene DEFINITIONS ::=
334 BEGIN
335
336 EXPORTS Gene-ref, Gene-nomenclature;
337
338 IMPORTS Dbtag FROM NCBI-General;
339
340 --*** Gene ***********************************************
341 --*
342 --* reference to a gene
343 --*
344
345 Gene-ref ::= SEQUENCE {
346 locus VisibleString OPTIONAL , -- Official gene symbol
347 allele VisibleString OPTIONAL , -- Official allele designation
348 desc VisibleString OPTIONAL , -- descriptive name
349 maploc VisibleString OPTIONAL , -- descriptive map location
350 pseudo BOOLEAN DEFAULT FALSE , -- pseudogene
351 db SET OF Dbtag OPTIONAL , -- ids in other dbases
352 syn SET OF VisibleString OPTIONAL , -- synonyms for locus
353 locus-tag VisibleString OPTIONAL , -- systematic gene name (e.g., MI0001, ORF0069)
354 formal-name Gene-nomenclature OPTIONAL
355 }
356
357 Gene-nomenclature ::= SEQUENCE {
358 status ENUMERATED {
359 unknown (0) ,
360 official (1) ,
361 interim (2)
362 } ,
363 symbol VisibleString OPTIONAL ,
364 name VisibleString OPTIONAL ,
365 source Dbtag OPTIONAL
366 }
367
368 END
369
370
371 --**********************************************************************
372 --
373 -- NCBI Organism
374 -- by James Ostell, 1994
375 -- version 3.0
376 --
377 --**********************************************************************
378
379 NCBI-Organism DEFINITIONS ::=
380 BEGIN
381
382 EXPORTS Org-ref;
383
384 IMPORTS Dbtag FROM NCBI-General;
385
386 --*** Org-ref ***********************************************
387 --*
388 --* Reference to an organism
389 --* defines only the organism.. lower levels of detail for biological
390 --* molecules are provided by the Source object
391 --*
392
393 Org-ref ::= SEQUENCE {
394 taxname VisibleString OPTIONAL , -- preferred formal name
395 common VisibleString OPTIONAL , -- common name
396 mod SET OF VisibleString OPTIONAL , -- unstructured modifiers
397 db SET OF Dbtag OPTIONAL , -- ids in taxonomic or culture dbases
398 syn SET OF VisibleString OPTIONAL , -- synonyms for taxname or common
399 orgname OrgName OPTIONAL }
400
401
402 OrgName ::= SEQUENCE {
403 name CHOICE {
404 binomial BinomialOrgName , -- genus/species type name
405 virus VisibleString , -- virus names are different
406 hybrid MultiOrgName , -- hybrid between organisms
407 namedhybrid BinomialOrgName , -- some hybrids have genus x species name
408 partial PartialOrgName } OPTIONAL , -- when genus not known
409 attrib VisibleString OPTIONAL , -- attribution of name
410 mod SEQUENCE OF OrgMod OPTIONAL ,
411 lineage VisibleString OPTIONAL , -- lineage with semicolon separators
412 gcode INTEGER OPTIONAL , -- genetic code (see CdRegion)
413 mgcode INTEGER OPTIONAL , -- mitochondrial genetic code
414 div VisibleString OPTIONAL } -- GenBank division code
415
416
417 OrgMod ::= SEQUENCE {
418 subtype INTEGER {
419 strain (2) ,
420 substrain (3) ,
421 type (4) ,
422 subtype (5) ,
423 variety (6) ,
424 serotype (7) ,
425 serogroup (8) ,
426 serovar (9) ,
427 cultivar (10) ,
428 pathovar (11) ,
429 chemovar (12) ,
430 biovar (13) ,
431 biotype (14) ,
432 group (15) ,
433 subgroup (16) ,
434 isolate (17) ,
435 common (18) ,
436 acronym (19) ,
437 dosage (20) , -- chromosome dosage of hybrid
438 nat-host (21) , -- natural host of this specimen
439 sub-species (22) ,
440 specimen-voucher (23) ,
441 authority (24) ,
442 forma (25) ,
443 forma-specialis (26) ,
444 ecotype (27) ,
445 synonym (28) ,
446 anamorph (29) ,
447 teleomorph (30) ,
448 breed (31) ,
449 gb-acronym (32) , -- used by taxonomy database
450 gb-anamorph (33) , -- used by taxonomy database
451 gb-synonym (34) , -- used by taxonomy database
452 culture-collection (35) ,
453 bio-material (36) ,
454 metagenome-source (37) ,
455 old-lineage (253) ,
456 old-name (254) ,
457 other (255) } , -- ASN5: old-name (254) will be added to next spec
458 subname VisibleString ,
459 attrib VisibleString OPTIONAL } -- attribution/source of name
460
461 BinomialOrgName ::= SEQUENCE {
462 genus VisibleString , -- required
463 species VisibleString OPTIONAL , -- species required if subspecies used
464 subspecies VisibleString OPTIONAL }
465
466 MultiOrgName ::= SEQUENCE OF OrgName -- the first will be used to assign division
467
468 PartialOrgName ::= SEQUENCE OF TaxElement -- when we don't know the genus
469
470 TaxElement ::= SEQUENCE {
471 fixed-level INTEGER {
472 other (0) , -- level must be set in string
473 family (1) ,
474 order (2) ,
475 class (3) } ,
476 level VisibleString OPTIONAL ,
477 name VisibleString }
478
479 END
480
481
482 --**********************************************************************
483 --
484 -- NCBI BioSource
485 -- by James Ostell, 1994
486 -- version 3.0
487 --
488 --**********************************************************************
489
490 NCBI-BioSource DEFINITIONS ::=
491 BEGIN
492
493 EXPORTS BioSource;
494
495 IMPORTS Org-ref FROM NCBI-Organism;
496
497 --********************************************************************
498 --
499 -- BioSource gives the source of the biological material
500 -- for sequences
501 --
502 --********************************************************************
503
504 BioSource ::= SEQUENCE {
505 genome INTEGER { -- biological context
506 unknown (0) ,
507 genomic (1) ,
508 chloroplast (2) ,
509 chromoplast (3) ,
510 kinetoplast (4) ,
511 mitochondrion (5) ,
512 plastid (6) ,
513 macronuclear (7) ,
514 extrachrom (8) ,
515 plasmid (9) ,
516 transposon (10) ,
517 insertion-seq (11) ,
518 cyanelle (12) ,
519 proviral (13) ,
520 virion (14) ,
521 nucleomorph (15) ,
522 apicoplast (16) ,
523 leucoplast (17) ,
524 proplastid (18) ,
525 endogenous-virus (19) ,
526 hydrogenosome (20) ,
527 chromosome (21) ,
528 chromatophore (22)
529 } DEFAULT unknown ,
530 origin INTEGER {
531 unknown (0) ,
532 natural (1) , -- normal biological entity
533 natmut (2) , -- naturally occurring mutant
534 mut (3) , -- artificially mutagenized
535 artificial (4) , -- artificially engineered
536 synthetic (5) , -- purely synthetic
537 other (255)
538 } DEFAULT unknown ,
539 org Org-ref ,
540 subtype SEQUENCE OF SubSource OPTIONAL ,
541 is-focus NULL OPTIONAL , -- to distinguish biological focus
542 pcr-primers PCRReactionSet OPTIONAL }
543
544 PCRReactionSet ::= SET OF PCRReaction
545
546 PCRReaction ::= SEQUENCE {
547 forward PCRPrimerSet OPTIONAL ,
548 reverse PCRPrimerSet OPTIONAL }
549
550 PCRPrimerSet ::= SET OF PCRPrimer
551
552 PCRPrimer ::= SEQUENCE {
553 seq PCRPrimerSeq OPTIONAL ,
554 name PCRPrimerName OPTIONAL }
555
556 PCRPrimerSeq ::= VisibleString
557
558 PCRPrimerName ::= VisibleString
559
560 SubSource ::= SEQUENCE {
561 subtype INTEGER {
562 chromosome (1) ,
563 map (2) ,
564 clone (3) ,
565 subclone (4) ,
566 haplotype (5) ,
567 genotype (6) ,
568 sex (7) ,
569 cell-line (8) ,
570 cell-type (9) ,
571 tissue-type (10) ,
572 clone-lib (11) ,
573 dev-stage (12) ,
574 frequency (13) ,
575 germline (14) ,
576 rearranged (15) ,
577 lab-host (16) ,
578 pop-variant (17) ,
579 tissue-lib (18) ,
580 plasmid-name (19) ,
581 transposon-name (20) ,
582 insertion-seq-name (21) ,
583 plastid-name (22) ,
584 country (23) ,
585 segment (24) ,
586 endogenous-virus-name (25) ,
587 transgenic (26) ,
588 environmental-sample (27) ,
589 isolation-source (28) ,
590 lat-lon (29) , -- +/- decimal degrees
591 collection-date (30) , -- DD-MMM-YYYY format
592 collected-by (31) , -- name of person who collected the sample
593 identified-by (32) , -- name of person who identified the sample
594 fwd-primer-seq (33) , -- sequence (possibly more than one; semicolon-separated)
595 rev-primer-seq (34) , -- sequence (possibly more than one; semicolon-separated)
596 fwd-primer-name (35) ,
597 rev-primer-name (36) ,
598 metagenomic (37) ,
599 mating-type (38) ,
600 linkage-group (39) ,
601 haplogroup (40) ,
602 other (255) } ,
603 name VisibleString ,
604 attrib VisibleString OPTIONAL } -- attribution/source of this name
605
606 END
607
608 --**********************************************************************
609 --
610 -- NCBI Protein
611 -- by James Ostell, 1990
612 -- version 0.8
613 --
614 --**********************************************************************
615
616 NCBI-Protein DEFINITIONS ::=
617 BEGIN
618
619 EXPORTS Prot-ref;
620
621 IMPORTS Dbtag FROM NCBI-General;
622
623 --*** Prot-ref ***********************************************
624 --*
625 --* Reference to a protein name
626 --*
627
628 Prot-ref ::= SEQUENCE {
629 name SET OF VisibleString OPTIONAL , -- protein name
630 desc VisibleString OPTIONAL , -- description (instead of name)
631 ec SET OF VisibleString OPTIONAL , -- E.C. number(s)
632 activity SET OF VisibleString OPTIONAL , -- activities
633 db SET OF Dbtag OPTIONAL , -- ids in other dbases
634 processed ENUMERATED { -- processing status
635 not-set (0) ,
636 preprotein (1) ,
637 mature (2) ,
638 signal-peptide (3) ,
639 transit-peptide (4) } DEFAULT not-set }
640
641
642
643 END
644 --********************************************************************
645 --
646 -- Transcription Initiation Site Feature Data Block
647 -- James Ostell, 1991
648 -- Philip Bucher, David Ghosh
649 -- version 1.1
650 --
651 --
652 --
653 --********************************************************************
654
655 NCBI-TxInit DEFINITIONS ::=
656 BEGIN
657
658 EXPORTS Txinit;
659
660 IMPORTS Gene-ref FROM NCBI-Gene
661 Prot-ref FROM NCBI-Protein
662 Org-ref FROM NCBI-Organism;
663
664 Txinit ::= SEQUENCE {
665 name VisibleString , -- descriptive name of initiation site
666 syn SEQUENCE OF VisibleString OPTIONAL , -- synonyms
667 gene SEQUENCE OF Gene-ref OPTIONAL , -- gene(s) transcribed
668 protein SEQUENCE OF Prot-ref OPTIONAL , -- protein(s) produced
669 rna SEQUENCE OF VisibleString OPTIONAL , -- rna(s) produced
670 expression VisibleString OPTIONAL , -- tissue/time of expression
671 txsystem ENUMERATED { -- transcription apparatus used at this site
672 unknown (0) ,
673 pol1 (1) , -- eukaryotic Pol I
674 pol2 (2) , -- eukaryotic Pol II
675 pol3 (3) , -- eukaryotic Pol III
676 bacterial (4) ,
677 viral (5) ,
678 rna (6) , -- RNA replicase
679 organelle (7) ,
680 other (255) } ,
681 txdescr VisibleString OPTIONAL , -- modifiers on txsystem
682 txorg Org-ref OPTIONAL , -- organism supplying transcription apparatus
683 mapping-precise BOOLEAN DEFAULT FALSE , -- mapping precise or approx
684 location-accurate BOOLEAN DEFAULT FALSE , -- does Seq-loc reflect mapping
685 inittype ENUMERATED {
686 unknown (0) ,
687 single (1) ,
688 multiple (2) ,
689 region (3) } OPTIONAL ,
690 evidence SET OF Tx-evidence OPTIONAL }
691
692 Tx-evidence ::= SEQUENCE {
693 exp-code ENUMERATED {
694 unknown (0) ,
695 rna-seq (1) , -- direct RNA sequencing
696 rna-size (2) , -- RNA length measurement
697 np-map (3) , -- nuclease protection mapping with homologous sequence ladder
698 np-size (4) , -- nuclease protected fragment length measurement
699 pe-seq (5) , -- dideoxy RNA sequencing
700 cDNA-seq (6) , -- full-length cDNA sequencing
701 pe-map (7) , -- primer extension mapping with homologous sequence ladder
702 pe-size (8) , -- primer extension product length measurement
703 pseudo-seq (9) , -- full-length processed pseudogene sequencing
704 rev-pe-map (10) , -- see NOTE (1) below
705 other (255) } ,
706 expression-system ENUMERATED {
707 unknown (0) ,
708 physiological (1) ,
709 in-vitro (2) ,
710 oocyte (3) ,
711 transfection (4) ,
712 transgenic (5) ,
713 other (255) } DEFAULT physiological ,
714 low-prec-data BOOLEAN DEFAULT FALSE ,
715 from-homolog BOOLEAN DEFAULT FALSE } -- experiment actually done on
716 -- close homolog
717
718 -- NOTE (1) length measurement of a reverse direction primer-extension
719 -- product (blocked by RNA 5'end) by comparison with
720 -- homologous sequence ladder (J. Mol. Biol. 199, 587)
721
722
723 END
724
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