source: trunk/lib/submit/embl_newsubmission_wl

Last change on this file was 5390, checked in by westram, 16 years ago
  • TAB-Ex
  • Property svn:eol-style set to native
  • Property svn:executable set to *
  • Property svn:keywords set to Author Date Id Revision
File size: 14.2 KB
Line 
1------------------------------------------------------
2
3EMBL NUCLEOTIDE SEQUENCE DATABASE SUBMISSION FORM
4
5HOW TO USE THIS FORM - PLEASE READ FIRST
6
71) WEBIN: THE WORLD WIDE WEB SUBMISSION TOOL
8============================================
9If you have access to the World Wide Web then DO NOT use this form. Use the
10WebIn form on the World Wide Web at
11
12           ##############################################
13           # http://www.ebi.ac.uk/submission/webin.html #
14           ##############################################
15
16If you do not have access to the World Wide Web then please use this form
17and email it to DATASUBS@EBI.AC.UK.
18
19It is only necessary to submit to one database. Public data are exchanged
20between EMBL, GenBank and DDBJ on a daily basis.
21
222) MULTIPLE SUBMISSIONS
23=======================
24If you have more than one but less than 25 sequences to submit, copy this
25form and send all the submissions together in one email with a note saying
26how many sequences you are sending.
27
283) BULK SUBMISSIONS
29===================
30If you have more than 25 related sequences to submit DO NOT send them all
31using this form. Instead email DATASUBS@EBI.AC.UK and include the following
32information
33a) how many sequences you are going to submit
34b) a short explanation of how the sequences are related
35c) what type of differences there are between the entries (e.g. isolate)
36d) one completed email submission form as an example
37You will be contacted by a curator who will create a template for you which
38you should then use to submit all of the sequences.
39
404) UPDATES
41==========
42DO NOT use this form for submitting updates or corrections.
43If you are sending an update please complete the update form available on
44the web at: http://www.ebi.ac.uk/ebi_docs/update.html or get a copy of the
45update form via anonymous FTP:
46ftp://ftp.ebi.ac.uk/pub/databases/embl/release/update.doc
47If you need help with updates contact UPDATE@EBI.AC.UK
48
495) PROTEIN SEQUENCES
50====================
51DO NOT use this form to submit protein sequences.
52For submissions to the SWISS-PROT protein sequence databank access the
53World Wide Web at http://www.ebi.ac.uk/ebi_docs/swissprot_db/swisshome.html
54or email DATALIB@EBI.AC.UK
55
566) ACCESSION NUMBERS AND CONFIDENTIALITY
57========================================
58Your data can be made public immediately, or they can be kept confidential
59until a release date which you provide. Confidential data are ALWAYS made
60available to the public after publication.
61
62If your data contain all the information we require we will assign unique
63accession numbers within two working days. We will email you to tell you
64the new accession numbers.
65
66You should submit your sequence data BEFORE you have galley proofs. We
67suggest that the following text be used to cite the accession number(s) in
68publication(s): "The nucleotide sequence data reported in this paper will
69appear in the DDBJ/EMBL/GenBank Nucleotide Sequence Database under the
70accession number(s) ________"
71
727) FORM FILLING INSTRUCTIONS
73============================
74
75<============== DO NOT EXCEED THIS LINE WIDTH IN YOUR REPLY ==============>
76
77To display this form properly choose a fixed width font (e.g. Courier) in
78your editor. If you are saving files in a word processing program then
79please save the file as TEXT ONLY WITH LINE BREAKS. (To do this in
80Microscoft Word you will need to choose File, Save as, Save file type as,
81and select Text only with line breaks). Please do not send files that are
82saved in Word or Wordperfect format. Processing of the submission may be
83delayed if your email is text wrapped, encoded or binhexed.
84
85  ########################################################################
86  # Fill in the form as follows:                                         #
87  # a) if there is a colon : then enter text (e.g. Last name    : Smith) #
88  # b) if there is an empty box [ ] and if the answer is yes then fill   #
89  #    the box with an X (e.g. Genomic DNA     [X])                      #
90  # c) if the option is not relevant then do not enter any text and/or   #
91  #    do not write an X in the box.                                     #
92  # d) DO NOT delete lines from this form.                               #
93  ########################################################################
94
958) ENTERING FEATURES AND LOCATIONS
96==================================
97Enter the feature key from the list given in Appendix I at the end of this
98document. Enter the locations, gene name, product name, and EC number,
99where appropriate. Use < and > in the locations to show whether the feature
100is partial at the 5' end and/or the 3' end. Mark with an X in the box [ ]
101if the feature is on the complementary strand and if you have experimental
102evidence for the feature.
103
104If you do not provide any features or adequate locations and names for the
105features you will be contacted for more information before an accession
106number is assigned to the sequence. For CDS features you must provide a gene
107name AND a product name, even if the product name is putative.
108
109If a CDS is partial at the 5' end then write the codon start number. This
110is the number (1,2 or 3) of the first base of the first complete codon of
111the translation. For example the following CDS is partial and the codon
112start is 2 because the first complete codon, T, starts with the base a,
113which is the second base in the feature.
114DNA         tacatcgatg...
115Translation  T  S  M...
116
117FEATURE EXAMPLE NO.1
118Feature key           :CDS
119>From                  :201
120To                    :500
121Gene name             :abcD
122Product name          :ABC repressor protein
123Codon start 1,2 or 3  :
124EC number             :
125Complementary strand  [ ]
126Experimental evidence [X]
127
128FEATURE EXAMPLE NO.2
129Feature key           :rRNA
130>From                  :<1
131To                    :>1500
132Gene name             :16S rRNA
133Product name          :16S ribosomal RNA
134Codon start 1,2 or 3  :
135EC number             :
136Complementary strand  [ ]
137Experimental evidence [ ]
138
139If you have further questions after reading this form please contact
140DATASUBS@EBI.AC.UK
141
142I.  CONFIDENTIAL STATUS
143
144Enter an X if you want these data to be confidential    [ ]
145If confidential write the release date here :
146(Date format DD-MMM-YYYY e.g. 30-JUN-1998)
147
148
149II.  CONTACT INFORMATION
150
151Last name            :$(LAST_NAME)           
152First name           :$(FIRST_NAME)         
153Middle initials      :
154Department           :$(DEPT)
155Institution          :$(INSTITUTION)
156Address              :$(ADDRESS)
157                     :
158                     :
159Country              :$(COUNTRY)
160Telephone            :$(PHONE)
161Fax                  :$(TELEFAX)
162Email                :$(MAIL)                                                         
163
164
165III. CITATION INFORMATION
166
167Author 1             :$(author_1)
168Author 2             :$(author_2)
169Author 3             :$(author_3)
170Author 4             :$(author_4)
171Author 5             :$(author_5)
172Author 6             :$(author_6)
173Author 7             :$(author_7)
174Author 8             :$(author_8)
175Author 9             :$(author_9)
176Author 10            :$(author_10)
177Author 11            :$(author_11)
178Author 12            :$(author_12)
179(e.g. Smith A.B.)
180(Copy line for extra authors)
181Title                :$(title)
182Journal              :$(journal)
183Volume               :$(volume)
184First page           :$(page_1)
185Last page            :$(page_2)
186Year                 :$(year_pub)
187Institute (if thesis):
188
189Publication status
190Mark one of the following
191In preparation       [ ]
192Accepted             [x]
193Published            [ ]
194Thesis/Book          [ ]
195No plans to publish  [ ]
196
197
198IV. SEQUENCE INFORMATION
199
200Sequence length (bp) :$(SEQ_LEN)
201
202Molecule type
203Mark one of the following
204Genomic DNA          [ ]
205cDNA to mRNA         [ ]
206rRNA                 [x]
207tRNA                 [ ]
208Genomic RNA          [ ]
209cDNA to genomic RNA  [ ]
210
211Mark if either of these apply
212Circular             [ ]
213Checked for vector
214contamination        [ ]
215
216
217V. SOURCE INFORMATION
218
219Organism             :$(full_name)
220Sub species          :
221Strain               :$(strain)
222Cultivar             :
223Variety              :
224Isolate/individual   :
225Developmental stage  :
226Tissue type          :
227Cell type            :
228Cell line            :
229Clone                :$(clone)
230Clone (if >1)        :
231Clone library        :
232Chromosome           :
233Map position         :
234Haplotype            :
235Natural host         :
236Laboratory host      :
237Macronuclear         [ ]
238
239Mark one if immunoglobulin
240or T cell receptor
241Germline             [ ]
242Rearranged           [ ]
243
244Mark one if viral
245Proviral             [ ]
246Virion               [ ]
247
248Mark one if from an organelle
249Chloroplast          [ ]
250Mitochondrion        [ ]
251Chromoplast          [ ]
252Kinetoplast          [ ]
253Cyanelle             [ ]
254Plasmid (not clone)  [ ]
255
256Further source information
257(e.g. taxonomy, specimen voucher etc)
258Note                 :$(tax)
259
260
261VI. FEATURES OF THE SEQUENCE
262
263
264YOU MUST DESCRIBE AT LEAST ONE FEATURE OF THE SEQUENCE OR THERE WILL BE A
265DELAY IN THE PROCESSING OF YOUR SUBMISSION
266
267
268Complete the block below for every feature you need to describe. If you
269have more than one feature copy the block as many times as you require. For
270help see 8) ENTERING FEATURES AND LOCATIONS above.
271
272 
273FEATURE NO.1
274Feature key           :$(seq_type)
275>From                  :$(start)
276To                    :$(end)
277Gene name             :$(gene)
278Product name          :$(gene_prod)
279Codon start 1,2 or 3  :
280EC number             :
281Complementary strand  [ ]
282Experimental evidence [ ]
283
284
285VII. SEQUENCE INFORMATION
286
287Enter the sequence data below
288(IUPAC nucleotide base codes, Nucl. Acids Res. 13: 3021-3030, 1985)
289
290BEGINNING OF SEQUENCE:
291$(SEQUENCE)
292
293END OF SEQUENCE
294
295
296Include the translation for each CDS feature below.
297
298
299BEGINNING OF TRANSLATION:
300
301
302END OF TRANSLATION
303
304
305---------------------------------------------------------------------------
306These data will be shared among the following databases: DDBJ Database
307(DNA Data Bank of Japan; Mishima, Japan); EMBL Nucleotide Sequence Database
308(EBI, Cambridge, UK); GenBank (NCBI, Bethesda, USA); SWISS-PROT Protein
309Sequence Database (Geneva, Switzerland and Heidelberg, FRG); International
310Protein Information Database in Japan (JIPID; Noda, Japan) Martinsried
311Institute For Protein Sequence Data (MIPS; Martinsried, FRG) National
312Biomedical Research Foundation Protein Identification Resource (NBRF-PIR;
313Washington, D.C., USA.)
314
315EMBL Data Submissions                     E-mail    datasubs@ebi.ac.uk
316European Bioinformatics Inst.             Telephone +44 (0)1223 494499
317Hinxton Hall, Hinxton                     Telefax   +44 (0)1223 494472
318Cambridge CB10 1SD, UK
319---------------------------------------------------------------------------
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353APPENDIX I FEATURE KEYS
354=======================
355A full description of features is found in the DDBJ/EMBL/GenBank Feature
356Table Definition Document at
357ftp://ftp.ebi.ac.uk/pub/databases/embl/release/ftable.doc
358and on the EBI website at
359http://www.ebi.ac.uk/ebi_docs/embl_db/ft/feature_table.html
360An abbreviated list of features keys is given below
361
362C_region         constant region of immunoglobulin light and heavy chain,
363                 and T-cell receptor alpha, beta and gamma chains
364CAAT_signal      eukaryotic promoter element; consensus=GG(C or T)CAATCT
365CDS              protein coding sequence (includes stop codon)
366conflict         the "same" sequence reported by different laboratories
367                 differ at this site or region       
368D-segment        diversity segment of immunoglobulin heavy chain and
369                 T-cell receptor beta-chain
370enhancer         cis-acting enhancer of eukaryotic promoter function
371exon             region that codes for part of spliced mRNA
372GC_signal        eukaryotic promoter element; consensus=GGGCGG
373intron           transcribed region excised by mRNA splicing
374J_segment        joining segment of immunoglobulin light and heavy chains,
375                 T-cell receptor alpha, beta and gamma-chains
376LTR              long terminal repeat
377mat_peptide      mature peptide coding region (does not include stop codon)
378                 or signal peptide
379misc_feature     region of biological interest which cannot be described
380                 by any other known feature
381mRNA             messenger RNA
382mutation         a related strain has an abrupt, inheritable change in the
383                 sequence
384polyA_signal     polyadenylation signal recognition region
385polyA_site       polyadenylation site to which adenine residues are added
386primer_bind      non-covalent primer binding site
387promoter         promoter region involved in transcription initiation
388protein_bind     non-covalent protein binding site on DNA or RNA
389RBS              ribosome binding site
390rep_origin       origin of replication
391repeat_region    region of genome containing repeating units
392repeat_unit      single repeat element
393rRNA             ribosomal RNA
394S_region         switch region of immunoglobulin heavy chains
395satellite        many tandem repeats of a short basic repeating unit
396sig_peptide      signal peptide coding region
397stem_loop        hair-pin loop structure in DNA or RNA
398STS              sequence tagged site
399TATA_signal      eukaryotic promoter element; consensus=TATA(A or T)A(A or T)
400terminator       transcription termination signal
401transit_peptide  transit peptide coding region
402tRNA             transfer RNA
403V_region         variable region of immunoglobulin light and heavy chains,
404                 and T-cell receptor alpha, beta, and gamma chains
405V_segment        variable segment of immunoglobulin light and heavy chains,
406                 and T-cell receptor alpha, beta, and gamma chains.
407variation        a related strain contains stable mutations from the same
408                 gene (e.g., RFLPs, polymorphisms)
4093'UTR            region at the 3' end of a mature transcript, following the
410                 stop codon
4115'UTR            region at the 5' end of a mature transcript, preceding the
412                 initiation
413-10_signal       prokaryotic promoter element, consensus=TAtAaT
414-35_signal       prokaryotic promoter element, consensus=TTGACa or TGTTGACA
415
416(Last change: 08-DEC-1998)
417(Wendy Baker, EMBL nucleotide sequence database curator)
418
419
420
421
422
423Agnes Leyen
424EMBL Outstation -  The European Bioinformatics Institute
425Wellcome Trust Genome Campus
426Cambridge CB10 1SD
427UK
428
429
430DATASUBMISSIONS:
431+44 1223 494499
432datasubs@ebi.ac.uk
433
434UPDATES:
435+44 1223 494499
436updates@ebi.ac.uk
437
438PERSONAL:
439+44 1223 494411
440leyen@ebi.ac.uk
441
Note: See TracBrowser for help on using the repository browser.