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EMBL NUCLEOTIDE SEQUENCE DATABASE SUBMISSION FORM
HOW TO USE THIS FORM - PLEASE READ FIRST
1) WEBIN: THE WORLD WIDE WEB SUBMISSION TOOL
============================================
If you have access to the World Wide Web then DO NOT use this form. Use the
WebIn form on the World Wide Web at
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# http://www.ebi.ac.uk/submission/webin.html #
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If you do not have access to the World Wide Web then please use this form
and email it to DATASUBS@EBI.AC.UK.
It is only necessary to submit to one database. Public data are exchanged
between EMBL, GenBank and DDBJ on a daily basis.
2) MULTIPLE SUBMISSIONS
=======================
If you have more than one but less than 25 sequences to submit, copy this
form and send all the submissions together in one email with a note saying
how many sequences you are sending.
3) BULK SUBMISSIONS
===================
If you have more than 25 related sequences to submit DO NOT send them all
using this form. Instead email DATASUBS@EBI.AC.UK and include the following
information
a) how many sequences you are going to submit
b) a short explanation of how the sequences are related
c) what type of differences there are between the entries (e.g. isolate)
d) one completed email submission form as an example
You will be contacted by a curator who will create a template for you which
you should then use to submit all of the sequences.
4) UPDATES
==========
DO NOT use this form for submitting updates or corrections.
If you are sending an update please complete the update form available on
the web at: http://www.ebi.ac.uk/ebi_docs/update.html or get a copy of the
update form via anonymous FTP:
ftp://ftp.ebi.ac.uk/pub/databases/embl/release/update.doc
If you need help with updates contact UPDATE@EBI.AC.UK
5) PROTEIN SEQUENCES
====================
DO NOT use this form to submit protein sequences.
For submissions to the SWISS-PROT protein sequence databank access the
World Wide Web at http://www.ebi.ac.uk/ebi_docs/swissprot_db/swisshome.html
or email DATALIB@EBI.AC.UK
6) ACCESSION NUMBERS AND CONFIDENTIALITY
========================================
Your data can be made public immediately, or they can be kept confidential
until a release date which you provide. Confidential data are ALWAYS made
available to the public after publication.
If your data contain all the information we require we will assign unique
accession numbers within two working days. We will email you to tell you
the new accession numbers.
You should submit your sequence data BEFORE you have galley proofs. We
suggest that the following text be used to cite the accession number(s) in
publication(s): "The nucleotide sequence data reported in this paper will
appear in the DDBJ/EMBL/GenBank Nucleotide Sequence Database under the
accession number(s) ________"
7) FORM FILLING INSTRUCTIONS
============================
<============== DO NOT EXCEED THIS LINE WIDTH IN YOUR REPLY ==============>
To display this form properly choose a fixed width font (e.g. Courier) in
your editor. If you are saving files in a word processing program then
please save the file as TEXT ONLY WITH LINE BREAKS. (To do this in
Microscoft Word you will need to choose File, Save as, Save file type as,
and select Text only with line breaks). Please do not send files that are
saved in Word or Wordperfect format. Processing of the submission may be
delayed if your email is text wrapped, encoded or binhexed.
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# Fill in the form as follows: #
# a) if there is a colon : then enter text (e.g. Last name : Smith) #
# b) if there is an empty box [ ] and if the answer is yes then fill #
# the box with an X (e.g. Genomic DNA [X]) #
# c) if the option is not relevant then do not enter any text and/or #
# do not write an X in the box. #
# d) DO NOT delete lines from this form. #
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8) ENTERING FEATURES AND LOCATIONS
==================================
Enter the feature key from the list given in Appendix I at the end of this
document. Enter the locations, gene name, product name, and EC number,
where appropriate. Use < and > in the locations to show whether the feature
is partial at the 5' end and/or the 3' end. Mark with an X in the box [ ]
if the feature is on the complementary strand and if you have experimental
evidence for the feature.
If you do not provide any features or adequate locations and names for the
features you will be contacted for more information before an accession
number is assigned to the sequence. For CDS features you must provide a gene
name AND a product name, even if the product name is putative.
If a CDS is partial at the 5' end then write the codon start number. This
is the number (1,2 or 3) of the first base of the first complete codon of
the translation. For example the following CDS is partial and the codon
start is 2 because the first complete codon, T, starts with the base a,
which is the second base in the feature.
DNA tacatcgatg...
Translation T S M...
FEATURE EXAMPLE NO.1
Feature key :CDS
>From :201
To :500
Gene name :abcD
Product name :ABC repressor protein
Codon start 1,2 or 3 :
EC number :
Complementary strand [ ]
Experimental evidence [X]
FEATURE EXAMPLE NO.2
Feature key :rRNA
>From :<1
To :>1500
Gene name :16S rRNA
Product name :16S ribosomal RNA
Codon start 1,2 or 3 :
EC number :
Complementary strand [ ]
Experimental evidence [ ]
If you have further questions after reading this form please contact
DATASUBS@EBI.AC.UK
I. CONFIDENTIAL STATUS
Enter an X if you want these data to be confidential [ ]
If confidential write the release date here :
(Date format DD-MMM-YYYY e.g. 30-JUN-1998)
II. CONTACT INFORMATION
Last name :$(LAST_NAME)
First name :$(FIRST_NAME)
Middle initials :
Department :$(DEPT)
Institution :$(INSTITUTION)
Address :$(ADDRESS)
:
:
Country :$(COUNTRY)
Telephone :$(PHONE)
Fax :$(TELEFAX)
Email :$(MAIL)
III. CITATION INFORMATION
Author 1 :$(author_1)
Author 2 :$(author_2)
Author 3 :$(author_3)
Author 4 :$(author_4)
Author 5 :$(author_5)
Author 6 :$(author_6)
Author 7 :$(author_7)
Author 8 :$(author_8)
Author 9 :$(author_9)
Author 10 :$(author_10)
Author 11 :$(author_11)
Author 12 :$(author_12)
(e.g. Smith A.B.)
(Copy line for extra authors)
Title :$(title)
Journal :$(journal)
Volume :$(volume)
First page :$(page_1)
Last page :$(page_2)
Year :$(year_pub)
Institute (if thesis):
Publication status
Mark one of the following
In preparation [ ]
Accepted [x]
Published [ ]
Thesis/Book [ ]
No plans to publish [ ]
IV. SEQUENCE INFORMATION
Sequence length (bp) :$(SEQ_LEN)
Molecule type
Mark one of the following
Genomic DNA [ ]
cDNA to mRNA [ ]
rRNA [x]
tRNA [ ]
Genomic RNA [ ]
cDNA to genomic RNA [ ]
Mark if either of these apply
Circular [ ]
Checked for vector
contamination [ ]
V. SOURCE INFORMATION
Organism :$(full_name)
Sub species :
Strain :$(strain)
Cultivar :
Variety :
Isolate/individual :
Developmental stage :
Tissue type :
Cell type :
Cell line :
Clone :$(clone)
Clone (if >1) :
Clone library :
Chromosome :
Map position :
Haplotype :
Natural host :
Laboratory host :
Macronuclear [ ]
Mark one if immunoglobulin
or T cell receptor
Germline [ ]
Rearranged [ ]
Mark one if viral
Proviral [ ]
Virion [ ]
Mark one if from an organelle
Chloroplast [ ]
Mitochondrion [ ]
Chromoplast [ ]
Kinetoplast [ ]
Cyanelle [ ]
Plasmid (not clone) [ ]
Further source information
(e.g. taxonomy, specimen voucher etc)
Note :$(tax)
VI. FEATURES OF THE SEQUENCE
YOU MUST DESCRIBE AT LEAST ONE FEATURE OF THE SEQUENCE OR THERE WILL BE A
DELAY IN THE PROCESSING OF YOUR SUBMISSION
Complete the block below for every feature you need to describe. If you
have more than one feature copy the block as many times as you require. For
help see 8) ENTERING FEATURES AND LOCATIONS above.
FEATURE NO.1
Feature key :$(seq_type)
>From :$(start)
To :$(end)
Gene name :$(gene)
Product name :$(gene_prod)
Codon start 1,2 or 3 :
EC number :
Complementary strand [ ]
Experimental evidence [ ]
VII. SEQUENCE INFORMATION
Enter the sequence data below
(IUPAC nucleotide base codes, Nucl. Acids Res. 13: 3021-3030, 1985)
BEGINNING OF SEQUENCE:
$(SEQUENCE)
END OF SEQUENCE
Include the translation for each CDS feature below.
BEGINNING OF TRANSLATION:
END OF TRANSLATION
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These data will be shared among the following databases: DDBJ Database
(DNA Data Bank of Japan; Mishima, Japan); EMBL Nucleotide Sequence Database
(EBI, Cambridge, UK); GenBank (NCBI, Bethesda, USA); SWISS-PROT Protein
Sequence Database (Geneva, Switzerland and Heidelberg, FRG); International
Protein Information Database in Japan (JIPID; Noda, Japan) Martinsried
Institute For Protein Sequence Data (MIPS; Martinsried, FRG) National
Biomedical Research Foundation Protein Identification Resource (NBRF-PIR;
Washington, D.C., USA.)
EMBL Data Submissions E-mail datasubs@ebi.ac.uk
European Bioinformatics Inst. Telephone +44 (0)1223 494499
Hinxton Hall, Hinxton Telefax +44 (0)1223 494472
Cambridge CB10 1SD, UK
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APPENDIX I FEATURE KEYS
=======================
A full description of features is found in the DDBJ/EMBL/GenBank Feature
Table Definition Document at
ftp://ftp.ebi.ac.uk/pub/databases/embl/release/ftable.doc
and on the EBI website at
http://www.ebi.ac.uk/ebi_docs/embl_db/ft/feature_table.html
An abbreviated list of features keys is given below
C_region constant region of immunoglobulin light and heavy chain,
and T-cell receptor alpha, beta and gamma chains
CAAT_signal eukaryotic promoter element; consensus=GG(C or T)CAATCT
CDS protein coding sequence (includes stop codon)
conflict the "same" sequence reported by different laboratories
differ at this site or region
D-segment diversity segment of immunoglobulin heavy chain and
T-cell receptor beta-chain
enhancer cis-acting enhancer of eukaryotic promoter function
exon region that codes for part of spliced mRNA
GC_signal eukaryotic promoter element; consensus=GGGCGG
intron transcribed region excised by mRNA splicing
J_segment joining segment of immunoglobulin light and heavy chains,
T-cell receptor alpha, beta and gamma-chains
LTR long terminal repeat
mat_peptide mature peptide coding region (does not include stop codon)
or signal peptide
misc_feature region of biological interest which cannot be described
by any other known feature
mRNA messenger RNA
mutation a related strain has an abrupt, inheritable change in the
sequence
polyA_signal polyadenylation signal recognition region
polyA_site polyadenylation site to which adenine residues are added
primer_bind non-covalent primer binding site
promoter promoter region involved in transcription initiation
protein_bind non-covalent protein binding site on DNA or RNA
RBS ribosome binding site
rep_origin origin of replication
repeat_region region of genome containing repeating units
repeat_unit single repeat element
rRNA ribosomal RNA
S_region switch region of immunoglobulin heavy chains
satellite many tandem repeats of a short basic repeating unit
sig_peptide signal peptide coding region
stem_loop hair-pin loop structure in DNA or RNA
STS sequence tagged site
TATA_signal eukaryotic promoter element; consensus=TATA(A or T)A(A or T)
terminator transcription termination signal
transit_peptide transit peptide coding region
tRNA transfer RNA
V_region variable region of immunoglobulin light and heavy chains,
and T-cell receptor alpha, beta, and gamma chains
V_segment variable segment of immunoglobulin light and heavy chains,
and T-cell receptor alpha, beta, and gamma chains.
variation a related strain contains stable mutations from the same
gene (e.g., RFLPs, polymorphisms)
3'UTR region at the 3' end of a mature transcript, following the
stop codon
5'UTR region at the 5' end of a mature transcript, preceding the
initiation
-10_signal prokaryotic promoter element, consensus=TAtAaT
-35_signal prokaryotic promoter element, consensus=TTGACa or TGTTGACA
(Last change: 08-DEC-1998)
(Wendy Baker, EMBL nucleotide sequence database curator)
Agnes Leyen
EMBL Outstation - The European Bioinformatics Institute
Wellcome Trust Genome Campus
Cambridge CB10 1SD
UK
DATASUBMISSIONS:
+44 1223 494499
datasubs@ebi.ac.uk
UPDATES:
+44 1223 494499
updates@ebi.ac.uk
PERSONAL:
+44 1223 494411
leyen@ebi.ac.uk