DNA Data Bank of Japan DNA Database Release 66.0, Jun. 2006, including 58,176,628 entries, 62,945,843,881 bases ------------------------------------------------------------------------------- Table of contents ------------------------------------------------------------------------------- 1. Introduction 1.1. Announcement for changes in the present release 1.2. Announcement for the forthcoming changes 2. DDBJ flat file format 2.1. LOCUS line 2.2. DEFINITION line 2.3. ACCESSION line 2.4. VERSION line 2.5. KEYWORDS line 2.6. SOURCE line 2.7. REFERENCE line 2.8. COMMENT line 2.9. FEATURES line 2.10. BASE COUNT line 2.11. ORIGIN line 3. Dataset categories 3.1. Division categories 3.2. TPA separated from primary dataset 3.3. Notice for patented data 4. DDBJ staff 5. Acknowledgment 6. File Contents 6.1. File categories 6.2. File types 7. Sample of the contents in each file 7.1. Part of the contents in the file 'ddbjbct1.seq' 7.2. Part of the contents in the file 'ddbjbct1.acc' 7.3. Part of the contents in the file 'ddbjbct1.aut' 7.4. Part of the contents in the directory file 'ddbjbct1.dir' 7.5. Part of the contents in the file 'ddbjbct1.idx' 7.6. Part of the contents in the file 'ddbjbct1.jou' 7.7. Part of the contents in the file 'ddbjbct1.key' 7.8. Part of the contents in the file 'ddbjbct1.org' 7.9. Part of the contents in the short directory file 'ddbjbct1.sdr' 7.10. Part of the contents in the accession number index file 'ddbjacc1.idx' 7.11. Part of the contents in the keyword phrase index file 'ddbjkey1.idx' 7.12. Part of the contents in the journal citation index file 'ddbjjou1.idx' 7.13. Part of the contents in the gene name index 'ddbjgen.idx' 8. Release history 9. File list ------------------------------------------------------------------------------- 1. Introduction This database contains nucleotide sequence data for any organism, not only those with DNA genomes but also those with RNA genomes. This database may be copied and redistributed without permission on the condition that all the statements in this release note are reproduced in each copy. See also '3.3. Notice for patented data' below. The present release contains the newest data prepared by the DNA Data Bank of Japan (DDBJ), GenBank (*), and European Molecular Biology Laboratory/European Bioinformatics Institute (EMBL/EBI) as of May 26, 2006. This unified database was made possible thanks to the international collaboration among the three data banks. All the entries have accordingly been annotated using the feature keys common to them. *'GenBank' is a trademark of NIH, USA, and is operated by National Center for Biotechnology Information (NCBI) at NIH. 1.1. Announcement for changes in the present release Nothing particular. 1.2. Announcement for the forthcoming changes Split of files: At present, all files of a DDBJ release except some indexes (ddbjacc#.idx, ddbjjou#.idx, and ddbjkey#.idx) have 300 MB storage capacity as shown at the sections, '6. File Contents' and '9. File list'. From the release 68, December 2006, we will change the maximum file size from 300 MB to 1.5 GB, because the network capacity has been remarkably increased. Each file named as ddbj***##.seq will have at most 1.5 GB storage capacity like as the index files by then. 2. DDBJ flat file format The database is a collection of "entry" which is the unit of the data. The entries submitted to databanks were processed and publicized according to the DDBJ format for distribution (flat file). The flat file includes the sequence and the information of submitters, references, source organisms, and "feature" information, etc. The items of the DDBJ flat file are explained at following; ------------------------------------------------------------------------------- LOCUS AB000000 450 bp mRNA linear HUM 08-JUL-2002 DEFINITION Homo sapiens GAPD mRNA for glyceraldehyde-3-phosphate dehydrogenase, partial cds. ACCESSION AB000000 VERSION AB000000.1 KEYWORDS . SOURCE Homo sapiens ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 450) AUTHORS Mishima,H. and Shizuoka,T. TITLE Direct Submission JOURNAL Submitted (30-NOV-2000) to the DDBJ/EMBL/GenBank databases. Hanako Mishima, National Institute of Genetics, DNA Data Bank of Japan; Yata 1111, Mishima, Shizuoka 411-8540, Japan (E-mail:mishima@supernig.nig.ac.jp, Tel:81-55-981-6853, Fax:81-55-981-6849) REFERENCE 2 (sites) AUTHORS Mishima,H., Shizuoka,T. and Fuji,I. TITLE Glyceraldehyde-3-phosphate dehydrogenase expressed in human liver JOURNAL Unpublished (2002) COMMENT Human cDNA sequencing project. FEATURES Location/Qualifiers source 1..450 /chromosome="12" /clone="GT200015" /clone_lib="lambda gt11 human liver cDNA (GeneTech. No.20)" /map="12p13" /mol_type="mRNA" /organism="Homo sapiens" /tissue_type="liver" CDS 86..>450 /codon_start=1 /gene="GAPD" /product="glyceraldehyde-3-phosphate dehydrogenase" /protein_id="BAA12345.1" /transl_table=1 /translation="MAKIKIGINGFGRIGRLVARVALQSDDVELVAVNDPFITTDYMT YMFKYDTVHGQWKHHEVKVKDSKTLLFGEKEVTVFGCRNPKEIPWGETSAEFVVEYTG VFTDKDKAVAQLKGGAKKV" BASE COUNT 102 a 119 c 131 g 98 t ORIGIN 1 cccacgcgtc cggtcgcatc gcacttgtag ctctcgaccc ccgcatctca tccctcctct 61 cgcttagttc agatcgaaat cgcaaatggc gaagattaag atcgggatca atgggttcgg 121 gaggatcggg aggctcgtgg ccagggtggc cctgcagagc gacgacgtcg agctcgtcgc 181 cgtcaacgac cccttcatca ccaccgacta catgacatac atgttcaagt atgacactgt 241 gcacggccag tggaagcatc atgaggttaa ggtgaaggac tccaagaccc ttctcttcgg 301 tgagaaggag gtcaccgtgt tcggctgcag gaaccctaag gagatcccat ggggtgagac 361 tagcgctgag tttgttgtgg agtacactgg tgttttcact gacaaggaca aggccgttgc 421 tcaacttaag ggtggtgcta agaaggtctg // ------------------------------------------------------------------------------- 2.1. LOCUS line The format of LOCUS line in the flat file is shown below; --------- -------- Positions Contents --------- -------- 01-05 'LOCUS' 06-12 spaces 13-28 Locus name 29-29 space 30-40 Length of sequence, right-justified 41-41 space 42-43 'bp' 44-47 spaces 48-54 DNA, RNA, mRNA, pre-RNA, rRNA, scRNA, snRNA, snoRNA, tRNA, left justified 55-55 space 56-63 'linear' followed by two spaces, or 'circular' 64-64 space 65-67 The division code (see '3.1. Division categories') 68-68 space 69-79 Date, in the form dd-MMM-yyyy (e.g., 08-JUL-2002) ------------------------------------------------------------------------------ 2.2. DEFINITION line The definition briefly describes the information of gene(s). "DEFINITION" is constructed by each of the three data banks. 2.3. ACCESSION line This line shows accession number of the entry data. A unique accession number is issued to the data submitter by each of the three data banks. The accession number is composed of 1 alphabet character and 5 digits (ex. A12345) or 2 alphabet characters and 6 digits (ex. AB123456). The former style was used in 1980s, but later the latter style was introduced because of data explosion. All the entries designated by the accession numbers with the prefixes given below have been collected and processed by DDBJ, and the rest have been done by GenBank and EMBL/EBI. ------------------------------------------------------------------------------- C, D, E, AB, AG, AK, AP, AT, AU, AV, BA, BB, BD, BJ, BP, BR, BS, BW, BY, CI, CJ, DA, DB, DD, DE, DF ------------------------------------------------------------------------------- You can find the list of the prefixes of the accession numbers at the following URL; http://www.ddbj.nig.ac.jp/sub/prefix.html If multiple entries are united to an entry, or if an entry is extensively modified after the submission, the responsible data banks may assign a new accession number to it. In these cases, the new accession number is called the primary accession number, and the old accession number(s) is/are called the secondary accession number(s). In the flat file, the primary accession number is indicated first, then the secondary accession number(s) follows. You can find the same updated entry with both the primary and the secondary accession numbers. 2.4. VERSION line This line consists of an accession number and a version number, like "AB123456.1", in which the digit(s) after the period is a version number. The data open to public for the first time is version number as "1". The reason for adding VERSION is that since a released sequence sometimes revised by the submitter, the accession number alone cannot specify the sequence in question causing the user a trouble. The number is increased by one every time when a revised sequence is made public. 2.5. KEYWORDS line The data banks describe this line, if necessary. In many cases, the categories of the data (EST, HTG etc.), gene names and product names included in "KEYWORDS". 2.6. SOURCE line This line shows the scientific name on organism from which the sequence is obtained and an organelle type if the sequence is derived from an organelle other than the nucleus. 2.7. REFERENCE line The information on the submitters and references related to the submitted sequence is indicated in REFERENCE line. 2.8. COMMENT line. The information about an entry that can not be described using FEATURES or the other fields. 2.9. FEATURES line Biological features of a submitted sequence data are described with "Feature" key (the biological nature of the annotated feature), "Location" (the region of the sequence which corresponds to Feature), and "Qualifier" (supplementary information about Feature). The "Feature" and "Qualifier" keys used in the present release is defined by DDBJ/EMBL/GenBank Feature Table: Definition (Version 6.5 April, 2006). The document is continuously updated every half year. You can find its newest version on URL; http://www.ddbj.nig.ac.jp/FT/full_index.html 2.10. BASE COUNT line In the BASE COUNT line of the DDBJ flat file, 9 digits are allocated for each number of a (adenine), c (cytosine), g(guanine) and t (thymine). In the case of RNA sequence, uracil is indicated as "t" according to the rule of the international nucleotide database. In accordance with the relaxation of sequence length limitation, GenBank had already dropped the BASE COUNT line from their flat file format from GenBank Release 138 (Oct. 2003). DDBJ has decided to maintain the BASE COUNT line in our flat file format from the view that GC contents are still important information to characterize the sequence. 2.11. ORIGIN line The sequence data starts from the next line of ORIGIN. The sequence is indicated as lower case letters, delimited by space per 10 bases, starts a new line by 60 bases. The numbers described at left side of lines mean the ordinal number of the top base of the line. 3. Dataset categories There have been a number of genome projects going on worldwide. Among them human genome projects have probably been most productive and yielded a large number of ordinary sequences, huge amounts of genome sequences and EST (expressed sequence tags). Thus, we DDBJ have the human (HUM) division solely for human sequences and the primate (PRI) division for non-human primate sequences, while PRI division of GenBank database contains human sequences too. Note that the other divisions such as EST, GSS, and HTC may also contain human sequences. The present release is divided into 21 categories of organisms and others. See also '6.1. File categories' and '9. File list' below. The contents of the 21 categories are shown in the following. 3.1. Division categories The first 20 divisions are given below; HUM; human PRI; primates (other than human) ROD; rodents MAM; mammals (other than primates and rodents) VRT; vertebrates (other than mammals) INV; invertebrates (animals other than vertebrates) PLN; plants, fungi, plastids (eukaryotes other than animals) BCT; bacteria (including both Eubacteria and Archaea) VRL; viruses PHG; bacteriophages ENV; sequences obtained via environmental sampling methods SYN; synthetic constructs EST; expressed sequence tags; short single pass cDNA sequences GSS; genome survey sequences; short single pass genomic sequences HTC; high throughput cDNA sequences; The sequence submitted from cDNA sequencing projects except for EST. This division is to include unfinished high throughput cDNA sequences, each of which has 5'UTR and 3'UTR at both ends and part of a coding region. The sequence may also include introns. When the sequence becomes finished later, it moves to the corresponding taxonomic division. HTG; high throughput genomic sequences The sequence submitted mainly from genome sequencing projects which regarded a clone as a sequencing unit. STS; sequence tagged sites The tag site for genome sequencing. The information of chromosome, map, PCR_condition is mandatory for this division. PAT; patented data The data submitted to JPO (Japan Patent Office), EPO (European Patent Office), or USPTO (United States Patent and Trademark Office). See also '3.3. Notice for patented data' in below. UNA; the data not annotated The UNA division is not used for recently submitted sequences. CON; Contig / Constructed To conjugate a series of entries, such as those submitted from a genome project, each of data banks constructs an entry and assign an accession number to a large scale sequence dataset. Such entries are classified into the CON division. The entry in the CON division has the information of joined accession numbers instead of the sequence data. The corresponding entries of the CON entry have been submitted to other divisions. The entries and bases in the CON division are not counted in the released numbers given on the top of the release note. 3.2. TPA separated from primary dataset TPA (Third Party Annotation) data are also available. The TPA data are a complement to the existing DDBJ/EMBL/GenBank comprehensive database of primary nucleotide sequences, which typically result from direct sequencing of cDNAs, ESTs, genomic DNAs etc. Primary entries are defined to be data for which the submitting group has done the sequencing and annotation, and as 'owner' of these data has privileges to submit updates/corrections etc. Primary entries used to build a TPA sequence are those that have been experimentally determined and are publicly available in the DDBJ/EMBL/GenBank databases. They may not be from a proprietary database. The entries and bases in TPA are not counted in the released numbers given on the top of the release note. See also the following URLs; http://www.ddbj.nig.ac.jp/sub/tpa-e.html http://www.insdc.org/TPA.html 3.3. Notice for patented data This release includes PAT division for patented data as described above. The patented data are those which the Japanese Patent Office (JPO), United States Patent and Trademark Office (USPTO), and the European Patent Office (EPO) collected, processed and released. The prefixes of accession numbers for the patented data are shown below; ----------------------- JPO : E, BD, DD USPTO: I, AR EPO : A, AX, CQ, CS ----------------------- Note also that unauthorized use of the patented data may cause legal issues for which DDBJ takes no responsibility. 4. DDBJ staff This release is published by the following DDBJ staff. Gojobori T, Tateno Y, Nishikawa K, Sugawara H, Saitou N, Okubo K, Ikeo K, Suzuki Y, Fukuchi S, Kinjo A, Barrero R, Abe T, Sumiyama K, Ogasawara O, Aono H, Atsumi T, Ejima M, Fukuda D, Gojobori M, Hikino Y, Hirai T, Honda K, Hoshi N, Ichikawa K, Ishida K,, Kawamoto T, Kohira J, Koike T, Kosuge T, Kusakabe A, Kuwana Y, Li C, Lin Y, Maesako H, Mamiya K, Maruyama N, Mashima J, Miyazawa S, Mizunuma T, Murakata N, Nagira S, Nagura M, Nishida S, Nishinomiya N, Nozaki A, Okido T, Sakai K, Shigemoto Y, Shiozawa H, Sugimoto K, Sugiyama F, Suzuki S, Tsuboi M, Tsutsui H, Yamada H, Yamamoto K, Yamamoto M, and Yokoyama E Center for Information Biology and DNA Data Bank of Japan National Institute of Genetics Research Organization of Information and Systems Mishima 411-8540, Japan Phone: +81 55 981 6853 FAX: +81 55 981 6849 E-mail: ddbj@ddbj.nig.ac.jp (for general inquiry) ddbjsub@ddbj.nig.ac.jp (for data submission) ddbjupdt@ddbj.nig.ac.jp (for updates and notification of publication) WWW: http://www.ddbj.nig.ac.jp/ (for DDBJ WWW server) http://sakura.ddbj.nig.ac.jp/ (for DDBJ sequence data submission system) 5. Acknowledgment We are grateful to NCBI and EMBL/EBI for a firm friendship and an excellent collaboration with us. We also thank the Japanese Patent Office for a steady cooperation with us. The operation of DDBJ is supported by the Ministry of Education, Culture, Sports, Science and Technology, and we would gratefully note this here. DDBJ uses the Super-SINET computer network for data collection, data exchange and various services. 6. File Contents 6.1. File categories This release covers 21 categories (see also '3. Dataset categories'.) of organisms and others as follows: ------------------------------------------------------------------------------ ddbjbct*** Category for bacteria ddbjcon*** Category for CON (contig sequences) ddbjenv*** Category for ENV (environmental samples) ddbjest*** Category for EST (expressed sequence tags) ddbjgss*** Category for GSS (genome survey sequences) ddbjhtc*** Category for HTC (high throughput cDNA sequences) ddbjhtg*** Category for HTG (high throughput genomic sequences) ddbjhum*** Category for human ddbjinv*** Category for invertebrates ddbjmam*** Category for mammals other than primates and rodents ddbjpat*** Category for patents ddbjphg*** Category for phages ddbjpln*** Category for plants ddbjpri*** Category for primates other than human ddbjrod*** Category for rodents ddbjsts*** Category for STS (sequence tagged sites) ddbjsyn*** Category for synthetic DNAs ddbjtpa*** Category for TPA (Third Party Annotation) ddbjuna*** Category for unannotated sequences ddbjvrl*** Category for viruses ddbjvrt*** Category for vertebrates other than mammals ------------------------------------------------------------------------------ Some of above in the present release are recorded in multiple ddbj***.seq files, each of which at most has 300 MB storage capacity as follows, respectively. --------------------- ddbjbct : 13 files ddbjenv : 3 files ddbjest : 412 files ddbjgss : 139 files ddbjhtc : 8 files ddbjhtg : 69 files ddbjhum : 23 files ddbjinv : 7 files ddbjmam : 2 files ddbjpat : 21 files ddbjpln : 15 files ddbjpri : 3 files ddbjrod : 20 files ddbjsts : 12 files ddbjvrl : 5 files ddbjvrt : 9 files --------------------- 6.2. File types The index files included in this release are ddbjacc#.idx, ddbjgen.idx, ddbjjou#.idx, and ddbjkey#.idx. All of them except ddbjgen.idx are recorded in multiple ddbj****.idx files, each of which at most has 1.5 GB storage capacity. We have also included a program by which to make the index files not presented in this release. For the use of the program, see the files, seq2indexes.doc, seq2indexes.c, and seq2indexes.h in this release. Each category then has the following nine types of files. Note that all the files except for ddbj***.seq are created by the user by use of seq2indexes as mentioned above. ------------------------------------------------------------------------------ ddbj***.seq List of an entry in DDBJ format, see 7.1. ddbj***.acc List of the accession numbers, see 7.2. ddbj***.aut List of the authors, see 7.3. ddbj***.dir List of the short directory in DDBJ style, see 7.4. ddbj***.idx List of indices, see 7.5. ddbj***.jou List of the journals, see 7.6. ddbj***.key List of the key words, see 7.7. ddbj***.org List of the species names, see 7.8. ddbj***.sdr List of the short directory in DDBJ style, see 7.9. ------------------------------------------------------------------------------ 7. Sample of the contents in each file 7.1. Part of the contents in the file 'ddbjbct1.seq' This shows all pieces of information on one entry in DDBJ format. ------------------------------------------------------------------------------ LOCUS D87069 993 bp mRNA linear BCT 14-APR-2000 DEFINITION Escherichia coli mRNA for RNA polymerase sigma subunit, truncated form of sigma-38, complete cds. ACCESSION D87069 VERSION D87069.1 KEYWORDS RNA polymerase sigma subunit, truncated form of sigma-38. SOURCE Escherichia coli ORGANISM Escherichia coli Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae; Escherichia. REFERENCE 1 (bases 1 to 993) AUTHORS Jishage,M. TITLE Direct Submission JOURNAL Submitted (14-AUG-1996) to the DDBJ/EMBL/GenBank databases. Miki Jishage, National Institute of Genetics, Molecular Genetics; Yata 1111, Mishima, Shizuoka 411, Japan (E-mail:mjishage@lab.nig.ac.jp, Tel:0559-81-6742, Fax:0559-81-6746) REFERENCE 2 (bases 1 to 993) AUTHORS Jishage,M. and Ishihama,A. TITLE Variation in RNA polymerase sigma subunit composition within different stocks of Escherichia coli starin W3110 JOURNAL Unpublished (1996) REFERENCE 3 AUTHORS Ivanova,A., Renshaw,M., Guntaka,R. and Eisenstark,A. TITLE DNA base sequence variability in katF (putative sigma factor) gene Escherichia coli JOURNAL Nucleic Acids Res. 20, 5479-5480 (1992) REFERENCE 4 AUTHORS Takayanagi,Y., Tanaka,K. and Takahashi,H. TITLE Structure of the 5' upstream region and the regulation of the rpoS gene of Escherichia coli JOURNAL Mol. Gen. Genet. 243, 525-531 (1994) COMMENT FEATURES Location/Qualifiers source 1..993 /mol_type="mRNA" /organism="Escherichia coli" /strain="W3110" CDS 1..810 /note="the gene has four single base changes, resulting in two amino acid substitutions and an amber mutation" /product="RNA polymerase sigma subunit, truncated form of sigma-38" /protein_id="BAA13238.1" /transl_table=11 /translation="MSQNTLKVHDLNEDAEFDENGVEVFDEKALVEYEPSDNDLAEEE LLSQGATQRVLDATQLYLGEIGYSPLLTAEEEVYFARRALRGDVASRRRMIESNLRLV VKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMN QTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNER ITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK" variation 75 /citation=[3] /replace="t" variation 97 /citation=[3] /replace="t" variation 99 /citation=[3] /replace="t" variation 808 /citation=[3] /replace="t" BASE COUNT 254 a 223 c 291 g 225 t ORIGIN 1 atgagtcaga atacgctgaa agttcatgat ttaaatgaag atgcggaatt tgatgagaac 61 ggagttgagg tttttgacga aaaggcctta gtagaatatg aacccagtga taacgatttg 121 gccgaagagg aactgttatc gcagggagcc acacagcgtg tgttggacgc gactcagctt 181 taccttggtg agattggtta ttcaccactg ttaacggccg aagaagaagt ttattttgcg 241 cgtcgcgcac tgcgtggaga tgtcgcctct cgccgccgga tgatcgagag taacttgcgt 301 ctggtggtaa aaattgcccg ccgttatggc aatcgtggtc tggcgttgct ggaccttatc 361 gaagagggca acctggggct gatccgcgcg gtagagaagt ttgacccgga acgtggtttc 421 cgcttctcaa catacgcaac ctggtggatt cgccagacga ttgaacgggc gattatgaac 481 caaacccgta ctattcgttt gccgattcac atcgtaaagg agctgaacgt ttacctgcga 541 accgcacgtg agttgtccca taagctggac catgaaccaa gtgcggaaga gatcgcagag 601 caactggata agccagttga tgacgtcagc cgtatgcttc gtcttaacga gcgcattacc 661 tcggtagaca ccccgctggg tggtgattcc gaaaaagcgt tgctggacat cctggccgat 721 gaaaaagaga acggtccgga agataccacg caagatgacg atatgaagca gagcatcgtc 781 aaatggctgt tcgagctgaa cgccaaatag cgtgaagtgc tggcacgtcg attcggtttg 841 ctggggtacg aagcggcaac actggaagat gtaggtcgtg aaattggcct cacccgtgaa 901 cgtgttcgcc agattcaggt tgaaggcctg cgccgtttgc gcgaaatcct gcaaacgcag 961 gggctgaata tcgaagcgct gttccgcgag taa // ------------------------------------------------------------------------------ 7.2. Part of the contents in the file 'ddbjbct1.acc' The first column refers to the secondary accession number, second column to the locus name, and third to the primary accession number. The primary number may be the same as the secondary number. They are arranged in the ascending order of the secondary accession numbers. ------------------------------------------------------------------------------ D00681 -> AB028210 AB028210 D10012 -> AB010832 AB010832 D10013 -> AB010832 AB010832 D10048 -> AB008452 AB008452 D13563 -> AB018435 AB018435 D13614 -> AB006206 AB006206 D13762 -> AB063629 AB063629 D14537 -> AB040412 AB040412 D14604 -> AB001637 AB001637 D14607 -> AB027308 AB027308 ------------------------------------------------------------------------------ 7.3. Part of the contents in the file 'ddbjbct1.aut' For each author name given on the left to the arrow, the corresponding locus name and primary accession number are respectively listed on the right. They are arranged in the alphabetical order of the author names. ------------------------------------------------------------------------------ Aarestrup,F.M.Threlfall,E.J. -> AF393510 AF393510 Aarnikunnas,J. -> AY090766 AY090766 Aarnio,T. -> AY792975 AY792975 Aarnio,T. -> AY792976 AY792976 Aarnio,T. -> AY792977 AY792977 Aarnio,T. -> AY792978 AY792978 Aarnio,T. -> AY792979 AY792979 Aarnio,T. -> AY792980 AY792980 Aarnio,T. -> AY792981 AY792981 Aarnio,T. -> AY792982 AY792982 ------------------------------------------------------------------------------ 7.4. Part of the contents in the directory file 'ddbjbct1.dir' For each locus name given in the first column, the corresponding primary accession number, molecular type, number of nucleotide pairs, and description for the locus are respectively listed. They are arranged in the alphabetical order of the locus names. ------------------------------------------------------------------------------ AAC133631 AJ133631 DNA 1482 Alicyclobacillus acidoterrestris 16S rRNA gene, strain DSM 3922T. AAC133789 AJ133789 DNA 3097 Alicyclobacillus acidocaldarius cyclomaltodex trinase gene region. AAC243194 AJ243194 DNA 1720 Alicyclobacillus acidocaldarius kdpA gene. AAC252160 AJ252160 DNA 1638 Alicyclobacillus acidocaldarius cysA gene for putative ABC-transporter ATP-binding protein. AAC252161 AJ252161 DNA 8690 Alicyclobacillus acidocaldarius maltose/maltodextrine transport gene region (malEFGR genes, cdaA gene and glcA gene). AAC289685 AJ289685 DNA 453 Actinobacillus actinomycetemcomitans partial infB gene for translation initiation factor IF2, strain CCUG13227 T (ATCC33384, NCTC9710). AAC289686 AJ289686 DNA 453 Actinobacillus actinomycetemcomitans partial infB gene for translation initiation factor IF2, strain HK666. AAC289687 AJ289687 DNA 453 Actinobacillus actinomycetemcomitans partial infB gene for translation initiation factor IF2, strain HK1662. AAC289694 AJ289694 DNA 453 Actinobacillus actinomycetemcomitans partial infB gene for translation initiation factor IF2, strain HK1651. ------------------------------------------------------------------------------ 7.5. Part of the contents in the file 'ddbjbct1.idx' The first column refers to the locus name, second column to the starting site of the locus in byte, and third to its ending site in byte. They are arranged in the alphabetical order of the locus names. ------------------------------------------------------------------------------ %***************************** #AAC133631 1125664347 1125667802 #AAC133789 1125786300 1125794416 #AAC243194 1136871421 1136876093 #AAC252160 1146107711 1146112332 #AAC252161 1146112333 1146131350 #AAC289685 1155353186 1155356047 #AAC289686 1155356048 1155358781 #AAC289687 1155358782 1155361517 #AAC289694 1155377972 1155380768 #AAC308623 1167555889 1167560983 ------------------------------------------------------------------------------ 7.6. Part of the contents in the file 'ddbjbct1.jou' This gives information on the journal in which sequence data were published. ------------------------------------------------------------------------------ Yi Chuan Xue Bao 29 (12), 1111-1117 (2002) -> AY601668 AY601668 Yi Chuan Xue Bao 29 (12), 1111-1117 (2002) -> AY603420 AY603420 Yi Chuan Xue Bao 30 (4), 364-369 (2003) -> AF526379 AF526379 Yonsei Med. J. 39 (6), 520-525 (1998) -> AF373217 AF373217 Yonsei Med. J. 39 (6), 520-525 (1998) -> AF373218 AF373218 Z. Lebensm.-Unters. -Forsch., A Eur. Food Res. Technol. 209, 83-87(1999). -> ABA7623 AJ007623 Z. Lebensm.-Unters. -Forsch., A Eur. Food Res. Technol. 209, 83-87(1999). -> ABA7624 AJ007624 Zb. Bioteh. Fak. Univ. Ljubl. Kmet. Supl. 79(1), 107-113(2002). -> ASP012466 AJ012466 Zb. Bioteh. Fak. Univ. Ljubl. Kmet. Supl. 79(1), 19-26(2002). -> ASP012466 AJ012466 Zentralbl. Bakteriol. 286 (1), 1-8 (1997) -> AF192489 AF192489 Zentralbl. Bakteriol. 290, 37-49(2000). -> LPN7311 AJ007311 Zentralbl. Bakteriol. 291, 345-352(2001). -> LPN300467 AJ300467 Zentralbl. Bakteriol. 292, 207-214(2002). -> ECO459584 AJ459584 Zhi Wu Bao Hu Xue Hui Hui Kan 44, 233-244 (2002) -> AF540014 AF540014 Zhi Wu Bing Li Xue Bao 34 (1), 80-85 (2004) -> AY447045 AY447045 Zhi Wu Bing Li Xue Hui Kan 12, 57-64 (2003) -> AF450275 AF450275 Zhiwu Baohuxue Hui Huikan 44, 185-208 (2002) -> AY122057 AY122057 Zhiwu Binglixue Huikan 6, 207-208 (1997) -> AF149819 AF149819 Zhongguo Jiaqin 25 (Supplement 1), 60-71 (2003) -> AY615358 AY615358 Zhongguo Kang Sheng Su Za Zhi 21, 94-97 (2003) -> AY293073 AY293073 Zhongguo Kang Sheng Su Za Zhi 28, 96-100 (2003) -> AY293071 AY293071 Zhongguo Kang Sheng Su Za Zhi 28, 96-100 (2003) -> AY293072 AY293072 Zhongguo Lin Chuang Yao Li Xue Za Zhi 19, 190-195 (2003) -> AY536040 AY536040 Zhongguo Nong Ye Ke Xue 36(1), 17-25 (2003) -> AY555768 AY555768 Zhonghua Liu Xing Bing Xue Za Zhi 24, 291-295 (2003) -> AY279003 AY279003 Zhonghua Min Guo Wei Sheng Wu Ji Mian Yi Xue Za Zhi (2003) In press -> AY299484 AY299484 Zhonghua Min Guo Wei Sheng Wu Ji Mian Yi Xue Za Zhi 22 (5), 489-492 (2002) -> AY382160 AY382160 Zool. Sci. 14, 701-706 (1997) -> AB002286 AB002286 Zool. Sci. 14, 701-706 (1997) -> AB002287 AB002287 Zool. Sci. 14, 701-706 (1997) -> AB002288 AB002288 Zool. Sci. 14, 701-706 (1997) -> AB002289 AB002289 Zool. Sci. 14, 701-706 (1997) -> AB002290 AB002290 Zool. Sci. 14, 701-706 (1997) -> AB002291 AB002291 Zoolog. Sci. 17, 983-989 (2000) -> AB038366 AB038366 Zoolog. Sci. 17, 983-989 (2000) -> AB038367 AB038367 Zoolog. Sci. 17, 983-989 (2000) -> AB038368 AB038368 Zoolog. Sci. 17, 983-989 (2000) -> AB038369 AB038369 Zoolog. Sci. 17, 983-989 (2000) -> AB038370 AB038370 ------------------------------------------------------------------------------ 7.7. Part of the contents in the file 'ddbjbct1.key' For the locus and accession number respectively given on the right to the arrow, the corresponding keywords are listed on the left. ------------------------------------------------------------------------------ Synechococcus sp. DNA for intrinsic membrane protein, malK-like protein, cyanase, complete cds. -> AB000100 AB000100 cynS; cyanase; cynD; malK-like protein; cynB; intrinsic membrane protein. -> AB000100 AB000100 Direct Submission -> AB000100 AB000100 Identification and nitrogen regulation of the cyanase gene from the cyanobacteri a Synechocystis sp. strain PPC 6803 and Synechococcus sp. strain PPC 7942 -> AB000100 AB000100 Sequence updated (31-Mar-1997) by: Tatsuo Omata Sequence updated (14-Aug-1997) -> AB000100 AB000100 Sphingomonas sp. 16S ribosomal RNA. -> AB000106 AB000106 16S rRNA. -> AB000106 AB000106 Direct Submission -> AB000106 AB000106 Sphingomonas sp. VT1 16s rRNA -> AB000106 AB000106 Synechococcus sp. gene for ribosomal proteins, complete cds. -> AB000111 AB000111 tRNA pseudouridine synthase I; 50S ribosomal protein L17; DNA-dircted RNA polymerase alpha chain; 30S Ribosomal Protein S11; 30S ribosomal protein S13; 50S ribosomal protein L36; adenylate kinase; preprotein translocase SecY subunit; 50S ribosomal protein L15; 30S ribosomal protein S5; 50S ribosomal protein L18; 50S ribosomal protein L6; 30S ribosomal protein S8; 50S ribosomal protein L5; 50S ribosomal protein L24; 50S ribosomal protein L14; 30S ribosomal protein S17; 50S ribosomal protein L29; 50S ribosomal protein L16; 30S ribosomal protein S3; 50S ribosomal protein L22; 30S ribosomal protein S19; 50S ribosomal protein L2; 50S ribosomal protein L23; 50S ribosomal protein L4; 50S ribosomal protein L3. -> AB000111 AB000111 Direct Submission -> AB000111 AB000111 ------------------------------------------------------------------------------ 7.8. Part of the contents in the file 'ddbjbct1.org' For the locus and accession number respectively given on the right to the arrow, the corresponding taxonomic names are listed on the left. They are arranged in the alphabetical order of the species names. ------------------------------------------------------------------------------ 'Flavobacterium' lutescens 'Flavobacterium' lutescens Bacteria; Proteobacteria; gamma subdivision; Pseudomonadaceae; Pseudomonas. -> AB035478 AB035478 'Flavobacterium' lutescens 'Flavobacterium' lutescens Bacteria; Proteobacteria; gamma subdivision; Pseudomonadaceae; Pseudomonas. -> AB042983 AB042983 'Fragaria multicipita' phytoplasma 'Fragaria multicipita' phytoplasma Bacteria; Firmicutes; Mollicutes; Acholeplasmatales; Acholeplasmataceae; Candidatus Phytoplasma. -> AF036354 AF036354 'Fragaria multicipita' phytoplasma 'Fragaria multicipita' phytoplasma Bacteria; Firmicutes; Mollicutes; Acholeplasmatales; Acholeplasmataceae; Candidatus Phytoplasma. -> AF190224 AF190224 'Fragaria multicipita' phytoplasma 'Fragaria multicipita' phytoplasma Bacteria; Firmicutes; Mollicutes; Acholeplasmatales; Acholeplasmataceae; Candidatus Phytoplasma. -> AF190225 AF190225 'Helichrysum bracteatum' phytoplasma 'Helichrysum bracteatum' phytoplasma Bacteria; Firmicutes; Mollicutes; Acholeplasmatales; Acholeplasmataceae; Candidatus Phytoplasma. -> AF515771 AF515771 'Momordica charantia' phytoplasma 'Momordica charantia' phytoplasma Bacteria; Firmicutes; Mollicutes; Acholeplasmatales; Acholeplasmataceae; Candidatus Phytoplasma. -> PHY431368 AJ431368 'Rehmannia glutinosa var. purpurea' phytoplasma 'Rehmannia glutinosa var. purpurea' phytoplasma Bacteria; Firmicutes; Mollicutes; Acholeplasmatales; Acholeplasmataceae; Candidatus Phytoplasma. -> AF335107 AF335107 'Rhizomonas' sp. 'Rhizomonas' sp. Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Sphingomonas. -> UBA132327 AJ132327 'Vinca minor' phytoplasma 'Vinca minor' phytoplasma Bacteria; Firmicutes; Mollicutes; Acholeplasmatales; Acholeplasmataceae; Candidatus Phytoplasma. -> AY144608 AY144608 ------------------------------------------------------------------------------ 7.9. Part of the contents in the short directory file 'ddbjbct1.sdr' The short directory file contains brief descriptions of all of the sequence entries contained in the DDBJ style. ------------------------------------------------------------------------------ AC133631 Alicyclobacillus acidoterrestris 16S rRNA gene, strain DSM 1482bp AAC133789 Alicyclobacillus acidocaldarius cyclomaltodextrinase gene 3097bp AAC243194 Alicyclobacillus acidocaldarius kdpA gene. 1720bp AAC252160 Alicyclobacillus acidocaldarius cysA gene for putative 1638bp AAC252161 Alicyclobacillus acidocaldarius maltose/maltodextrine 8690bp AAC289685 Actinobacillus actinomycetemcomitans partial infB gene for 453bp AAC289686 Actinobacillus actinomycetemcomitans partial infB gene for 453bp AAC289687 Actinobacillus actinomycetemcomitans partial infB gene for 453bp AAC289694 Actinobacillus actinomycetemcomitans partial infB gene for 453bp AAC308623 Alicyclobacillus acidocaldarius celA gene for cellulase. 1778bp AAC417690 Actinobacillus actinomycetemcomitans mukB gene. 4491bp AAC419840 Acetobacter aceti 16S rRNA gene, strain LMG 1531. 1440bp AAC430786 Actinobacillus actinomycetemcomitans partial fur gene for 1246bp AAC493667 Alicyclobacillus acidocaldarius subsp. rittmannii 16S rRNA 1472bp AAC496806 Alicyclobacillus acidocaldarius 16S rRNA gene, strain DSM 1507bp ------------------------------------------------------------------------------ In addition to the tables for the four following index files are included in this release. These files were prepared for BCT, ENV, EST, GSS, HTC, HTG, HUM, INV, MAM, PAT, PHG, PLN, PRI, ROD, STS, SYN, UNA, VRL, and VRT divisions. Accession number index file Keyword phrase index file Journal citation index file Gene name index file A brief description is given for each file in the above section, '3. Dataset categories'. 7.10. Part of the contents in the accession number index file 'ddbjacc1.idx' The following excerpt from the accession number index file illustrates the format of the index. ------------------------------------------------------------------------------ D00001 ECPBPA BCT X04516 D00002 ECPYRC BCT X04469 D00003 HUMP450M HUM D00003 D00004 FLBFLBL40 VRL D00004 D00005 IBAMEM682 VRL D00005 D00006 BACPNS1981 BCT D00006 D00007 CHKCALGRP VRT D00007 D00008 ECPNTAB BCT X04195 D00009 DROPER1 INV D00009 ------------------------------------------------------------------------------ 7.11. Part of the contents in the keyword phrase index file 'ddbjkey1.idx' Keyword phrases consist of names for gene products and other characteristics of sequence entries. ------------------------------------------------------------------------------ "COAT PROTEIN SMO511347 VRL AJ511347 'TNPA GENE UBA564903 BCT AJ564903 'ZINC-FINGER' MOTIF PRNS53 VRL X60546 (+) MATING TYPE SURFACE PROTEIN ABGPSSP PLN M94861 (1,3 TABETGLUB PLN Z22874 (1,3)-BETA-D-GLUCAN BINDING PROTEIN AJ606470 INV AJ606470 (1,3)BETA-GLUCAN SYNTHASE NCU09275 PLN U09275 (1,4)-BETA-D-ARABINOXYLAN ARABINOFURANOHYDROLASE ANAXHA PLN Z78011 ANTUAXHA PLN Z78010 (1,6)-BETA-GLUCAN BIOSYNTHESIS YSAKRE1A PLN M81588 (1-3)-BETA-GLUCANASE NTSP41AGN PLN X81560 PA13BGPT PLN X57794 (1-3,1-4)-BETA-D-GLUCANASE HVBDG PLN X52572 (1-4)-BETA-MANNAN ENDOHYDROLASE CAR278996 PLN AJ278996 CAR293305 PLN AJ293305 (2',5'-OLIGOISOADENYLATE SYNTHETASE-DEPENDENT) AL138776 HUM AL138776 (2'-5') OLIGO(A) SYNTHASE E16 SSO4G06 EST F14610 (2'-5')OLIGOADENYLATE SYNTHETASE HSA225089 HUM AJ225089 HUMSYN25A HUM D00068 SSA225090 MAM AJ225090 (6')-IB' AMINOGLYCOSIDE ACETYLTRANSFERASE AXY278514 BCT AJ278514 PAE291609 BCT AJ291609 (8,11)-LINOLEOYL DESATURASE COF245938 PLN AJ245938 ------------------------------------------------------------------------------ 7.12. Part of the contents in the journal citation index file 'ddbjjou1.idx' The journal citation index file lists all of the citations that appear in the references. ------------------------------------------------------------------------------ (ER) AAPS PHARMSCI. 4 (3), DOI 10.1208/PS040315 (2002) AY170916 ROD AY170916 (ER) AM. J. HUM. GENET. 76 (1) (2004) IN PRESS AY753209S1 HUM AY753209 AY753209S2 HUM AY753210 (ER) ARCH. VIROL. (2004) IN PRESS AF531505 VRL AF531505 AY518899 VRL AY518899 AY518900 VRL AY518900 AY518901 VRL AY518901 AY518902 VRL AY518902 AY518903 VRL AY518903 AY518904 VRL AY518904 AY518905 VRL AY518905 AY518906 VRL AY518906 AY518907 VRL AY518907 AY518908 VRL AY518908 AY518909 VRL AY518909 AY518910 VRL AY518910 AY518911 VRL AY518911 AY518912 VRL AY518912 AY518913 VRL AY518913 AY518914 VRL AY518914 AY518915 VRL AY518915 AY518916 VRL AY518916 AY518917 VRL AY518917 AY518918 VRL AY518918 AY518919 VRL AY518919 AY518920 VRL AY518920 AY518921 VRL AY518921 AY518922 VRL AY518922 AY518923 VRL AY518923 AY518924 VRL AY518924 AY518925 VRL AY518925 AY518926 VRL AY518926 AY518927 VRL AY518927 AY518928 VRL AY518928 AY518929 VRL AY518929 AY518930 VRL AY518930 AY518931 VRL AY518931 AY518932 VRL AY518932 AY521234 VRL AY521234 AY521235 VRL AY521235 AY521236 VRL AY521236 AY521237 VRL AY521237 AY521238 VRL AY521238 (ER) ARTERIOSCLER. THROMB. VASC. BIOL. (2004) IN PRESS AY563557 HUM AY563557 (ER) BIOCHEM. BIOPHYS. RES. COMMUN. 325 (1), 203-214 (2004) AY563137 HUM AY563137 (ER) BIOCHEM. J./10.1042/BJ20030293 HSA496460 HUM AJ496460 ------------------------------------------------------------------------------ 7.13. Part of the contents in the gene name index file 'ddbjgen.idx' This file lists all the gene names that appear in the feature table. ------------------------------------------------------------------------------ 'ARR BX927156 BCT BX927156 'BGLG BX927156 BCT BX927156 'BGLS BX927148 BCT BX927148 'BGLY' BX927156 BCT BX927156 'BRNQ AF305888 BCT AF305888 'COMK AL591983 BCT AL591983 AL596172 BCT AL596172 'CRCB BX927155 BCT BX927155 'CRTI BX927155 BCT BX927155 'DPPE LDDIPEP BCT Z34898 'FIC BX936398 BCT BX936398 ------------------------------------------------------------------------------ 8. Release history Release Date Entries Bases Comments 66 06/06 58,176,628 62,945,843,881 65 03/06 55,890,995 60,564,721,635 TPA subcategories started 64 12/05 52,272,669 56,098,558,378 Some index files split 63 09/05 47,741,593 52,246,110,341 62 06/05 45,249,444 49,158,155,283 ENV started Version for release note started 61 03/05 43,118,204 47,099,081,750 Changed style of release note 60 12/04 40,583,945 44,416,752,273 /db_xref="H-inv:**" started 59 09/04 37,926,117 42,245,956,937 58 06/04 34,917,581 39,812,635,108 57 03/04 32,693,678 38,008,449,840 56 12/03 30,405,173 36,079,046,032 55 09/03 27,753,140 34,280,225,489 54 06/03 25,149,821 32,162,041,177 53 02/03 23,250,813 29,711,299,332 52 12/02 20,354,812 26,931,456,316 51 09/02 18,401,358 22,782,404,136 TPA started 50 06/02 17,260,693 20,158,357,982 49 04/02 16,503,157 18,579,627,226 48 01/02 15,016,100 16,197,713,855 47 10/01 13,266,610 14,145,671,645 46 07/01 12,313,759 13,037,646,166 45 04/01 11,434,113 12,207,092,905 HTC division started 44 01/01 10,165,597 11,136,298,841 43 10/00 8,666,551 10,034,532,698 42 07/00 7,554,995 8,880,721,093 41 04/00 5,962,608 6,409,581,885 CON division started 40 01/00 5,388,125 4,762,696,173 RNA division terminated 39 10/99 4,810,773 3,728,000,562 NID and PID discarded 38 07/99 4,294,369 3,098,519,597 37 03/99 3,311,627 2,375,261,951 VERSION, /protein_id started 36 01/99 3,073,166 2,190,425,560 35 10/98 2,759,261 1,957,341,169 34 07/98 2,412,785 1,708,580,623 33 04/98 2,174,769 1,479,303,279 32 01/98 1,956,669 1,300,950,613 31 10/97 1,731,532 1,139,869,464 Adoption of the unified taxonomy database 30 07/97 1,534,115 992,788,339 NID and PID terminated 29 04/97 1,270,194 841,415,232 28 01/97 1,154,120 756,785,219 HTG division started ORG division terminated 27 10/96 936,697 608,103,057 GSS division started 26 07/96 835,552 551,932,448 25 04/96 744,490 499,300,364 /translation started 24 01/96 637,508 431,771,652 23 10/95 569,757 390,694,350 22 07/95 437,588 322,982,425 HUM division started 21 04/95 274,596 250,875,023 20 01/95 239,689 231,299,557 19 10/94 204,332 205,274,131 18 07/94 185,230 192,473,021 17 04/94 169,957 179,942,209 16 01/94 154,626 165,017,628 15 10/93 131,649 147,224,690 14 07/93 120,350 138,686,333 13 04/93 112,067 129,784,445 12 01/93 97,683 120,815,244 EST division started 11 07/92 65,693 84,839,075 10 01/92 59,317 77,805,556 GenBank/EMBL inclusion started 9 07/91 1,130 2,002,124 8 01/91 879 1,573,442 7 07/90 681 1,154,211 6 01/90 496 841,236 5 07/89 395 679,378 4 01/89 302 535,985 3 07/88 230 345,850 2 01/88 142 199,392 1 07/87 66 108,970 Started with DDBJ only ------------------ Since release 65 ------------------ Introduction of two types of TPA entries: According to the decision of ICM 2005, TPA data set is now classified into two categories, "TPA:experimental" and "TPA:inferential", to distinguish TPA annotation supported by wet-lab. experimental evidence and that inferred. The retrofit to divide TPA entries into two categories starts from the release 65. You can find the description of the two TPA categories at the following URLs; http://www.ddbj.nig.ac.jp/sub/tpa-e.html http://www.insdc.org/TPA.html See also '3.2. TPA separated from primary dataset'. ------------------ Since release 64 ------------------ Split of index files: In the present release, some of index files (ddbjacc.idx, ddbjjou.idx, and ddbjkey.idx) have been greater than 2 GB in the file size. So, these have been recorded in multiple ddbj****.idx files, each of which at most has 1.5 GB storage capacity as follows, respectively. See also 6.2., 7.10., 7.11., 7.12. and 9. ------------------ Since release 62 ------------------ Release version number is introduced: DDBJ has started to include the item, 'version', for its release note, which indicates a version for its periodical release. It is expressed like '62.0', in which the digit(s) after the period is a version number. The reason for adding the version number is that a released data is sometimes revised due to urgent and necessary corrections. The number is increased by one every time when a revised periodical release is made public until the next release. Introduction of ENV division: Recently, the submissions of the sequences derived from environmental samples have rapidly increased. To accommodate such submissions, a new division, ENV, has been created (See also '3.1. Division categories'). This division contains the sequences obtained via direct molecular isolation such as PCR, DGGE, or any anonymous method. In the past, the sequences derived from environmental samples belonged to taxonomic divisions, mainly BCT. At DDBJ, the retrofit to transfer relevant entries from taxonomic divisions to the ENV division starts in the present release, and ends by the next periodical release. Please note that during this transitional period, some entries to be eventually placed in the ENV division will be found in other divisions. Strand information is removed: The strand information of LOCUS line in the flat file has been removed as shown below. See also '2.1. LOCUS line'. ---------------------------------------------------------------------------- Old (-rel. 61): 44-44 space 45-47 spaces, ss- (single-stranded), ds- (double-stranded), or ms- (mixed-stranded) New (rel. 62-): 44-47 spaces ---------------------------------------------------------------------------- ------------------ Since release 61 ------------------ The style of release note (this file) has been changed. Some entries have the sequential format for the secondary accession numbers in the ACCESSION line, in order to make the expression of secondary accession numbers in the past short. For example; ------------------------------------------------------------------------------ Before; ACCESSION AB000802 D85885 D85886 D85887 After; ACCESSION AB000802 D85885-D85887 ------------------------------------------------------------------------------ See also '2.3. ACCESSION line'. ------------------ Since release 60 ------------------ The cross-reference to the H-invitational has been included. ------------------ Since release 56 ------------------ The three data banks have agreed that the maximum length limitation (350 kb) of a submitted sequence be relaxed. The BASE COUNT line of the DDBJ flat file format has been changed, corresponding to the relaxation of the maximum sequence length restriction in the entry that had been practiced at DDBJ/EMBL/GenBank International Nucleotide Sequence Databases. In the BASE COUNT line of the DDBJ flat file, 6 digits had been allocated for each number of a, c, g, t and other bases in the sequence. Hereafter, in the new flat file format, 9 digits are allocated for each number of a, c, g and t, while the numbers of other bases are removed. In accordance with the relaxation of sequence length limitation, GenBank had already dropped the BASE COUNT line from their flat file format from GenBank Release 138 (Oct. 2003). We DDBJ have decided to maintain the BASE COUNT line in our flat file format from the view that GC contents are still important information to characterize the sequence. The changes in the BASE COUNT line are shown below. ---------------------------------------------------------------------------- Old (-rel. 55): 1 6 11 16 21 26 31 36 41 46 51 56 61 66 71 |----|----|----|----|----|----|----|----|----|----|----|----|----|----| BASE COUNT 123456 a 123456 c 123456 g 123456 t 123456 others New (rel. 56-): 1 6 11 16 21 26 31 36 41 46 51 56 61 66 71 |----|----|----|----|----|----|----|----|----|----|----|----|----|----| BASE COUNT 123456789 a 123456789 c 123456789 g 123456789 t ---------------------------------------------------------------------------- The SOURCE in the flat file is revisited and revised if necessary in accordance with the unified taxonomy database common to the three data banks. ------------------ Since release 54 ------------------ '/sequenced_mol' qualifier has been changed to '/mol_type' qualifier. We accordingly completed retrofitting the pertinent entries. This change was made on the agreement at the INSD collaborative meeting in 2002. ------------------ Since release 51 ------------------ The TPA (Third Party Annotation) dataset has been available. The dataset is a complement to the existing DDBJ/EMBL/GenBank database of the primary nucleotide sequences which were obtained from direct sequencing of cDNAs, ESTs, genomic DNAs etc. The format of LOCUS line in the flat file has been changed as shown below to adjust to the GenBank format. ------------------------------------------------------------------------------ Old (-rel. 50): LOCUS AB000001 660 bp DNA PLN 01-FEB-2001 New (rel. 51-): LOCUS AB000001 660 bp DNA linear PLN 01-FEB-2001 ------------------------------------------------------------------------------ ------------------ Since release 45 ------------------ The HTC (High Throughput cDNA) division has been included. This is to include unfinished high throughput cDNA sequences, each of which has 5'UTR and 3'UTR at both ends and part of a coding region. The sequence may also include introns. When the sequence becomes finished later, it moves to the corresponding taxonomic division. The sequence is accompanied with a keyword, HTC (High Throughput cDNA), which is dropped when the sequence is finished and moved to a taxonomic division. ------------------ Since release 41 ------------------ The CON division has been included. This division is to show the order of related sequences in a genome, and expressed by join and the accession numbers of the sequences. The contents of the CON division are compiled by the three data banks not by the data submitter. ------------------ Since release 40 ------------------ The RNA division was terminated. The RNA data have been redistributed according to the category of the organism. Therefore, you will find a human RNA sequence, for example, in the HUM division. ------------------ Since release 37 ------------------ The three data banks include the item VERSION in the flat file, which indicates a version of a submitted nucleotide sequence. It is expressed like AB123456.1, in which the digit(s) after the period is a version number. The reason for adding VERSION is that since a released sequence sometimes revised by the submitter, the accession number alone cannot specify the sequence in question causing the user a trouble. The number is increased by one every time when a revised sequence is made public. Accordingly, the translated protein sequence will be accompanied with a /protein_id which is expressed as BAA12345.1, in which the digit(s) after the period is again a version number. The number is increased by one when the corresponding nucleotide sequence is revised and the protein sequence is changed as a result, and when the revised protein sequence is made public. ------------------ Since release 31 ------------------ We have started adopting the unified taxonomy database to unify the biological source of the sequence. The database is made up with scientific names, ID of unidentified organisms, and synthetic constructs etc. ------------------ Since release 30 ------------------ NID and PID were terminated. This change was made on the agreement at the INSD collaborative meeting in 1999. ------------------ Since release 28 ------------------ The HTG (High Throughput Genomic sequence) has been included. This division was created to cope with genome project teams which deal with a clone as a sequencing unit. We terminated the ORG (Organelle) division. Thus, if you are interested in human mitochondrial sequences, for example, you are now advised to refer to the HUM division. ------------------ Since release 27 ------------------ The GSS division has been included. GSS stands for Genome Survey Sequence, which is similar to EST, except that GSS is genomic DNA whereas EST is cDNA. ------------------ Since release 25 ------------------ DDBJ release contains amino acid sequences that were translated from the corresponding nucleotide sequences of the database. In the translation we paid much attention to the fact that some species or organella have a codon different from the universal one, and used the proper codon table. ------------------ Since release 22 ------------------ The HUM division has been included. Human genome projects have probably been most productive and yielded a large number of sequences Thus, we have the human (HUM) division solely for human sequences and the primate (PRI) division for non-human primate sequences. ------------------ Since release 12 ------------------ The EST (Expressed Sequence Tag) division has been included. The number of ESTs has been increasing at an enormous rate and is expected to be growing even more rapidly in the future. Thus, we created a division for ESTs ------------------ Since release 10 ------------------ The sequences submitted to GenBank or EMBL have been included in the release. 9. File list The files in this release are arranged in the following order with non-labeled format. ----------------------------------------------------------------------- file name file size ----------------------------------------------------------------------- ddbjrel.txt (DDBJ release note) 110621 ddbjacc1.idx (Accession number index file 1) 1499999999 ddbjacc2.idx (Accession number index file 2) 768735925 ddbjgen.idx (Gene name index file) 86531194 ddbjjou1.idx (Journal citation index file 1) 1472825249 ddbjjou2.idx (Journal citation index file 2) 1118985087 ddbjkey1.idx (Keyword phrase index file 1) 1497087093 ddbjkey2.idx (Keyword phrase index file 2) 769086148 ----------------------------------------------------------------------- file name number of entries number of bases file size ----------------------------------------------------------------------- ddbjbct1.seq 26105 127613826 305721147 ddbjbct2.seq 3767 132753890 304209052 ddbjbct3.seq 3304 131734719 299194821 ddbjbct4.seq 65183 105643919 299000184 ddbjbct5.seq 12931 126007055 305298407 ddbjbct6.seq 58323 111437103 299000067 ddbjbct7.seq 9678 135969927 299403735 ddbjbct8.seq 183 127425687 303692240 ddbjbct9.seq 68 134715696 299051844 ddbjbct10.seq 64 136057483 302166216 ddbjbct11.seq 2157 133127164 299002840 ddbjbct12.seq 64013 108602984 299002762 ddbjbct13.seq 3396 9022474 24585383 ddbjenv1.seq 112299 83089649 299002020 ddbjenv2.seq 107465 93721524 299001767 ddbjenv3.seq 19242 19709045 55298510 ddbjest1.seq 89091 33671886 299001620 ddbjest2.seq 94344 37773125 299002548 ddbjest3.seq 95052 37040156 299002425 ddbjest4.seq 89215 28137921 299000672 ddbjest5.seq 93794 36046591 299001142 ddbjest6.seq 97166 38574744 299001070 ddbjest7.seq 98022 37885035 299002910 ddbjest8.seq 97489 37569834 299000844 ddbjest9.seq 97572 38631400 299003034 ddbjest10.seq 99257 38874489 299002841 ddbjest11.seq 97584 38934068 299002840 ddbjest12.seq 96525 42974301 299000791 ddbjest13.seq 103634 42410548 299001401 ddbjest14.seq 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ddbjgss26.seq 91310 41000418 299002458 ddbjgss27.seq 96588 55483658 299000315 ddbjgss28.seq 90620 44314811 299002819 ddbjgss29.seq 74663 36533062 299000851 ddbjgss30.seq 73422 35644224 299001805 ddbjgss31.seq 76572 33558513 299002613 ddbjgss32.seq 82303 48359601 299002770 ddbjgss33.seq 74973 40360157 299000605 ddbjgss34.seq 90629 47524709 299002332 ddbjgss35.seq 75233 30789685 299003185 ddbjgss36.seq 90176 42493426 299000551 ddbjgss37.seq 74241 40653557 299002517 ddbjgss38.seq 95939 51412296 299000618 ddbjgss39.seq 91671 58400310 298999937 ddbjgss40.seq 100255 49977638 299000371 ddbjgss41.seq 95604 52156261 299000423 ddbjgss42.seq 107844 66473771 299001988 ddbjgss43.seq 111256 72350610 299002063 ddbjgss44.seq 109429 61086705 299001948 ddbjgss45.seq 108846 51199411 299000413 ddbjgss46.seq 106233 45392587 299000173 ddbjgss47.seq 110149 73542143 299002002 ddbjgss48.seq 113957 64500025 298999996 ddbjgss49.seq 109777 62687979 299001626 ddbjgss50.seq 96516 67390502 299002059 ddbjgss51.seq 91991 60784784 299000843 ddbjgss52.seq 98165 57544908 299001486 ddbjgss53.seq 101678 56236440 299000625 ddbjgss54.seq 109262 77181534 299001802 ddbjgss55.seq 105084 75224158 299000250 ddbjgss56.seq 117646 75396797 299002328 ddbjgss57.seq 105571 65735562 299000650 ddbjgss58.seq 91468 47422065 299000380 ddbjgss59.seq 116364 66079782 299000530 ddbjgss60.seq 110456 55581404 299002394 ddbjgss61.seq 107347 72785615 299003137 ddbjgss62.seq 92938 100248883 299002297 ddbjgss63.seq 108479 89672865 299002159 ddbjgss64.seq 103200 68706533 299003013 ddbjgss65.seq 82446 57444337 299001447 ddbjgss66.seq 107811 80159481 299001484 ddbjgss67.seq 110314 71948964 299000371 ddbjgss68.seq 111337 70986058 299001225 ddbjgss69.seq 115421 76266439 299001501 ddbjgss70.seq 128303 68075194 299000349 ddbjgss71.seq 127758 68789856 299000447 ddbjgss72.seq 129247 66840680 299001399 ddbjgss73.seq 129641 66325196 299001748 ddbjgss74.seq 129722 66218638 299001063 ddbjgss75.seq 128948 67232155 299001985 ddbjgss76.seq 119756 79774113 299000213 ddbjgss77.seq 113889 89680172 299001213 ddbjgss78.seq 111955 88476984 299001136 ddbjgss79.seq 111705 86398147 299000556 ddbjgss80.seq 116048 58356737 299000277 ddbjgss81.seq 118213 35563355 299001907 ddbjgss82.seq 111146 55446759 299001670 ddbjgss83.seq 103607 62041866 299002939 ddbjgss84.seq 114033 81240750 299001869 ddbjgss85.seq 99205 83842931 299001987 ddbjgss86.seq 100201 91277111 299002598 ddbjgss87.seq 113778 62365051 299002321 ddbjgss88.seq 97637 54652835 299000529 ddbjgss89.seq 104010 71655464 299001286 ddbjgss90.seq 101239 71385721 299001012 ddbjgss91.seq 104624 73505877 298999965 ddbjgss92.seq 108309 71353869 299002192 ddbjgss93.seq 110268 67794063 299002624 ddbjgss94.seq 111299 88371971 299001938 ddbjgss95.seq 139627 84719776 299001234 ddbjgss96.seq 135161 87483441 299001754 ddbjgss97.seq 111815 62539566 299001826 ddbjgss98.seq 104228 65019654 299000264 ddbjgss99.seq 119005 83241536 299001511 ddbjgss100.seq 123138 89059535 299002313 ddbjgss101.seq 121368 91238821 299001760 ddbjgss102.seq 121123 91043092 299001705 ddbjgss103.seq 108241 64559823 299001380 ddbjgss104.seq 95655 56471740 299002603 ddbjgss105.seq 94678 58319134 299000412 ddbjgss106.seq 94657 58319600 299000946 ddbjgss107.seq 94866 57705880 299002252 ddbjgss108.seq 98696 62878928 299000715 ddbjgss109.seq 109666 72932952 299002012 ddbjgss110.seq 105208 66754311 299001228 ddbjgss111.seq 108624 67762934 299000898 ddbjgss112.seq 100075 77741511 299002409 ddbjgss113.seq 112223 59953495 299002278 ddbjgss114.seq 111415 67301484 299001597 ddbjgss115.seq 102622 70155774 299002065 ddbjgss116.seq 107818 82806142 299001140 ddbjgss117.seq 98603 55097185 299000683 ddbjgss118.seq 109636 65335461 299001982 ddbjgss119.seq 113971 69489073 299000226 ddbjgss120.seq 108978 69670588 299001039 ddbjgss121.seq 104927 74059444 299000977 ddbjgss122.seq 103007 70549524 299002272 ddbjgss123.seq 101311 56052444 299001573 ddbjgss124.seq 100321 65551834 299001152 ddbjgss125.seq 98790 86603943 299000734 ddbjgss126.seq 101059 70636140 299001987 ddbjgss127.seq 100304 69636915 299001297 ddbjgss128.seq 101053 68493754 299001322 ddbjgss129.seq 100086 70002358 299002270 ddbjgss130.seq 105339 73293565 299002212 ddbjgss131.seq 105267 74451035 299001203 ddbjgss132.seq 79008 73007954 299002662 ddbjgss133.seq 100347 78270111 299000162 ddbjgss134.seq 97459 82504159 299001694 ddbjgss135.seq 99976 65017165 299001136 ddbjgss136.seq 116122 73781186 299002344 ddbjgss137.seq 119162 74493307 299000876 ddbjgss138.seq 110215 71698632 299000977 ddbjgss139.seq 92019 47610784 244619535 ddbjhtc1.seq 42086 65451186 299000266 ddbjhtc2.seq 33889 75582523 299003031 ddbjhtc3.seq 33238 80491455 299000844 ddbjhtc4.seq 81417 51721676 299004179 ddbjhtc5.seq 86125 84726213 299003229 ddbjhtc6.seq 77497 92618673 299003408 ddbjhtc7.seq 76063 79462007 299000647 ddbjhtc8.seq 9212 7198131 27100046 ddbjhtg1.seq 1565 225473555 299027633 ddbjhtg2.seq 3362 221524874 299187513 ddbjhtg3.seq 3038 223597585 299021128 ddbjhtg4.seq 1896 223358825 299058341 ddbjhtg5.seq 1521 221473014 299048080 ddbjhtg6.seq 1499 221576348 299017941 ddbjhtg7.seq 1537 221164788 299020198 ddbjhtg8.seq 1333 225449941 299072078 ddbjhtg9.seq 1752 218836707 299211619 ddbjhtg10.seq 1141 228882375 299089752 ddbjhtg11.seq 898 229968920 299106072 ddbjhtg12.seq 890 229969994 299280449 ddbjhtg13.seq 968 229865711 299287445 ddbjhtg14.seq 923 229904361 299208627 ddbjhtg15.seq 2137 210147528 299437388 ddbjhtg16.seq 1401 222618163 299055411 ddbjhtg17.seq 1013 228743123 299265156 ddbjhtg18.seq 1031 228367092 299103363 ddbjhtg19.seq 1061 228402041 299240853 ddbjhtg20.seq 1001 228540267 299176219 ddbjhtg21.seq 933 229678008 299138618 ddbjhtg22.seq 1031 228980913 299485060 ddbjhtg23.seq 1093 227809133 299061234 ddbjhtg24.seq 1100 227864959 299178070 ddbjhtg25.seq 1109 227910615 299194321 ddbjhtg26.seq 1038 228957368 299326864 ddbjhtg27.seq 1132 227315774 299278250 ddbjhtg28.seq 1064 228409532 299041972 ddbjhtg29.seq 990 229446676 299171928 ddbjhtg30.seq 1045 228774336 299342470 ddbjhtg31.seq 1146 227697980 299215643 ddbjhtg32.seq 1124 227639330 299084080 ddbjhtg33.seq 1255 226540511 299256543 ddbjhtg34.seq 1386 224436040 299134007 ddbjhtg35.seq 1599 223825175 299250470 ddbjhtg36.seq 1384 224057205 299036402 ddbjhtg37.seq 1329 229015358 299130817 ddbjhtg38.seq 1505 228136276 299098037 ddbjhtg39.seq 1400 228837992 299174401 ddbjhtg40.seq 1280 228538250 299138022 ddbjhtg41.seq 1173 227190884 299044184 ddbjhtg42.seq 1262 226864690 299136565 ddbjhtg43.seq 1074 226786600 299210802 ddbjhtg44.seq 1270 226765732 299052088 ddbjhtg45.seq 1156 226921459 299171711 ddbjhtg46.seq 1132 226253162 299206841 ddbjhtg47.seq 1144 226020326 299156489 ddbjhtg48.seq 1290 225788571 299151736 ddbjhtg49.seq 1181 226540983 299085776 ddbjhtg50.seq 1362 222769591 299117058 ddbjhtg51.seq 1235 226029241 299296441 ddbjhtg52.seq 1223 226281351 299228555 ddbjhtg53.seq 1171 226144693 299239074 ddbjhtg54.seq 1362 225832334 299206576 ddbjhtg55.seq 1431 223059190 299083099 ddbjhtg56.seq 1501 221582664 299012059 ddbjhtg57.seq 1486 220764431 299193809 ddbjhtg58.seq 1504 220764418 299072138 ddbjhtg59.seq 1479 223716612 299154667 ddbjhtg60.seq 1655 223517368 299075425 ddbjhtg61.seq 1504 227131190 299138059 ddbjhtg62.seq 1472 228563972 299145137 ddbjhtg63.seq 1307 227807279 299049826 ddbjhtg64.seq 1833 228671963 299236705 ddbjhtg65.seq 1157 231765364 299103830 ddbjhtg66.seq 1235 231770162 299156993 ddbjhtg67.seq 1022 216742079 299221219 ddbjhtg68.seq 1370 231366203 299255062 ddbjhtg69.seq 501 69586830 90366417 ddbjhum1.seq 16576 187234439 299091479 ddbjhum2.seq 1658 213567608 299020704 ddbjhum3.seq 1627 223293492 299043763 ddbjhum4.seq 1417 216761051 299172550 ddbjhum5.seq 1461 214736666 299044447 ddbjhum6.seq 1485 213830840 299011229 ddbjhum7.seq 1571 208462509 299007698 ddbjhum8.seq 1678 216880451 299190882 ddbjhum9.seq 1556 213744362 299199182 ddbjhum10.seq 1839 214149474 299048034 ddbjhum11.seq 1940 213689156 299012454 ddbjhum12.seq 36436 162777522 299013741 ddbjhum13.seq 69886 97023520 299001163 ddbjhum14.seq 17551 174192573 299005012 ddbjhum15.seq 2839 219987417 299149544 ddbjhum16.seq 2061 222855766 299069988 ddbjhum17.seq 2497 220601880 299104637 ddbjhum18.seq 4741 215258424 299084255 ddbjhum19.seq 2061 213703552 299035402 ddbjhum20.seq 56344 100502504 299001263 ddbjhum21.seq 34628 107508291 299002208 ddbjhum22.seq 55017 130706788 299000837 ddbjhum23.seq 29381 55713363 129129253 ddbjinv1.seq 19025 193841100 299060081 ddbjinv2.seq 1148 196589651 299006038 ddbjinv3.seq 73572 102801964 299001224 ddbjinv4.seq 71002 103364952 299063401 ddbjinv5.seq 95356 85614457 299003512 ddbjinv6.seq 80793 95437201 299009861 ddbjinv7.seq 27888 95874581 209859982 ddbjmam1.seq 65019 132616743 299000524 ddbjmam2.seq 33910 58821399 152748981 ddbjpat1.seq 253014 87770034 299000052 ddbjpat2.seq 212254 101235929 299000934 ddbjpat3.seq 178455 122694288 299018754 ddbjpat4.seq 192366 107620158 299003892 ddbjpat5.seq 165766 97290972 299001616 ddbjpat6.seq 130020 130849053 299000855 ddbjpat7.seq 151319 112145326 299000124 ddbjpat8.seq 156644 103587641 299001467 ddbjpat9.seq 174703 60647680 299001232 ddbjpat10.seq 119551 71942794 299002766 ddbjpat11.seq 131933 61245720 299000784 ddbjpat12.seq 130878 74699984 299000034 ddbjpat13.seq 171235 57070217 299001344 ddbjpat14.seq 174087 83366751 299000260 ddbjpat15.seq 131147 129464315 299000585 ddbjpat16.seq 146610 114902400 299157163 ddbjpat17.seq 137261 118584792 299000107 ddbjpat18.seq 129619 117901724 299001080 ddbjpat19.seq 121526 91676433 299019513 ddbjpat20.seq 129467 79689242 299000970 ddbjpat21.seq 76708 21566644 86988044 ddbjphg.seq 3092 19597727 48160200 ddbjpln1.seq 39049 147212707 299005598 ddbjpln2.seq 1545 201327026 299007275 ddbjpln3.seq 20756 168257853 299005437 ddbjpln4.seq 89684 93170026 299000605 ddbjpln5.seq 80871 81438247 299008421 ddbjpln6.seq 38286 76300380 299034205 ddbjpln7.seq 6644 190959854 299227103 ddbjpln8.seq 1547 203531604 299117646 ddbjpln9.seq 668 223192190 303067747 ddbjpln10.seq 7132 225441235 299000228 ddbjpln11.seq 79517 80667065 299002582 ddbjpln12.seq 90423 93101393 299000862 ddbjpln13.seq 47805 126582559 299026734 ddbjpln14.seq 76401 112436671 299000401 ddbjpln15.seq 27643 54206428 141240189 ddbjpri1.seq 8583 212103610 299054459 ddbjpri2.seq 28066 191153548 299077098 ddbjpri3.seq 6251 26850200 47050699 ddbjrod1.seq 10494 203053923 299040071 ddbjrod2.seq 1107 207338610 299258443 ddbjrod3.seq 1073 207951026 299172994 ddbjrod4.seq 1108 208437725 299068061 ddbjrod5.seq 1165 214923353 299108733 ddbjrod6.seq 1164 215328593 299189854 ddbjrod7.seq 1185 217589224 299132809 ddbjrod8.seq 1189 218126796 299239434 ddbjrod9.seq 1225 221422576 299144583 ddbjrod10.seq 1151 220822125 299143260 ddbjrod11.seq 1208 221600714 299051292 ddbjrod12.seq 1144 217869901 299304281 ddbjrod13.seq 1161 221055703 299244213 ddbjrod14.seq 22879 189140509 299013649 ddbjrod15.seq 14569 202826961 299017452 ddbjrod16.seq 1437 231149753 299001311 ddbjrod17.seq 13636 211152955 299004319 ddbjrod18.seq 44887 82438544 299003662 ddbjrod19.seq 8231 216864932 299009722 ddbjrod20.seq 35456 41001539 128023563 ddbjsts1.seq 97026 44510209 299001386 ddbjsts2.seq 95589 48290629 299001664 ddbjsts3.seq 96198 40326668 299002965 ddbjsts4.seq 64650 38047549 299003629 ddbjsts5.seq 64933 37772516 299002619 ddbjsts6.seq 64680 38095677 299001331 ddbjsts7.seq 66633 45739100 299003684 ddbjsts8.seq 68566 52572160 299001129 ddbjsts9.seq 68575 52180144 299001513 ddbjsts10.seq 74364 49360927 299002405 ddbjsts11.seq 101835 42500436 299001164 ddbjsts12.seq 18148 6325595 43189363 ddbjsyn.seq 26142 38076999 117737176 ddbjuna.seq 213 116305 439875 ddbjvrl1.seq 86035 77073300 299000158 ddbjvrl2.seq 84906 76912136 299001049 ddbjvrl3.seq 82350 81118693 299002401 ddbjvrl4.seq 79676 84191260 299000572 ddbjvrl5.seq 32967 31147914 115248834 ddbjvrt1.seq 55451 145531760 299001747 ddbjvrt2.seq 31940 178050002 299077977 ddbjvrt3.seq 87170 94292524 299001952 ddbjvrt4.seq 34917 112440726 299096302 ddbjvrt5.seq 1464 230697434 299211902 ddbjvrt6.seq 1552 230061438 299143925 ddbjvrt7.seq 12574 212783266 299000567 ddbjvrt8.seq 15294 207731413 299035347 ddbjvrt9.seq 48269 57768066 171846829 ------------------------------------------------------------------------------ Total 58176628 62945843881 224883513044 ddbjcon.seq 770197 0 1764262099 ddbjtpa.seq 5067 18845016 39976573 The entries and bases in the CON division and TPA dataset are not counted in the numbers given on the top of the release note or 'Total' on the above table.