DNA Data Bank of Japan DNA Database Release 7, July 1990 681 entries, 1154211 bases, 41264 lines This data base may be copied and redistributed freely, without advance permission, provided that this statement is reproduced with each copy. All entries included in this release have been created by DDBJ and will be incorporated into future releases of EMBL and GenBank databases. Entries created by DDBJ in the EMBL and GenBank databases may be identified, because their accession numbers begin with the letter "D". Prepared by: Sanzo Miyazawa Manager/Database Administrator Hidenori Hayashida Scientific Reviewer Yukiko Yamazaki/Eriko Hatada/Hiroaki Serizawa Annotators/reviewers Motono Horie/Shigeko Suzuki/Yumiko Sato Secretaries/typists DNA Data Bank of Japan National Institute of Genetics Center for Genetic Information research Laboratory of Genetic Information Analyses 1111 Yata Mishima, Shizuoka 411 Japan Phone: +81 559 75 0771 x647 FAX: +81 559 75 6040 E-mail: ddbj@ddbj.nig.ac.jp Files included: 1) ddbjrel.txt: release notes; this document 2) ddbjsub.txt: a data submission form 3) netserv.man: a brief manual of network DB server 4) ddbj.dna: DNA data 5) ddbj.cds: peptide coding sequences extracted from ddbj.dna 6) ddbj.pep: peptide sequences translated from ddbj.cds 7) ddbj.dir: a short directory file 8) ddbj.acc: an accession number index file 9) ddbj.aut: an author name index file 10) ddbj.jou: a journal name index file The 5th and 6th files above were generated by using "seqext" and "pepttr" programs made by Dr. Jim Fickett in GenBank, Los Alamos National Laboratory. The index files from the 7th through the 10th file above may include longer lines than 80 characters. If distribution tapes are written in the fixed size records of 80 bytes, longer lines than 80 characters will be folded in those files. Acknowledgements: We thank GenBank for helps, especially for providing us with such tools that are useful for quality control in data entry. Appendix 1. DDBJ database release history Release date Entries Bases Lines -------------------------------------------- 7 07/90 681 1154211 41264 6 01/90 496 841236 29682 5 07/89 395 679378 23895 4 01/89 302 535985 18713 3 07/88 230 345850 13773 2 01/88 142 199392 8238 1 07/87 66 108970 4291 Appendix 2. The DNA sequence file, ddbj.dna The format of the DNA sequence file is the same as one of GenBank data which is described in the release note of GenBank Release 63. Example: -------------------------------------------------------------------------------- LOCUS BOVCYT2 269 bp ds-DNA MAM 31-OCT-1989 DEFINITION Bovine cytochrome P-450 (11beta) gene, exon 2. ACCESSION D00450 KEYWORDS cytochrome; cytochrome P-450; steroid hormone. SEGMENT 2 of 8 SOURCE Bovine adrenal DNA, clone lambdaB11beta(7-1). ORGANISM Bos taurus Eukaryota; Metazoa; Chordata; Vertebrata; Tetrapoda; Mammalia; Eutheria; Artiodactyla. REFERENCE 1 (bases 1 to 269) AUTHORS Hashimoto,T., Morohashi,K. and Omura,T. TITLE Cloning and characterization of bovine cytochrome P-450(11beta) genes JOURNAL J. Biochem. 105, 676-679 (1989) STANDARD full staff_entry COMMENT FEATURES from to/span description pept / 57 / 212 cytochrome P-450(11beta) gene, exon 2 refnumbr 58 60 numbered codon 81 in [1] BASE COUNT 49 a 74 c 110 g 36 t ORIGIN 1 agcggggacc aggcaggaca cggcccctca gcagaccgca gagctctgcc ccacaggtac 61 gacgtgggag ggagacacat ggtgttcgtg atgctgcccg aggacgtgga gaggctgcag 121 caggcggaca gccatcaccc tcagcggatg atcctggagc cctggctggc ctaccgacag 181 gctcgcgggc acaagtgtgg cgtgttcttg ctgtgagggc cggtgggggt gcggagggag 241 gggcagggcg gcctgggtgc agagagcac // ... -------------------------------------------------------------------------------- Appendix 3. The peptide coding sequence file, ddbj.cds, extracted from ddbj.dna Example: -------------------------------------------------------------------------------- ID BOVCYT2 cytochrome P-450 (11beta) gene, exon 2 LOCUS BOVCYT2 269 bp ds-DNA MAM 31-OCT-1989 ACCESSION D00450 ORGANISM Bos taurus Eukaryota; Metazoa; Chordata; Vertebrata; Tetrapoda; Mammalia; Eutheria; Artiodactyla. FEATURES from to/span description pept / 57 / 212 2 cytochrome P-450(11beta) gene, exon 2 COMPLETE 5':n 3':n LENGTH 156 ORIGIN 1 gtacgacgtg ggagggagac acatggtgtt cgtgatgctg cccgaggacg tggagaggct 61 gcagcaggcg gacagccatc accctcagcg gatgatcctg gagccctggc tggcctaccg 121 acaggctcgc gggcacaagt gtggcgtgtt cttgct // ... -------------------------------------------------------------------------------- Appendix 4. The peptide sequence file, ddbj.pep, translated from ddbj.cds Example: -------------------------------------------------------------------------------- ID BOVCYT2 cytochrome P-450 (11beta) gene, exon 2 LOCUS BOVCYT2 269 bp ds-DNA MAM 31-OCT-1989 ACCESSION D00450 ORGANISM Bos taurus Eukaryota; Metazoa; Chordata; Vertebrata; Tetrapoda; Mammalia; Eutheria; Artiodactyla. FEATURES from to/span description pept / 57 / 212 2 cytochrome P-450(11beta) gene, exon 2 COMPLETE 5':n 3':n LENGTH 51 ORIGIN Translated using phase 2 1 ydvggrhmvf vmlpedverl qqadshhpqr milepwlayr qarghkcgvf l // ... -------------------------------------------------------------------------------- Appendix 5. The short directory file, ddbj.dir Example: Entry name #Acc bp Definition ---------------------------------------------------------------------------- AAUFUL D00573 ss-mRNA 1370 + Mushroom (A. aurantia) mRNA for fucose ... ACAADH1 D90004 ds-DNA 2467 Acetobacter aceti(K6033) alcohol ... ACH5SRR D00106 ss-rRNA 114 Achromobacter xylosoxidans GIFU 543 ... ACH5SRRX D00107 ss-rRNA 120 Achromobacter cycloclastes IAM 1013 ... ... YSKURA3A D00431 ds-DNA 1764 + Yeast orotidine 5'-phosphate .. YSOGAPDH D00134 ds-DNA 2159 Zygosaccharomyces rouxii, ... ----------------------------------------------------------------------------- '+' means new or updated entries. Appendix 6. The accession number index file, ddbj.acc Example: #Acc Entry name #Primary accession --------------------------------------------- D00001 -> ECOPBPA D00001 ... D00629 -> VACB12R D00629 D90001 -> HSGMD5GA D90001 ... D90186 -> CE2SSIA D90186 J00614 -> MUSPRIMP D00570 ... X52093 -> STYFLG D00498 --------------------------------------------- Appendix 7. The author name index file, ddbj.aut Example: Author Entry name #Accession --------------------------------------- Abe,K. -> RICGLUT D00584 Abe,M. -> GOTGHRA D00476 ... shimada,K. -> HUMLD78 D00045 tlausen,H.Z. -> LPV76VP1 D00056 --------------------------------------- Appendix 8. The journal name index file, ddbj.jou Example: Jounral name Entry name #Accession ---------------------------------------------------------------- Acta Obst. Gynaec. Jpn. 35, 1133-1142 (1983) -> MUSPRIMP D00570 Agric. Biol. Chem. 47, 441-444 (1983) -> BOVCAS D00412 Agric. Biol. Chem. 49, 2725-2731 (1985) -> MPOCPUP D00379 ... Zool. Sci. (1990) In press -> RATPGHA D00575 Zool. Sci. (1990) In press -> RATTSHB D00578 ----------------------------------------------------------------