Relay-Version: version B 2.10 5/3/83; site utzoo.UUCP Path: utzoo!utgpu!water!watmath!uunet!ig!daemon From: daemon@ig.UUCP Newsgroups: bionet.molbio.seqnet Subject: SEQNET Bulletin Message-ID: <4196@ig.ig.com> Date: Tue, 24-Nov-87 22:35:54 EST Article-I.D.: ig.4196 Posted: Tue Nov 24 22:35:54 1987 Date-Received: Sat, 28-Nov-87 05:42:05 EST Sender: daemon@presto.ig.com Lines: 222 From: MJB1@VMS-SUPP.CAM.AC.UK Bulletin_# 49 From: MA11 24 Nov 87 Drosophila codon table 3.0 Date: 24 Nov 87 From: MA11 Subject: Codon tables To: seqnet Drosophila Codon Table Version 3.0 Michael Ashburner, Department of Genetics, University of Cambridge, Cambridge, England. Telephone 44-(0)223-333969 Electronic mail:ma11@uk.ac.cam.phx November 20 1987 These Tables are supplied with the understanding that they can be freely used for research, although if quoted in any publication a suitable acknowledgement (e.g. Michael Ashburner, personal communication) would be appreciated. I will automatically post new versions on the SEQNET and BIONET Bulletin Boards. These will generally be compiled whenever enough new data warrents the work. I am very happy to include new sequences that have not yet made the Sequence Data Banks, if these can be sent to me by electronic mail with sufficient data for the coding sequences to be extracted. If anyone should need the files of coding sequences that have been used to generate these tables please send me a message. Two series of Table are included, one for "host" genes and one for orfs carried by transposable elements. For each series you have a codon table, a base composition and the names of the sequences used to compile these. By and large these sequences are taken from the EMBL, GENBANK or DAYHOFF Libraries. However some have been privately communicated to me. All sequences have been checked that they translate but many are incomplete. Hence, for example, the number of sequences is greater than the number of TER codons. The latest versions of the databanks used are EMBL V13.0 and GENBANK V52.0. // Table 1A: Codons of "host" genes: TTT 401 TCT 256 TAT 416 TGT 254 TTC 1075 TCC 902 TAC 1006 TGC 743 TTA 91 TCA 218 TAA 50 TGA 15 TTG 572 TCG 689 TAG 22 TGG 486 CTT 264 CCT 288 CAT 413 CGT 448 CTC 523 CCC 1002 CAC 735 CGC 814 CTA 253 CCA 491 CAA 458 CGA 268 CTG 1734 CCG 669 CAG 1554 CGG 294 ATT 631 ACT 344 AAT 732 AGT 325 ATC 1237 ACC 1222 AAC 1222 AGC 777 ATA 225 ACA 313 AAA 491 AGA 169 ATG 1084 ACG 568 AAG 1998 AGG 226 GTT 476 GCT 686 GAT 1198 GGT 798 GTC 773 GCC 1870 GAC 1153 GGC 1495 GTA 179 GCA 408 GAA 602 GGA 988 GTG 1307 GCG 533 GAG 2139 GGG 175 Total=43748 // Table 1B: Base composition of "host" genes: T=25951 C=37217 A=30973 G=37107 Nucleotides=131256 // Table 1C: "Host" gene sequences used for Tables 1A and 1B [EMBL/GENBANK Acession numbers] M14643; alpha-tubulin-1 M14644; alpha-tubulin-2 M14645; alpha-tubulin-3 M14646; alpha-tubulin-4 K00667-K00669; Actin 5C K00670;K00671; Actin 42A J01064; Actin 79B K00674;K00675; Actin 87E J01065; Actin 88F Z00030; Alcohol dehydrogenase and 3' ORF X04695; amd X04569-X04570; amylase-2 X03788-X03791; Antp M14549; bicoid X04896; bsg25D M14131; C1A9 nuclear protein K01042; c-ash M11281; c-myb (13E) K01960; c-ras1 (85D) M10759;M10803;M10804; c-ras2 (64B) X02200; c-ras3 (62B) M11917; c-src (64B) X02305; c-src4 Y00133; calmodulin X03062; caudal M13219; choline acetyl transferase X02497; chorion genes s18-1, s15-1 and s19-1 V00200; collagen-like gene fragments [two genes] X01761; cytochrome c gene DC3 X01760; cytochrome c gene DC4 M13373; Deformed X04426; dopa decarboxylase M14978-14982; dunce X04521; eip28/29 Cherbas; eip40 M11744; Elongation factor (48D) M10017; engrailed K03416;K03417;K034018; epidermal growth factor homolog Richmond; Esterase-6 X05138; eve X00854;K01951; ftz M11254; Gapdh-1 M11255; Gapdh-2 J02527; glycinimide ribotide transformylase (GART) M13786; Gpdh [exon 3] J01085; heat shock cognate 70C [exon 1] K01296;K01297; heat shock cognate 87D [exons 1 & 2] J02569; heat shock cognate 88E X04073; Histone H1 Dayhoff; Histone H2A Dayhoff; Histone H2B Dayhoff; Histone H3 Dayhoff; Histone H4 V00209; hsp22 V00210; hsp23 V00211; hsp26 V00212; hsp27 V00213;V00214; hsp70 [87A] J01104;J01105; hsp70 [87C] X03810; hsp82 Y00274; hunchback M13568; Insulin-like receptor protein-1 M14778; Insulin-like receptor protein-2 K03057;K03058; invected X04227; l(2)37Cc V00202; larval cuticle protein I [44D] V00203; larval cuticle proteins II & III [44D] V00204; larval cuticle proteins H, D and L. X03872; LSP1-alpha X03873; LSP1-beta X03874; LSP1-gamma X03758; metallothionein (Mtn) M12741; myosin-heavy chain [exons A & C] M10125; myosin-light chain X04016; nicotinic acetylcholine receptor (AChR) K02315; ninaE (opsin) M11664; Notch Y00043; ospsin R7 specific M12896; opsin at 91D M15762; pen#9b M11969; period Y00402; Phosphoenolpyruvate carboxykinase M14548; prd X05076;Y00042; protein kinase C X00848; ribosomal protein rp49 X05016; ribosomal protein rp1A M11798; RNA polymerase II-215 Y00308; rosy X04813; rudimentary X01918; Sgs3, Sgs7, Sgs8 J01135;J01136; Sgs4 X04269; Sgs5 X04513; snake X03121; sry K03277; tropomyosin I M15466; tropomyosin II X02989; trypsin-like enzyme, alpha-chain X05723;Y00206; Ubx X01802; vitelline membrane protein X02974; white Chia; yellow V00248; Yolk protein-1 J01157; Yolk protein-2 M15898; Yolk protein-3 // Table 2A: Codon table TE genes: TTT 366 TCT 129 TAT 264 TGT 108 TTC 200 TCC 120 TAC 230 TGC 107 TTA 351 TCA 197 TAA 1 TGA 1 TTG 195 TCG 74 TAG 0 TGG 108 CTT 216 CCT 112 CAT 187 CGT 64 CTC 104 CCC 104 CAC 165 CGC 38 CTA 199 CCA 271 CAA 396 CGA 99 CTG 105 CCG 52 CAG 160 CGG 22 ATT 463 ACT 205 AAT 620 AGT 180 ATC 175 ACC 171 AAC 403 AGC 145 ATA 447 ACA 374 AAA 888 AGA 260 ATG 199 ACG 64 AAG 282 AGG 83 GTT 181 GCT 160 GAT 330 GGT 130 GTC 106 GCC 129 GAC 305 GGC 107 GTA 188 GCA 222 GAA 566 GGA 148 GTG 113 GCG 63 GAG 227 GGG 39 Total=12718 // Table 2B: Base composition TE genes: T=9774 C=7350 A=14591 G=6439 Nucleotides=38154 // Table 2C: TE genes used for Tables 2A and 2B: [EMBL/GENBANK Accession numbers] X01472; 17.6 element X03431; 297 element X04132;X03733; 412 element X02599; copia element [Saigo] V00246; FB4 X03734; gypsy element X01748; HB1 X04705; hobo Finnegan I element O'Hare; P element X01747; transposon HB2 X02600; virus like particle RNA (VLP H-RNA) //