(none)
MA11 at PHOENIX.CAMBRIDGE.AC.UK
MA11 at PHOENIX.CAMBRIDGE.AC.UK
Mon Feb 19 11:40:29 EST 1990
Drosophila Codon Tables
Version 8.2
November 15 1989
Michael Ashburner,
Department of Genetics,
University of Cambridge,
Cambridge, England.
Telephone 44-(0)223-333969
Electronic mail:ma11 at uk.ac.cam.phx
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 BIOSCI Bulletin Board.
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 Tables 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 V20.0 and GENBANK V61.0.
The "host" gene coding sequences are from a total of 687.482-kb of sequenced
DNA.
//
Table 1A: Base composition of "host" genes:
T=65551 C=93013 Y=0 Pyrimidine=158564
A=79558 G=91689 R=0 Purine=171247
N=9 Nucleotides=329820
Deletions=0 Characters=329820
//
Table 1B: Codons of "host" genes:
TTT 1040 TCT 687 TAT 1061 TGT 633
TTC 2639 TCC 2287 TAC 2262 TGC 1744
TTA 345 TCA 649 TAA 102 TGA 40
TTG 1525 TCG 1986 TAG 57 TGG 1069
CTT 749 CCT 712 CAT 1218 CGT 1083
CTC 1360 CCC 2288 CAC 1966 CGC 1963
CTA 682 CCA 1358 CAA 1451 CGA 752
CTG 4204 CCG 1876 CAG 4362 CGG 751
ATT 1605 ACT 862 AAT 2189 AGT 1070
ATC 2860 ACC 2727 AAC 3067 AGC 2160
ATA 659 ACA 922 AAA 1310 AGA 450
ATG 2715 ACG 1450 AAG 4495 AGG 632
GTT 1123 GCT 1660 GAT 2979 GGT 1986
GTC 1683 GCC 4362 GAC 2692 GGC 3635
GTA 513 GCA 1200 GAA 1772 GGA 2310
GTG 3066 GCG 1515 GAG 4886 GGG 479
Total=109935
//
Table 1C: "Host" gene sequences used for Tables 1A and 1B
The numbers after the names indicate the number of codons (including the
N-terminal met); if this number is bracketed then the coding sequence is
incomplete; if the number of codons is followed by a '.' then the terminator
is included.
[EMBL/GENBANK Acession numbers]
M26267; 67B gene 1, 239.
X07311; 67B gene 2, 112.
X06542; 67B gene 3, 170.
M14643; alpha-tubulin-1, 452.
M14644; alpha-tubulin-2, 451.
M14645; alpha-tubulin-3, 451.
M14646; alpha-tubulin-4, 463.
M20419; beta-tubulin-1, 448.
M16922; beta-tubulin-2, 447.
M16923; beta-tubulin-3, 455.
X16134; Abdominal-B-M (Abdb-B), 492.
X13168; Abdominal-B-r (Abdb-B-r), 528.
X05893; acetyl cholinesterase, 650.
M17120; achaete, 202.
K00667-K00669; actin 5C, 377.
K00670;K00671; actin 42A, 377.
J01064; actin 79B, 377.
K00674;K00675; actin 87E, 377.
J01065; actin 88F, 377.
Z00030; alcohol dehydrogenase, 257.
Z00030;Kreitman; 3' orf to Adh, 273.
X04569; amylase-1, 495.
X03788-X03791; Antp, 379.
M18432; Aprt, 184.
X12550; asense, 397.
X14476; ATP-ase-alpha-subunit, 1029.
X13107;Y00226; awd, 154.
X07870; bicoid, 495.
X04896; bsg25D, 742.
M20630; bw, 676.
M14131; C1A9 nuclear protein, 162.
M19690-92;M18402; c-abl, 1521.
X05939; c-myb (13E), 698.
X07181; c-raf, 667.
K01960; c-ras1 (85D), 190.
M10759;M10803;M10804; c-ras2 (64B), 196.
X02200; c-ras3 (62B), 183.
M11917; c-src (64B), 553.
M16599; c-src4 (28C), 591.
X05948-X05951; calmodulin, 150.
M18655; cAMP-dependent-protein-kinase-catalytic (Dpck), 354.
M18656; cGMP-dependent-protein-kinase-catalytic (Dg1),[473]
M16534;J03452; casein-hydrolase-alpha-chain, 337.
M16534;J03452; casein-hydrolase-beta-chain, 216.
M21069;M21070 caudal, 473.
M19008-M19017; chaoptin, 1135.
M13219; choline acetyl transferase, [729.]
X02947; chorion gene s15-1, 116.
X02497; chorion gene s18-1, 273.
X02947; chorion gene s19-1, 374.
X05245; chorion gene s36, 287.
X05245; chorion gene s38, 307.
V00200; collagen-like gene fragments, [469]
J02727; collagen-IV, [712.]
X05144; crumbs (EGF-like at 95F), [293]
X07985; cut, 2176.
X01761; cytochrome c gene DC3, 106.
X01760; cytochrome c gene DC4, 109.
J13148 daughterless, 711.
X05136; Deformed, 591.
X06289; Delta, 881.
X04426; dopa decarboxylase, 512.
M23702; dorsal, 678.
J03957; D-cholecytokinin-like (Dsk), 129.
M14978-14982; dunce, 363.
X04521; eip28/29, 256.
X04024; eip40, 394.
X15087; eip74EF, 884.
X15586; eip75B, 1444.
X15657; element-binding-factor-1, 1064.
X06869; elongation factor-1, alpha F1 (48D), 464.
X06870; elongation factor-1, alpha F2, 464.
X15805; elongation factor-2, 845.
M10017; engrailed, 553.
M20571; E(spl), 720.
M15961; esterase-6, 549.
X05138; even-skipped, 377.
M20545; fasciclin I, 653.
J03232; FMRF-amide, 343.
M18281; follicle cell protein @ 3C, 211.
J03177; fork-head, 511.
X14153; fs(1)K10, 464.
M23221; fsh, 2039.
X00854;K01951; fushi tarazu, 414.
M11254; Gapdh-1, 333.
M11255; Gapdh-2, 333.
J02932; Glued, 1320.
M22567;J04083; G-protein beta subunit, 341.
J02527;K02461; glycinimide ribotide transformylase (GART), 1354.
J04567 Gpdh, 352.
J01085; heat shock cognate 70C [exon 1], [68]
K01296;K01297; heat shock cognate 87D [exons 1 & 2], [70]
J02569; heat shock cognate 88E, [104]
X04073; Histone H1, 257.
Dayhoff; Histone H2A, [122]
X07485; Histone H2A variant, 142.
Dayhoff; Histone H2B, [118]
Dayhoff; Histone H3, [122]
Dayhoff; Histone H4, [72]
M21329; HMG-coenzyme A reductase, 917.
Y00843; homoeobox protein H2.0, 411.
V00209; hsp22, 175.
V00210; hsp23, 187.
V00211; hsp26, 209.
V00212; hsp27, 214.
V00213;V00214; hsp70 [87A], [345.]
J01104;J01105; hsp70 [87C], 642.
X03810; hsp82, 718.
Y00274; hunchback, 759.
M13568; Insulin-like receptor protein-1 (Dir-b) [1096.]
M14778; Insulin-like receptor protein-2, (Dir-a) [300]
X05273; invected, 577.
X13331; knirps, 430.
X14153; knirps-related, 648.
X03414; Kruppel, 467.
X04227; l(2)37Cc, 327.
X05991; l(2)37Cs, 246.
X04695; l(2)amd, 511.
X05426; l(2)gl, 1161.
M13014;X12834; labial, 636.
X07278; lamin, 622.
M19525; lamimin B1, 1788.
X07802; laminin B2, [1297.]
V00202; larval cuticle protein-1 [44D], 131.
V00203; larval cuticle protein-2 [44D], 127.
V00203; larval cuticile protein-3 [44D], 112.
V00204; larval visceral protein-D [44D], 509.
V00204; larval visceral protein-H [44D], 522.
V00204; larval visceral protein-L [44D], 506.
X12549; lethal-of-scute 258.
X03872; LSP1-alpha, [70]
X03873; LSP1-beta, [100]
X03874; LSP1-gamma, [105]
X03758; metallothionein-A (MtnA), 41.
M16250; metallothionein-B (MtnB), 44.
Y00795; mp20, 184.
Y00219; mst355a, 265.
Y00831; mst(3)gl-9 sperm protein, 57.
J02788; myosin-heavy chain, 270.
M10125; myosin-alkali-light chain, 156.
M11947; myosin-light-chain-2, 223.
J03251; myospheroid, 847.
X04016; nicotinic acetylcholine receptor (Ard), 522.
X07194; nicotinic acetylcholine receptor, alpha subunit,
(AcrB) 568.
M20230; ninaC, 1502.
J03138; norpA, 1096.
M11664; Notch, 2704.
K02315; opsin, ninaE, 374.
M12896; opsin, Rh2, 381.
M17718; opsin, Rh3, 384.
M17719;M17730; opsin, Rh4, 379.
X13693; otu, 812.
M14548; paired, 614.
M24285; para, [1821]
M21201; paragonial peptide (PapB), 56.
M25662; pecanex, [1929.]
M15762; pen#9b, 366.
M11969; period, 1128.
Y00402; Phosphoenolpyruvate carboxykinase, 648.
M14548; paired, 614.
X05076;Y00042; protein kinase C, 640.
Y07510; protein phosphatase (pp55A), 315.
M19059; PS2 antigen, 1395.
J02527;K02461; pupal cuticle protein (Gart), 185.
Y00504; ribosomal protein rp21C, 113.
X14247; ribosomal protein rpS31, 115.
X00848; ribosomal protein rp49, 134.
X05016; ribosomal protein rpA1, 114.
X13382; ribosomal protein rpL1, 408.
M21045; ribosomal protein S14A, 152.
M21045; ribosomal protein S14B, 152.
X05709; RNA polymerase II-140, 1124.
M11798; RNA polymerase II-215, [470]
M19537; RNA polymerase II-215 [409.]
Y00308; rosy, 1336.
X04813; rudimentary, 2357.
M17119; scute T4, 346.
X03121; serendipity-alpha, 531.
X03121; serendipity-beta, 352.
X03121; serendipity-delta, 431.
J03158; sevenless, 2555.
X01918; Sgs3, 308.
J01135;J01136; Sgs4, [141]
X04269; Sgs5, 164.
X01918; Sgs7, 75.
X01918; Sgs8, 76.
X07131;Y00847; Shaker, 617.
M19020; single minded, 656.
Y00288; snail, 391.
X04513; snake, 431.
Y00228; su(Hw), 945.
Y00367; superoxide dismutase, 154.
M21159; Tcp1, 558.
M19140; ter, 429.
M19494; tko, 141.
J02682; Toll, 1098.
M17478; tra, 198.
M23633; tra-2, 180.
K03277; tropomyosin I, T-isoform, [198]
M15466; tropomyosin II, 286.
M18635; trp, 265.
X02989; trypsin-like enzyme, alpha-chain, 257.
X14569; twist, 491.
X05723;Y00206; Ubx, 390.
X12945;X12946; vasa, 661.
X01802; vitelline membrane protein (Vm34C.1), [96]
M18280; vitelline membrane protein (Vm26A.2), 142.
X02974; white, 697.
M17230; wingless, 469.
Chia; yellow, 542.
V00248; yolk protein-1, 441.
J01157; yolk protein-2, 460.
M15898; yolk protein-3, 421.
Y00049; zeste, 576.
X07450; zipper, 501.
//
Table 2A: Codon table TE genes:
TTT 439 TCT 176 TAT 314 TGT 143
TTC 266 TCC 163 TAC 295 TGC 150
TTA 407 TCA 252 TAA 10 TGA 2
TTG 288 TCG 103 TAG 2 TGG 166
CTT 271 CCT 142 CAT 255 CGT 100
CTC 164 CCC 140 CAC 228 CGC 83
CTA 256 CCA 341 CAA 512 CGA 137
CTG 172 CCG 89 CAG 246 CGG 46
ATT 543 ACT 261 AAT 720 AGT 228
ATC 251 ACC 219 AAC 490 AGC 205
ATA 505 ACA 450 AAA 1047 AGA 326
ATG 269 ACG 114 AAG 418 AGG 135
GTT 242 GCT 245 GAT 414 GGT 175
GTC 158 GCC 197 GAC 424 GGC 165
GTA 249 GCA 312 GAA 696 GGA 205
GTG 188 GCG 100 GAG 350 GGG 75
Total=16734
//
Table 2B: Base composition TE genes:
T=12512 C=10084 Y=0 Pyrimidine=22596
A=18309 G=9297 R=0 Purine=27606
N=0 Nucleotides=50202
Deletions=0 Characters=50202
//
Table 2C: TE genes used for Tables 2A and 2B:
[EMBL/GENBANK Accession numbers]
X01472; 17.6 element, 1975
X03431; 297 element, 1944
X07656; 1731 element, 273 & 982
X04132;X03733; 412 element, 128, 104, 455. & 1237
X02599; copia element [Saigo], 1410
M17214; F-element, 123. & 860.
M12927; gypsy, 452., 1036. & 510.
X01748; HB1, 149.
X04705; hobo, 644
M14954; I element, 430. & 1087.
M14653; mariner (mauritiana), 345.
O'Hare; P element, 792.
X02600; virus like particle RNA (VLP H-RNA), 1289 & 146
Savakis; minos element (hydei), 362.
//
More information about the Mol-evol
mailing list
Send comments to us at biosci-help [At] net.bio.net
