From: GOLD::UK%"[email-masked]" 17-FEB-1990 08:21
To: gilbertd@IUBACS

Via:        UK.AC.CAM.PHX; 17 FEB 90  9:54:00 GMT
Date:       Sat, 17 Feb 90 09:54:25 GMT
From:       [email-masked]
To:         gilbertd@IUBACS
 
Here is the last version. In fact it may be the final version as i don't
see it changing very much.
michael ashburner
                   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:[email-masked]
 
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.
//