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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)
//