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Started by BIORELAY
Tue, 24 May 1988 17:49
SEQNET Bulletin RELAY ONLY: reply to SEQNET@UK.AC.CAM.BIO
Author: BIORELAY
Date: Tue, 24 May 1988 17:49
Date: Tue, 24 May 1988 17:49
314 lines
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15097 bytes
From: BIORELAY@BIO.CAM.AC.UK
From: SEQNET@UK.AC.CAM.PHX 24-MAY-1988 11:16
To: SEQNET
Subj:
Date: Tue, 24 May 88 11:15:05 BST
From: SEQNET@UK.AC.CAM.PHX
To: seqnet@UK.AC.CAM.BIO
Message-ID: <9E900D0A61660C30@UK.AC.CAM.PHX>
(Message number 2)
Accepted: 11:13:07 24 May 88
Submitted: 16:16:20 21 May 88
IPMessageId: 9E8C8AC803CD4E90
From: MA11
To: seqnet
Drosophila Codon Table
Version 4.0
Michael Ashburner,
Department of Genetics,
University of Cambridge,
Cambridge, England.
Telephone 44-(0)223-333969
Electronic mail:ma11@uk.ac.cam.phx
May 18 1988
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 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 V15.0 and GENBANK V55.0.
//
Table 1A: Codons of "host" genes:
TTT 477 TCT 341 TAT 521 TGT 323
TTC 1270 TCC 1071 TAC 1187 TGC 899
TTA 147 TCA 291 TAA 61 TGA 18
TTG 687 TCG 831 TAG 28 TGG 560
CTT 362 CCT 371 CAT 521 CGT 552
CTC 605 CCC 1201 CAC 910 CGC 927
CTA 298 CCA 631 CAA 598 CGA 344
CTG 1986 CCG 814 CAG 1877 CGG 316
ATT 787 ACT 437 AAT 912 AGT 404
ATC 1417 ACC 1418 AAC 1442 AGC 909
ATA 282 ACA 399 AAA 593 AGA 209
ATG 1304 ACG 672 AAG 2304 AGG 259
GTT 577 GCT 864 GAT 1414 GGT 1034
GTC 897 GCC 2164 GAC 1333 GGC 1805
GTA 226 GCA 522 GAA 770 GGA 1233
GTG 1527 GCG 660 GAG 2491 GGG 205
Total = 52495
//
Table 1A in Staden format:
===========================================
F TTT 477. S TCT 341. Y TAT 521. C TGT 323.
F TTC1270. S TCC1071. Y TAC1187. C TGC 899.
L TTA 147. S TCA 291. * TAA 61. * TGA 18.
L TTG 687. S TCG 831. * TAG 28. W TGG 560.
===========================================
L CTT 362. P CCT 371. H CAT 521. R CGT 552.
L CTC 605. P CCC1201. H CAC 910. R CGC 927.
L CTA 298. P CCA 631. Q CAA 598. R CGA 344.
L CTG1986. P CCG 814. Q CAG1877. R CGG 316.
===========================================
I ATT 787. T ACT 437. N AAT 912. S AGT 404.
I ATC1417. T ACC1418. N AAC1442. S AGC 909.
I ATA 282. T ACA 399. K AAA 593. R AGA 209.
M ATG1304. T ACG 672. K AAG2304. R AGG 259.
===========================================
V GTT 577. A GCT 864. D GAT1414. G GGT1034.
V GTC 897. A GCC2164. D GAC1333. G GGC1805.
V GTA 226. A GCA 522. E GAA 770. G GGA1233.
V GTG1527. A GCG 660. E GAG2491. G GGG 205.
===========================================
TOTAL CODONS= 52495.
//
Table 1B: Base composition of "host" genes:
T = 31458 C = 44456 Y = 0 Pyrimidine = 75914
A = 37333 G = 44242 R = 0 Purine = 81575
N = 8 Nucleotides = 157497
//
Table 1C: "Host" gene sequences used for Tables 1A and 1B
The numbers after the names indicate the number of codons (excluding ter but
including N-terminal met); if this number if bracketed then the coding
sequence is incomplete.
[EMBL/GENBANK Acession numbers]
M14643; alpha-tubulin-1, 450
M14644; alpha-tubulin-2, 449
M14645; alpha-tubulin-3, 450
M14646; alpha-tubulin-4, 462
M16922; beta-tubulin-2, 446
M16922; beta-tubulin-3, 448
X05893; acetyl cholinesterase, 649
X06384;Y00212; actin 5C, [137]
K00670;K00671; actin 42A, [308]
J01064; actin 79B, 376
K00674;K00675; actin 87E, [93]
J01065; actin 88F, 376
Z00030; alcohol dehydrogenase, 256
Z00030; 3' orf to Adh, [145]
X04695; a-methyl-dopa resistant (amd), 510
X04569; amylase-1, 494
X03788-X03791; Antp, 378
M14549; bicoid, [71]
X04896; bsg25D, 741
M14131; C1A9 nuclear protein, 161
K01042; c-ash, [275]
X05939; c-myb (13E), 697
K01960; c-ras1 (85D), 189
M10759;M10803;M10804; c-ras2 (64B), 195
X02200; c-ras3 (62B), 182
M11917; c-src (64B), 552
M16599; c-src4 (28C), 590
Y00133; calmodulin, [128]
M16534;J03452; casein-hydrolase-alpha-chain, 336
M16534;J03452 casein-hydrolase-beta-chain, 215
X03062; caudal, [197]
M13219; choline acetyl transferase, [728]
X02947; chorion gene s15-1, 115
X02497; chorion gene s18-1, 272
X02947; chorion gene s19-1, 373
X05245; chorion gene s36, 286
X05245; chorion gene s38, 306
V00200; collagen-like gene fragments, [589]
J02727; collagen-IV, [711]
X05144; crumbs (EGF-like at 95F), [293]
X01761; cytochrome c gene DC3, 105
X01760; cytochrome c gene DC4, 108
X05136; Deformed, 590
X05140; Delta, [200]
X04426; dopa decarboxylase, 511
M14978-14982; dunce, 362
X04521; eip28/29, 255
X04024; eip40, 393
M11744; elongation factor (48D), 463
M10017; engrailed, 552
M15961; esterase-6, 548
X05138; even-skipped, 376
X00854;K01951; fushi tarazu, 413
M11254; Gapdh-1, 332
M11255; Gapdh-2, 332
J02527;K02461; glycinimide ribotide transformylase (GART), 1353
M13786; Gpdh [exon 3], [40]
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, 256
Dayhoff; Histone H2A, [122]
Dayhoff; Histone H2B, [118]
Dayhoff; Histone H3, [122]
Dayhoff; Histone H4, [72]
V00209; hsp22, 174
V00210; hsp23, 186
V00211; hsp26, 208
V00212; hsp27, 213
V00213;V00214; hsp70 [87A], [347]
J01104;J01105; hsp70 [87C], 641
X03810; hsp82, 717
Y00274; hunchback, 757
M13568; Insulin-like receptor protein-1, [1095]
M14778; Insulin-like receptor protein-2, [300]
X05273; invected, 576
X03414; Kruppel, 466
X04227; l(2)37Cc, 326
X05426; lethal(2)giant larva, 1160
V00202; larval cuticle protein-1 [44D], 130
V00203; larval cuticle protein-2 [44D], 126
V00203; larval cuticile protein-3 [44D], 112
V00204; larval visceral protein-D [44D], 508
V00204; larval visceral protein-H [44D], 522
V00204; larval visceral protein-L [44D], 505
X03872; LSP1-alpha, [70]
X03873; LSP1-beta, [100]
X03874; LSP1-gamma, [105]
X03758; metallothionein (Mtn), 40
Y00831; mst(3)gl-9 sperm protein, 56
J02788; myosin-heavy chain, 269
M10125; myosin-light chain, 155
X04016; nicotinic acetylcholine receptor (AChR), 521
M11664; Notch, 2703
Y00043; ospsin R7 specific, 383
K02315; opsin, ninaE, 373
M12896; opsin at 91D, 373
M15762; pen#9b, 365
M11969; period, 1127
Y00402; Phosphoenolpyruvate carboxykinase, 647
M14548; paired, 613
X05076;Y00042; protein kinase C, 639
J02527;K02461; pupal cuticle protein (Gart), 184
X05016; ribosomal protein rpA1, 113
X00848; ribosomal protein rp49, 133
X05709; RNA polymerase II-140, 1123
M11798; RNA polymerase II-215, [470]
Y00308; rosy, 1335
X04813; rudimentary, 2356
X01918; Sgs3, 307
J01135;J01136; Sgs4, [141]
X04269; Sgs5, 163
X01918; Sgs7, 74
X01918; Sgs8, 75
Y00288; snail, 390
X04513; snake, 430
X03121; serendipity-alpha, 530
X03121; serendipity-beta, 351
X03121; serendipity-delta, 430
Y00367; superoxide dismutase, 213
K03277; tropomyosin I, T-isoform, [198]
M15466; tropomyosin II, 285
X02989; trypsin-like enzyme, alpha-chain, 256
X05723;Y00206; Ubx, 389
X01802; vitelline membrane protein, [96]
X02974; white, 541
Chia; yellow, 696
V00248; yolk protein-1, 459
J01157; yolk protein-2, 459
M15898; yolk protein-3, 420
Y00049; zeste, 575
//
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 2A in Staden format:
===========================================
F TTT 366. S TCT 129. Y TAT 264. C TGT 108.
F TTC 200. S TCC 120. Y TAC 230. C TGC 107.
L TTA 351. S TCA 197. * TAA 1. * TGA 1.
L TTG 195. S TCG 74. * TAG 0. W TGG 108.
===========================================
L CTT 216. P CCT 112. H CAT 187. R CGT 64.
L CTC 104. P CCC 104. H CAC 165. R CGC 38.
L CTA 199. P CCA 271. Q CAA 396. R CGA 99.
L CTG 105. P CCG 52. Q CAG 160. R CGG 22.
===========================================
I ATT 463. T ACT 205. N AAT 620. S AGT 180.
I ATC 175. T ACC 171. N AAC 403. S AGC 145.
I ATA 447. T ACA 374. K AAA 888. R AGA 260.
M ATG 199. T ACG 64. K AAG 282. R AGG 83.
===========================================
V GTT 181. A GCT 160. D GAT 330. G GGT 130.
V GTC 106. A GCC 129. D GAC 305. G GGC 107.
V GTA 188. A GCA 222. E GAA 566. G GGA 148.
V GTG 113. A GCG 63. E GAG 227. G GGG 39.
===========================================
TOTAL CODONS= 12718.
//
Table 2B: Base composition TE genes:
T = 9774 C = 7350 Y = 0 Pyrimidine = 17124
A = 14591 G = 6439 R = 0 Purine = 21030
N = 0 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)
//
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