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PMID: 6159596 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't

Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type.

Nucleic acids research ·Vol. 8 ·No. 9 ·1980-05-10 ·Pages 1893-912

Grantham R, Gautier C, Gouy M

Abstract

The poor printing of our previous Figure 2 (1) is corrected. Codon usage in mRNA sequences just published is also given. A new correspondence analysis is done, based on simultaneous comparison in all mRNA of use of the 61 codons. This analysis reinforces our claim that most genes in a genome, or genome type, have the same coding strategy; that is, they show similar choices among synonymous codons, or among degenerate bases (2). Like analysis on frequency variation in the amino acids coded reveals an entirely different pattern.

MeSH Terms
Animals Base Sequence Bombyx/genetics Cattle Chickens/genetics Codon/genetics Genes Humans Mice RNA, Bacterial/genetics RNA, Fungal/genetics RNA, Messenger/genetics RNA, Viral/genetics Rabbits Sea Urchins/genetics Species Specificity
Chemicals
Codon RNA, Bacterial RNA, Fungal RNA, Messenger RNA, Viral
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Grantham R
Gautier C
Gouy M
References (72)
72 references, click to expand
  1. A-protein gene of bacteriophage MS2.
    Nature. 1975 Jul 24;256(5515):273-8 PMID: 806810
  2. Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene.
    Nature. 1976 Apr 8;260(5551):500-7 PMID: 1264203
  3. Nucleotide sequence of bacteriophage phi X174 DNA.
    Nature. 1977 Feb 24;265(5596):687-95 PMID: 870828
  4. The primary structure of rabbit beta-globin mRNA as determined from cloned DNA.
    Cell. 1977 Apr;10(4):571-85 PMID: 558827
  5. Rat insulin genes: construction of plasmids containing the coding sequences.
    Science. 1977 Jun 17;196(4296):1313-9 PMID: 325648
  6. Human beta-globin messenger RNA. III. Nucleotide sequences derived from complementary DNA.
    J Biol Chem. 1977 Jul 25;252(14):5040-53 PMID: 68958
  7. The nucleotide sequence of a viral DNA.
    Sci Am. 1977 Dec;237(6):54-67 PMID: 929160
  8. Nucleotide sequence and amplification in bacteria of structural gene for rat growth hormone.
    Nature. 1977 Dec 8;270(5637):486-94 PMID: 339105
  9. Construction and analysis of recombinant DNA for human chorionic somatomammotropin.
    Nature. 1977 Dec 8;270(5637):494-9 PMID: 593368
  10. Nucleotide sequence of cro, cII and part of the O gene in phage lambda DNA.
    Nature. 1978 Mar 30;272(5652):410-4 PMID: 264238
  11. Nucleotide sequence at the 5' extremity of tobacco-mosaic-virus RNA. 2. The coding region (nucleotides 69-236).
    Eur J Biochem. 1978 Mar 15;84(2):521-31 PMID: 639801
  12. Complete nucleotide sequence of SV40 DNA.
    Nature. 1978 May 11;273(5658):113-20 PMID: 205802
  13. The genome of simian virus 40.
    Science. 1978 May 5;200(4341):494-502 PMID: 205947
  14. Sequence of a mouse germ-line gene for a variable region of an immunoglobulin light chain.
    Proc Natl Acad Sci U S A. 1978 Mar;75(3):1485-9 PMID: 418414
  15. Sequence of chicken ovalbumin mRNA.
    Nature. 1978 Jun 29;273(5665):723-8 PMID: 661981
  16. Genes and spacers of cloned sea urchin histone DNA analyzed by sequencing.
    Cell. 1978 Jul;14(3):655-71 PMID: 688387
  17. Gene K, a new overlapping gene in bacteriophage G4.
    Nature. 1978 Apr 6;272(5653):510-5 PMID: 692656
  18. Nucleotide sequence of the ampicillin resistance gene of Escherichia coli plasmid pBR322.
    Proc Natl Acad Sci U S A. 1978 Aug;75(8):3737-41 PMID: 358200
  19. Antibody diversity.
    Science. 1978 Oct 6;202(4363):11-7 PMID: 99815
  20. Nucleotide sequence of turnip yellow mosaic virus coat protein mRNA.
    Cell. 1978 Sep;15(1):113-22 PMID: 699035
  21. The primary sequence of rabbit alpha-globin mRNA.
    Cell. 1978 Sep;15(1):43-54 PMID: 699050
  22. Nucleotide sequence of the O gene and of the origin of replication in bacteriophage lambda DNA.
    Nucleic Acids Res. 1978 Sep;5(9):3141-56 PMID: 704348
  23. Determination of the first half of the coat protein cistron of bacteriophage Qbeta as an application of a mapping procedure for RNA fragments.
    J Biol Chem. 1978 Dec 10;253(23):8390-9 PMID: 361741
  24. Nucleotide sequence of bacteriophage G4 DNA.
    Nature. 1978 Nov 16;276(5685):236-47 PMID: 714153
  25. DNA sequence of the bacteriophage gama cI gene.
    Nature. 1978 Nov 16;276(5685):301-2 PMID: 714163
  26. Nucleotide sequence of gene VII and of a hypothetical gene (IX) in bacteriophage M13.
    Nucleic Acids Res. 1978 Dec;5(12):4677-98 PMID: 370777
  27. Nucleotide sequence of the BK virus DNA segment encoding small t antigen.
    Proc Natl Acad Sci U S A. 1979 Feb;76(2):565-9 PMID: 218208
  28. Nucleotide sequence of the cro-cII-oop region of bacteriophage 434 DNA.
    Nucleic Acids Res. 1979 Mar;6(3):867-81 PMID: 375198
  29. Construction and analysis of recombinant DNAs containing a structural gene for rat prolactin.
    Nucleic Acids Res. 1979 Mar;6(3):915-30 PMID: 375200
  30. Nucleotide sequence of cloned cDNA for bovine corticotropin-beta-lipotropin precursor.
    Nature. 1979 Mar 29;278(5703):423-7 PMID: 221818
  31. Sequence of 1000 nucleotides at the 3' end of tobacco mosaic virus RNA.
    Nucleic Acids Res. 1979 Apr;6(4):1287-308 PMID: 109810
  32. Nucleotide sequence of the mitochondrial structural gene for subunit 9 of yeast ATPase complex.
    Proc Natl Acad Sci U S A. 1979 Apr;76(4):1663-7 PMID: 156363
  33. Nucleotide sequence of the ribosomal protein gene cluster adjacent to the gene for RNA polymerase subunit beta in Escherichia coli.
    Proc Natl Acad Sci U S A. 1979 Apr;76(4):1697-701 PMID: 377281
  34. Corticotropin and beta-endorphin: construction and analysis of recombinant DNA complementary to mRNA for the common precursor.
    Proc Natl Acad Sci U S A. 1979 May;76(5):2153-7 PMID: 221916
  35. Human growth hormone: complementary DNA cloning and expression in bacteria.
    Science. 1979 Aug 10;205(4406):602-7 PMID: 377496
  36. Sequence of the gene for iso-1-cytochrome c in Saccharomyces cerevisiae.
    Cell. 1979 Apr;16(4):753-61 PMID: 222467
  37. Viral, prokaryote and eukaryote genes contrasted by mRNA sequence indexes.
    FEBS Lett. 1978 Nov 1;95(1):1-11 PMID: 214340
  38. The DNA sequence of sea urchin (S. purpuratus) H2A, H2B and H3 histone coding and spacer regions.
    Cell. 1978 Nov;15(3):1033-44 PMID: 728984
  39. Complete sequence of constant and 3' noncoding regions of an immunoglobulin mRNA using the dideoxynucleotide method of RNA sequencing.
    Cell. 1978 Nov;15(3):1067-75 PMID: 103625
  40. The sequence of the chromosomal mouse beta-globin major gene: homologies in capping, splicing and poly(A) sites.
    Cell. 1978 Dec;15(4):1125-32 PMID: 569555
  41. Sequences of mouse immunoglobulin light chain genes before and after somatic changes.
    Cell. 1978 Dec;15(4):1133-44 PMID: 103630
  42. Nucleotide sequence of bacteriophage fd DNA.
    Nucleic Acids Res. 1978 Dec;5(12):4495-503 PMID: 745987
  43. A kappa-immunoglobulin gene is formed by site-specific recombination without further somatic mutation.
    Nature. 1979 Aug 2;280(5721):370-5 PMID: 111146
  44. Nucleotide sequence of the genes III, VI and I of bacteriophage M13.
    Nucleic Acids Res. 1979 Jun 25;6(8):2799-818 PMID: 379830
  45. Nucleotide sequence of the gene coding for the major protein of hepatitis B virus surface antigen.
    Nature. 1979 Aug 30;280(5725):815-9 PMID: 471053
  46. Isolation, cloning and sequence analysis of the cDNA for the alpha-subunit of human chorionic gonadotropin.
    Nature. 1979 Oct 4;281(5730):351-6 PMID: 481597
  47. Sequence analysis of cloned cDNA encoding part of an immunoglobulin heavy chain.
    Nucleic Acids Res. 1979 Jul 25;6(10):3305-21 PMID: 113776
  48. The primary structure of a glyceraldehyde-3-phosphate dehydrogenase gene from Saccharomyces cerevisiae.
    J Biol Chem. 1979 Oct 10;254(19):9839-45 PMID: 385592
  49. Molecular cloning and nucleotide sequence of the human growth hormone structural gene.
    Nucleic Acids Res. 1979 Sep 25;7(2):305-20 PMID: 386281
  50. Localization on the viral genome and nucleotide sequence of the gene coding for the two major polypeptides of the hepatitis B surface antigen (HBs Ag).
    Nucleic Acids Res. 1979 Sep 25;7(2):335-46 PMID: 493148
  51. Cloning and complete nucleotide sequence of mouse immunoglobulin gamma 1 chain gene.
    Cell. 1979 Oct;18(2):559-68 PMID: 115593
  52. The DNA sequence of Bombyx mori fibroin gene including the 5' flanking, mRNA coding, entire intervening and fibroin protein coding regions.
    Cell. 1979 Oct;18(2):591-600 PMID: 498286
  53. Complete nucleotide sequence of an influenza virus haemagglutinin gene from cloned DNA.
    Nature. 1979 Nov 29;282(5738):471-7 PMID: 503226
  54. Cloning and nucleotide sequence of DNA coding for bovine preproparathyroid hormone.
    Proc Natl Acad Sci U S A. 1979 Oct;76(10):4981-5 PMID: 388425
  55. Nucleotide sequences of trpA of Salmonella typhimurium and Escherichia coli: an evolutionary comparison.
    Proc Natl Acad Sci U S A. 1979 Oct;76(10):5244-8 PMID: 388433
  56. Nucleotide sequence analysis of the chloramphenicol resistance transposon Tn9.
    Nature. 1979 Dec 20-27;282(5741):864-9 PMID: 390403
  57. Isolation of the structural gene for alcohol dehydrogenase by genetic complementation in yeast.
    Nature. 1980 Jan 10;283(5743):214-6 PMID: 6985717
  58. Molecular cloning and sequence analysis of adult chicken betal globin cDNA.
    Nucleic Acids Res. 1979 Nov 10;7(5):1137-46 PMID: 514809
  59. Nucleotide sequence of a secondary attachment site for bacteriophage lambda on the Escherichia coli chromosome.
    Nucleic Acids Res. 1979 Nov 10;7(5):1335-41 PMID: 160033
  60. The evolution and sequence comparison of two recently diverged mouse chromosomal beta--globin genes.
    Cell. 1979 Nov;18(3):865-73 PMID: 519759
  61. The complete sequence of a chromosomal mouse alpha--globin gene reveals elements conserved throughout vertebrate evolution.
    Cell. 1979 Nov;18(3):875-82 PMID: 519760
  62. DNA sequence of the gene for the outer membrane lipoprotein of E. coli: an extremely AT-rich promoter.
    Cell. 1979 Dec;18(4):1109-17 PMID: 391404
  63. DNA sequence analysis of the transposon Tn3: three genes and three sites involved in transposition of Tn3.
    Cell. 1979 Dec;18(4):1153-63 PMID: 391406
  64. The nucleotide sequence preceding and including the beginning of the ilvE gene of the ilvGEDA operon of Escherichia coli K12.
    Nucleic Acids Res. 1979 Dec 20;7(8):2289-301 PMID: 392469
  65. The preferential codon usages in variable and constant regions of immunoglobulin genes are quite distinct from each other.
    Nucleic Acids Res. 1979 Dec 20;7(8):2431-8 PMID: 523321
  66. Unusual nucleotide sequences at the 5' end of actin genes in Dictyostelium discoideum.
    Proc Natl Acad Sci U S A. 1979 Dec;76(12):6206-10 PMID: 293714
  67. Five TGA "stop" codons occur within the translated sequence of the yeast mitochondrial gene for cytochrome c oxidase subunit II.
    Proc Natl Acad Sci U S A. 1979 Dec;76(12):6534-8 PMID: 230513
  68. The DNA sequence of an IS/-flanked transposon coding for resistance to chloramphenicol and fusidic acid.
    FEBS Lett. 1980 Jan 28;110(1):11-4 PMID: 7353655
  69. Sequence of the lactose permease gene.
    Nature. 1980 Feb 7;283(5747):541-5 PMID: 6444453
  70. Codon catalog usage and the genome hypothesis.
    Nucleic Acids Res. 1980 Jan 11;8(1):r49-r62 PMID: 6986610
  71. Genetic distances from mRNA sequences.
    Naturwissenschaften. 1980 Feb;67(2):93-4 PMID: 6990278
  72. Structure of two spliced mRNAs from the transforming region of human subgroup C adenoviruses.
    Nature. 1979 Oct 25;281(5733):694-6 PMID: 551290
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/8.9.1893
Published
1980-05-10
Pages
1893-912
Language
English
Region
England
NLM ID
0411011
PMCID
PMC324046
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/8.9.1893 PMC Full Text View journal details
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