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Table 4 The taxonomic distribution of nonsense codons in the GAU sequence among mitochondrial genomes

From: Probable presence of an ubiquitous cryptic mitochondrial gene on the antisense strand of the cytochrome oxidase I gene

  

a) 100 aminoacids upstream GSPP sequence

 

b) 100 aminoacids downstream GSPPP (GAU sequence)

 

c) 100 aminoacids downstream GAU sequence

 
  

Number of sequences with STOP codons

NoSC*

 

Number of sequences with STOP codons

NoSC*

 

Number of sequences with STOP codons

NoSC*

 
  

Position of last STOP codon starting from 5'

  

Position of 1rst STOP codon starting from 5'

  

Position of 1rst STOP codon starting from 5'

  
 

Phylum

10

20

30

40

50

60

70

80

90

100

  

10

20

30

40

50

60

70

80

90

100

  

10

20

30

40

50

60

70

80

90

100

  

Metazoa/Protostomia

Arthropoda

  

1

  

18

4

 

57

22

1

 

4

    

3

  

4

5

87

 

2

   

1

  

86

2

1

11

 
 

Annelida

      

1

 

2

2

            

5

         

1

 

4

 
 

Brachiopoda

     

1

  

2

             

3

        

1

  

2

 
 

Bryozoa

     

1

                

1

        

1

    
 

Chaetognatha

     

1

  

1

             

2

        

1

  

1

 
 

Entoprocta

      

1

 

1

        

1

    

1

        

2

    
 

Echiura

     

1

                

1

        

1

    
 

Mollusca

  

3

  

9

8

 

13

4

  

1

 

1

 

3

 

2

 

3

 

27

 

1

2

3

    

12

1

 

18

 
 

Priapulida

     

1

                

1

           

1

 
 

Onychophora

        

2

        

1

    

1

           

2

 

Metazoa/Deuterostomia

Chordata

      

11

 

76

798

  

1

751

92

36

3

 

1

  

1

  

4

824

20

 

12

 

1

16

  

8

 
 

Echinodermata

      

6

 

9

1

            

16

        

8

  

8

 
 

Hemichordata

      

1

 

1

             

2

        

2

    
 

Xenoturbellida

      

1

               

1

        

1

    

Metazoa/Pseudocoelomata

Nematoda

     

3

  

4

 

1

 

6

    

1

    

1

    

4

   

4

    

Metazoa/Acoelomata

Platyhelminthes

     

11

1

 

14

   

1

   

18

  

1

2

3

1

 

7

   

12

 

1

6

    

Metazoa/Cnidaria

Cnidaria

     

2

  

26

            

6

22

        

27

  

1

 

Metazoa (other)

Placozoa

     

1

2

               

3

           

3

 
 

Porifera

     

2

1

 

17

 

1

     

1

     

20

     

1

  

1

  

19

 

Fungi/Dikarya

Ascomycota

     

3

1

 

14

2

1

 

4

    

1

    

16

 

1

 

1

2

10

     

7

 

Fungi/Dikarya

Basidiomycota

  

1

  

1

   

2

  

4

         

1

     

5

       

Fungi

Blastocladiomycota

        

1

1

  

1

               

1

       

Fungi

Chytridiomycota

        

3

3

  

4

    

1

   

1

         

6

    

Viridiplantae

Chlorophyta

        

3

3

  

1

        

3

2

    

1

   

5

    
 

Streptophyta

        

15

4

         

17

 

2

        

18

1

    

Protists/stramenopiles

Bacillariophyta

        

1

             

1

           

1

 
 

Phaeophyceae

        

2

3

         

5

          

2

3

    

Eukaryota (other)

Eukaryota (other)

     

2

1

 

7

12

  

8

    

1

   

5

8

     

2

1

4

11

  

4

 
 

Total without STOP codons

           

4

           

223

           

90

 

Total with STOP codons

           

1229

           

1010

           

1143

  1. The table is divided into three main sections: a) 100 codons upstream of the GSPPP motif in the GAU sequence; b) 100 codons downstream, starting in the GSPPP motif; and c) 100 codons starting at codon 101 from the GSPPP motif. In each section (a, b and c), the 100 codons are divided into 10 groups of 10 codons each, and the table cells indicate the number of stop codons found in each division. For section (a), the cells indicate the position of the last stop codon starting from the 5' end and for sections (b) and (c) the position of the first stop codon starting from the 5' end. The cells in gray highlight sequences with a substantial portion without nonsense codons. NoSC* indicates the number of sequences without nonsense codons.