Skip to main content

Table 2 Most frequent tetranucleotide (4mer) motifs at polyadenylation [poly(A)] tail starting positions and most frequent hexanucleotide (6mer) motifs within 50 nucleotides upstream of poly(A) tail starting positions in each species

From: Motif types, motif locations and base composition patterns around the RNA polyadenylation site in microorganisms, plants and animals

Species/group

Mapped unique mRNA (No.)

Most frequent 4mer motif at the poly(A) sites1

%

Most frequent 6mer motif within 50 bases upstream2

%

Microorganisms

     

Fungi3

209

UUUA

7.2

AAUAAA

19.6

Protists 4

     

Blastocystis hominis

1 717

UUUG

5.01

AAGAAG

10.34

Chlamydomonas reinhardtii

176

UCCA

4.0

UGUAAC

31.3

Phytophthora infestans

63

CUCA

6.4

AAAAUA5

20.6

Trypanosoma cruzi

52

UUGA

19.2

UGUUUU

38.5

Dicotyledonous plants

     

Arabidopsis thaliana

4 431

UUUA

4.9

AAUAAA

13.4

Medicago truncatula

136

UUCA

9.6

UAUUUU

17.7

Populus trichocarpa

1 371

UUUA

5.6

UAUUUU

12.6

Solanum lycopersicum

450

UUUA

8.2

UAUUUU

12.9

Monocotyledonous plants

     

Oryza sativa

693

UUUA

7.4

AAUAAA

15.3

Sorghum bicolor

1 685

UUCA

5.5

AAUAAA

11.2

Zea mays

10 491

UUCA

4.6

AAUAAA

9.0

Animals

     

Apis mellifera

187

AAUA

9.6

AAUAAA

53.5

Bos taurus

2 679

UUUA

3.7

AAUAAA

63.6

Caenorhabditis elegans

389

UUUA

11.6

AAUAAA

50.6

Callithrix jacchus

79

CUUA

10.1

AAUAAA

55.7

Canis lupus familiaris

108

UUUA

8.3

AAUAAA

68.5

Ciona intestinalis

287

UUUA

6.3

AAUAAA

48.4

Danio rerio

7 246

UUUA

6.0

AAUAAA

61.7

Drosophila melanogaster

954

AACA

9.0

AAUAAA

59.0

Equus caballus

97

AUUA

7.2

AAUAAA

46.4

Gallus gallus

788

AACA

4.6

AAUAAA

58.8

Homo sapiens

30 499

UUUA

5.0

AAUAAA

58.2

Mus musculus

8 709

UUUA

5.4

AAUAAA

61.2

Oryctolagus cuniculus

224

AUUA

5.4

AAUAAA

59.8

Pongo abelii

1 965

CUCA

5.9

AAUAAA

58.5

Rattus norvegicus

14 263

UUUA

6.4

AAUAAA

56.0

Sus scrofa

8 114

GACA

8.1

AAUAAA

40.5

Taeniopygia guttata

808

UGCA

4.2

AAUAAA

59.9

Animal average

4 116

  

AAUAAA

53.9

  1. 1The last nucleotide in bold in the tetranucleotide is the poly(A) tail starting position of the poly(A) site.
  2. 2The AAUAAA motif could be found in 11.8% of unique poly(A) sites in monocotyledonous plants and in 11.9% of unique poly(A) sites in all plants (average of all four dicotyledonous plants and all three monocotyledonous plants together). The frequencies of these motifs are all significantly higher than the mean frequencies of hexanucleotide motifs in the region according to chi-test (P < 0.000001).
  3. 3Pooled from the 14 fungal species listed in Table 1.
  4. 4The protist Babesia bovis was found to also have A predominance at the poly(A) tail starting position: 18 of 23 mapped unique poly(A) sites were A (data not shown).
  5. 5AAUAAA was among the most frequent upstream motifs (11.11%). In EST-based mapping [207 unique poly(A) sites], AAUAAA was the most frequent but the frequency was only 16.91%, and AAAAUA became the second most frequent. The analysis results suggested a weak predominance of AAUAAA and some other A-rich motifs including AAAAUA.