Skip to main content

Advertisement

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.