Table 2 The motifs (tetra-, penta-nucleotides) extracted from different data sets (u > 1.64).

tetra- penta-

Motifs in upstream regions: ATGT TACC CCAA CCAT CCCA CCAG GTAC CACC ACCC TCCG CGGC CCGT TGGA GGAA AGGT GGGC TAGG CTAG GCCT CTCC GCGC [CCGG GGCC] TGTA ACCA TCCC CAGA AGAG GAGC ACTG CTGC TGAA GAAA AACC CGCT GGCT GAGG ACGC CGGG GGCA CAGG CCGC TCTC GGAC CGCC CGCG [GCTG] TATTG ATGTA ATACC CCATG ACATT TGTAC ACACC CACCC TGAAA AACCC ACCCA CCCAT CCAAG ATCCG GCCGT CCGTA CGTAC ACCGT CCGTC AAATG AGGTA CAAAC CGCTC CGGGC AAATT TATGG TCTAG CAGTG AGTGT CCTAG GTGGA GGATG ACGGA CTCCG TCCCA CCCAC CCTGG GGTGG CATAC CGGCA GCACG CGCGC [CCCCC CCGGC GGCAG CCTAT GGGAG GCCTA CCTAC AGGCC GGCCC GCCCT GCTAG TCCGC CCGCC CTCCA CGGCC GCTGG GGGCG] ACCAA CCCAG CCAGA CAGAC ACATC CCCAA AACTG AAACC CGGCT GAGGT CACGC CTCGG GCAGG GTTCC TTCCC CCCGC CCATC TCTCT GCCTC CTCTC CTCGC ACTGG CTGGA TCACC CACCA CCTCC CGTCC CGCCT CTGGC GGAAG GCGTC GTCCG GCGCA GCCGC ACGCG ACGGG TCGCG [AATCT CAAGA GACAG CAGAG AGAGC ACTGC TTGAA TCCGG GGCTC GGAAA GGCTG TCCCG CCGCT AGTAG TAGCT CTTTC TGCTG TCAGT AGCCT ACCAG CGGAA GCTGC GCCGA TGGGC CAGGC GGACT CTCAG CAGCG TCTGC CTGCG GGCGC GCTCC GCGCT]

tetra- penta-

Motifs in introns: TTAA TAAA AAAT AATT TTAT TATT TGGT TTCA GAAT ATTA AGAC ATAT TATC CATG CACG GGTC TAAAA AAATT TATTT ATTTG TAAAT ATTGA ATTTC TTTCA AGAAT AATTA TATCG ATTCA AATAT TATTC CAAGC ATATC GATAA TCACG CACGC CTATT ACCAC TGCTA ATTAT ATAGT TATTA ACGTG GATTG TGGTG [TTAAA GAATT]

The bolds are potential positive transcriptional regulatory elements of “set I upstream”, i.e. they are significantly over-represented in “set I upstream” relative to in “set II upstream”, and others are potential general transcriptional regulatory motifs. All of the motifs agree with “test sites”, except for those in bracket [ ]. The motifs in introns are all potential positive transcriptional regulatory elements, obtained by comparing “set I intron” to “set II intron”. The reverse complements are not listed.