Table 3.
iTriplet prediction using real biological sequences.
| Gene: | Preproinsulin (IEB1) promoter+5' UTR | Remarks | |
|---|---|---|---|
| iTriplet | GTYYGGAAAYTGCAGCYTCAGCCCC | <25,2> model | |
| PMSprune | CAGCCTCAGCCCCTT | Ref. [17] | |
| MITRA | CCTCAGCCCCC | Ref. [14] | |
| Published | CTCAGCCCCCAGCCATCTGCCGACCCCCCC | Transfac ID: R04457 | |
| Gene: | DHFR (promoter+5' UTR) | Remarks | |
| iTriplet | RWSTSGCGCSAAACY | <15,3> model | |
| PMSprune | ATTTCGTGGGCA | Ref. [17] | |
| MITRA | TGCAATTTCGCGCCAAAC | Ref. [14] | |
| Published | ATTTCGCGCCAAA | Transfac ID: R01928 | |
| Gene: | Metallothionein promoter+5' UTR | Remarks | |
| iTriplet | TTTTGCRCTCGYCCC | <15,1> model | |
| PMSprune | CTCTGCACACGGCCC | Ref. [17] | |
| MITRA | TGCGCCCGG | Ref. [14] | |
| Published | TGCGCCCGG | Transfac ID: R08298 | |
| Gene: | c-fos serum response element promoter+5' UTR | Remarks | |
| iTriplet | CCATATTAGGACATCTGCGT | <20,1> model | |
| PMSprune | CCAAATTTG | Ref. [17] | |
| MITRA | CCATATTAGGACA | Ref. [14] | |
| Published | CAGGATGTCCATATTAGGACATC | Transfac ID: R00466 | |
| 3'UTR Regulatory Elements | iTriplet Prediction only | Published | Remarks |
| AU-rich (ARE) | TTTTATTTATTTTT | WWTTATTTATTWW | <14,3> model |
| Cytoplasmic Polyadenylation element (CPE) | TTTTAAT | TTTTAT and TTTTAAT | <6,1> model |
| Pumillio binding element (PBE) | TKTWAATA | TGTAAATA | <8,1> model |
Motif predicted by iTriplet is presented in consensus sequence. Bold and underlined sequence represents correctly predicted nucleotide. Transfac IDs are obtained from TRANSFAC database [37]