Table 1 Candidates with desired binding sites adjacent to alternative polyadenylation sites. Identification of cDNAs with potential alternative 3' ends and various patterns – base composition, degenerate, and combinatorial patterns – located between 100 nucleotides upstream of the 3' end of the first EST set through the 3' end of the second EST set. # and ** cDNAs were used as examples for the alignment shown in Figure 4.
From: Fast-Find: A novel computational approach to analyzing combinatorial motifs
| Number of cDNAs with potential alternative 3' ends and search patterns | ||
|---|---|---|
| Search pattern | Number of Patterns | Number of cDNAs |
| A. Base composition | ||
| CstF64; U> = 4, G< = 4, A+C = 0 ;length = 8 | 163 | 276 |
| SXL; U> = 15, G< = 2, A+C = 0 ;length = 17 | 154 | 5 |
| SXL1; U> = 8, G+A+C = 0 ;length = 8 | 1 | 27 |
| SXL2; U> = 10, G< = 2, A+C = 0 ;length = 12 | 79 | 25 |
| B. Degenerate motifs | ||
| hnRNP F/H/H' (core); GGGA | 1 | 232 |
| hnRNP F/H/H'; GGGGA | 1 | 78 |
| Rbp1; DCADCUUA | 9 | 47 |
| PSI; RCYYCUURYRC | 12 | 8 |
| Rbp9; UUUNUUUU | 4 | 111 |
| C. Combinatorial motifs | ||
| CstF64 + SXL | 25,102 | 5# |
| CstF64 + hnRNP F/H/H' (core) | 163 | 178* |
| CstF64 + hnRNP F/H/H' | 163 | 59** |
| SXL + hnRNP F/H/H' (core) | 154 | 4*** |
| PSI + hnRNP F/H/H' (core) | 12 | 8*** |