3'-processing Analysis of S. cerevisiae mRNA Sequences

Tools
Sites in User Submitted Sequence
Sites in Known Genes
Check Results

Documentation
Output Format
Overview Plot
Top Sites
Full Site Detail

DSM/HMM Used
DSM Overview Plot
Empirical Positions
Nucleotide Frequency

List of Example Outputs

3'-end processing genes:
RNA14, RNA15, CLP1, YDH1(CFT2), YSH1, YHH1(CFT1), PCF11, PTA1, HRP1, PAP1
Genes with known sites internal to the CDS:
RNA14, CBP1, SIR1, AEP2
CYC1, and Mutagenesis Studies Thereof:
CYC1 (wt), CYC1-d512, CYC1d965, CYC1d966, CYC1d967, CYC1d968, CYC1d969, CYC1d970, CYC1d971, CYC1d972, CYC1d973, CYC1d974, CYC1d975, CYC1d976, CYC1d977, CYC1d978, CYC1d979, CYC1d980, CYC1d981, CYC1d982, CYC1d983, CYC1d984, CYC1d985, CYC1d1006, CYC1d1007, CYC1d1183, CYC1d1184, CYC1d1185, CYC1d1186, CYC1d1187, CYC1d1188, CYC1d1189, CYC1d1190, CYC1d1191, CYC1d1192, CYC1d1193, CYC1d1316, CYC1d1317, CYC1d1318, CYC1d1319, CYC1d1320, CYC1d1321, CYC1d1322, CYC1d1323, CYC1d1345, CYC1d1346, CYC1d1347, CYC1d1348, CYC1d1349, CYC1d1350, CYC1d1351, CYC1d1352, CYC1d1353, CYC1d1354, CYC1d1355, CYC1d1356, CYC1d1357, CYC1d1358, CYC1d1359, CYC1d1360, CYC1d1361, CYC1d1362, CYC1d1363, CYC1d1364, CYC1d1365, CYC1d1366, CYC1d1367, CYC1d1368, CYC1d1369, CYC1d1370
Other interesting genes:
SUA7 (known regulatory alternatives in the 3'-UTR),
BAP2 (predicted internal CDS site),
ACT1 (known regulatory alternatives in the 3'-UTR),
HIS3 (at least 13 reported alternative sites)
Example Output Caveats
- All example output gene sequences include 50 nt of 5'-sequence and 500 nt of 3'-sequence (and the first position is 0), so the CDS extends from position 50 to position L - 501, where L is the length of the sequence.
- These are of course predictions. There are a few verified genes where this method fails miserably- possible causes include a weak signal (or more accurately, one that diverges too greatly from the "average" pattern that we are using), or perhaps a different mechanism of 3'-end processing.