Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
18 hits were found for CCAGAUGAUGGUCAAAGCU (5 guide strand hits and 13 sense strand hits.)
Hits to Guide strand
| Accession | Gene | Start | End | Details of mismatches | Spec. Score | Mismatches | Contiguous | Jackson style specificity | Hits similar gene | HSP Score | HSP % Identity | HSP length | Gene Length | ||||||||||||||||||
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | |||||||||||||
| NM_152613 | WBP2NL | 409 | 427 | C | C | A | G | u | U | G | A | U | G | G | U | g | A | A | A | G | C | U | 38 | 2 | 7 | false | <90% | 2267 | |||
| NM_178171 | GSDM1 | 742 | 760 | a | C | A | G | c | U | G | A | U | G | G | U | C | A | A | A | G | g | c | 38 | 4 | 12 | c | false | <90% | 2166 | ||
| NM_007124 | UTRN | 7631 | 7649 | g | C | A | G | A | a | G | A | U | G | G | U | a | A | A | A | G | C | U | 24 | 3 | 6 | false | <90% | 12436 | |||
| NM_001173 | ARHGAP5 | 3649 | 3667 | C | C | A | G | A | U | G | A | U | a | G | U | C | A | A | A | a | u | c | -13 | 4 | 9 | c | false | <90% | 9601 | ||
| NM_001030055 | ARHGAP5 | 3649 | 3667 | C | C | A | G | A | U | G | A | U | a | G | U | C | A | A | A | a | u | c | -13 | 4 | 9 | c | false | <90% | 9604 | ||
Hits to Sense strand
| Accession | Gene | Start | End | Details of mismatches | Spec. Score | Mismatches | Contiguous | Jackson style specificity | Hits similar gene | HSP Score | HSP % Identity | HSP length | Gene Length | ||||||||||||||||||
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | |||||||||||||
| NM_001078176 | SLC29A1 | 785 | 803 | c | a | u | U | U | U | G | A | C | C | A | U | C | A | U | C | U | G | u | 62 | 4 | 15 | bc | false | <90% | 2146 | ||
| NM_001078175 | SLC29A1 | 892 | 910 | c | a | u | U | U | U | G | A | C | C | A | U | C | A | U | C | U | G | u | 62 | 4 | 15 | bc | false | <90% | 2253 | ||
| NM_004955 | SLC29A1 | 980 | 998 | c | a | u | U | U | U | G | A | C | C | A | U | C | A | U | C | U | G | u | 62 | 4 | 15 | bc | false | <90% | 2341 | ||
| NM_001078174 | SLC29A1 | 983 | 1001 | c | a | u | U | U | U | G | A | C | C | A | U | C | A | U | C | U | G | u | 62 | 4 | 15 | bc | false | <90% | 2344 | ||
| NM_001078177 | SLC29A1 | 1142 | 1160 | c | a | u | U | U | U | G | A | C | C | A | U | C | A | U | C | U | G | u | 62 | 4 | 15 | bc | false | <90% | 2503 | ||
| NM_001004469 | OR10J5 | 148 | 166 | u | G | C | a | U | U | G | A | C | C | A | U | C | A | U | C | U | c | c | 53 | 4 | 13 | c | false | <90% | 930 | ||
| NM_024837 | ATP8B4 | 1486 | 1504 | u | u | C | U | U | U | G | A | C | C | A | c | C | A | U | C | U | G | a | 47 | 4 | 9 | false | <90% | 5679 | |||
| NM_174893 | C17orf49 | 770 | 788 | c | c | C | U | U | U | G | A | C | C | u | U | C | A | U | C | U | G | a | 20 | 4 | 8 | c | false | <90% | 841 | ||
| NM_003439 | ZKSCAN1 | 719 | 737 | A | G | C | U | U | U | G | A | C | C | u | U | C | A | U | C | a | c | G | 12 | 3 | 10 | c | false | <90% | 5494 | ||
| NM_207521 | RTN4 | 1340 | 1358 | A | G | C | U | U | U | G | c | C | C | A | U | C | A | U | u | U | G | a | 6 | 3 | 7 | c | false | <90% | 4129 | ||
| NM_020532 | RTN4 | 2082 | 2100 | A | G | C | U | U | U | G | c | C | C | A | U | C | A | U | u | U | G | a | 6 | 3 | 7 | c | false | <90% | 4871 | ||
| NM_001001870 | MGC14376 | 222 | 240 | u | G | C | U | U | U | c | c | C | C | A | U | C | A | U | C | U | G | G | -30 | 3 | 11 | bc | false | <90% | 1303 | ||
| NM_032895 | MGC14376 | 304 | 322 | u | G | C | U | U | U | c | c | C | C | A | U | C | A | U | C | U | G | G | -30 | 3 | 11 | bc | false | <90% | 1385 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2473
View matched accessions
3 prime seed match details
Immunostimulatory motif search results
UGUGU - Judge et al. Sequence-dependent stimulation of the mammalian innate immune response by synthetic siRNA. Nat Biotechnol. 2005 Apr;23(4):457-62. (PMID: 15778705)
No Immunostimulatory motif found (UGUGU).
GUCCUUCAA - Hornung et al. Sequence-specific potent induction of IFN-alpha by short interfering RNA in plasmacytoid dendritic cells through TLR7. Nat Med. 2005 Mar;11(3):263-70. Epub 2005 Feb 20. (PMID: 15723075)
No Immunostimulatory motif found (GUCCUUCAA).
Settings used for search
Scores were calculated using scoring scheme SS1
Using AVG scoring mode.
Hit scores
| Parameter | Spec. Score cut-off | Colour | Comment |
| Hit to same gene | Colour | Hits to the same accession or genes with 100 percent identity (i.e. likely transcript variants). It is advisable to always check the genes hit. | |
| High scoring hit | ≥80 | Colour | Hits are very likely to cause an off-target effect |
| Medium scoring hit | <80¸≥40 | Colour | Hits with a small chance of causing an off target effect. |
| Low scoring hit | Colour | Hits very unlikely to cause an off-target effect |
The mismatches are colour coded based on the weighting of that position.
| Cut-off | Colour |
| Match | Colour |
| Wobble base pairs (G-U) | Colour |
| Critical bases (none) | Colour |
| 0.6 bits | Colour |
| 0.4 bits | Colour |
| 0.2 bits | Colour |
SpecificityServer is designed to help you identify potential non-specific matches to your siRNA. It incorporates the latest information about non-specific matches (sequence-specific only).
Designed by: Alistair Chalk, Quan Du, Zicai Liang and Erik L.L. Sonnhammer