Automatic recommendation
Not OK - siRNA is not specific
19 hits were found for CCAGCUUGAGAGCAAAGUU (10 guide strand hits and 9 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_018003 | UACA | 3658 | 3676 | C | C | A | G | C | U | U | G | A | G | A | G | a | A | A | A | G | g | a | 81 | 3 | 12 | false | <90% | 6873 | |||
| NM_001008224 | UACA | 3881 | 3899 | C | C | A | G | C | U | U | G | A | G | A | G | a | A | A | A | G | g | a | 81 | 3 | 12 | false | <90% | 7096 | |||
| NM_020242 | KIF15 | 2638 | 2656 | g | C | u | G | C | U | U | G | A | G | A | G | C | A | A | A | G | c | c | 70 | 4 | 14 | c | false | <90% | 4775 | ||
| NM_015635 | GAPVD1 | 3955 | 3973 | a | C | u | G | C | U | U | G | A | G | A | G | C | A | A | A | G | a | a | 70 | 4 | 14 | c | false | <90% | 6906 | ||
| NM_172069 | PLEKHH2 | 204 | 222 | a | C | A | G | C | U | U | G | A | G | A | G | a | c | A | A | G | U | U | 68 | 3 | 11 | false | <90% | 7027 | |||
| NM_017707 | DDEFL1 | 861 | 879 | g | C | A | G | C | U | U | G | A | G | A | G | C | A | g | A | G | a | g | 65 | 4 | 13 | c | false | <90% | 4050 | ||
| XM_937552 | LOC648502 | 1133 | 1151 | C | C | A | G | C | c | U | G | A | G | A | G | C | A | A | A | G | c | c | 29 | 3 | 11 | c | false | <90% | 10907 | ||
| XM_062871 | LOC643677 | 1133 | 1151 | C | C | A | G | C | c | U | G | A | G | A | G | C | A | A | A | G | c | c | 29 | 3 | 11 | c | false | <90% | 11201 | ||
| NM_003214 | TEAD3 | 2336 | 2354 | C | C | A | G | a | U | U | G | A | G | A | G | C | A | A | g | G | U | a | 17 | 3 | 10 | c | false | <90% | 2947 | ||
| NM_001008536 | TCHHL1 | 777 | 795 | C | C | A | G | C | c | a | G | A | G | A | G | C | A | A | A | G | U | g | -34 | 3 | 11 | bc | false | <90% | 3603 | ||
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_003324 | TULP3 | 1115 | 1133 | c | A | g | U | U | U | G | C | U | C | U | C | A | A | G | g | U | G | G | 52 | 3 | 12 | c | false | <90% | 2945 | ||
| NM_153690 | FAM43A | 2649 | 2667 | A | A | a | U | U | U | G | C | U | C | U | C | A | A | G | g | U | G | u | 49 | 3 | 12 | c | false | <90% | 3182 | ||
| NM_001010982 | AFMID | 631 | 649 | A | A | C | g | U | U | G | C | U | C | U | C | c | A | G | C | U | G | a | 47 | 3 | 8 | false | <90% | 1819 | |||
| NM_004979 | KCND1 | 4593 | 4611 | A | A | C | U | c | U | G | C | U | C | U | C | A | g | G | C | U | G | a | 24 | 3 | 8 | c | false | <90% | 4720 | ||
| NM_000088 | COL1A1 | 598 | 616 | A | A | C | U | U | U | G | C | U | C | c | C | c | A | G | C | U | G | u | 23 | 3 | 10 | false | <90% | 5927 | |||
| NM_173802 | MGC50559 | 1509 | 1527 | c | A | C | U | U | U | G | C | U | C | c | C | A | g | G | C | U | G | G | 17 | 3 | 9 | c | false | <90% | 2078 | ||
| NM_001042430 | C14orf140 | 1173 | 1191 | c | A | C | U | U | U | G | C | U | C | c | C | A | A | G | g | U | G | G | 10 | 3 | 9 | c | false | <90% | 1578 | ||
| NM_024643 | C14orf140 | 1688 | 1706 | c | A | C | U | U | U | G | C | U | C | c | C | A | A | G | g | U | G | G | 10 | 3 | 9 | c | false | <90% | 2093 | ||
| XR_018754 | LOC648949 | 156 | 174 | g | A | C | U | U | g | G | C | U | C | U | g | A | A | G | C | U | G | G | 0 | 3 | 7 | false | <90% | 3015 | |||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2921
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