Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
30 hits were found for CCUCUUGUCCUCCAAUUUG (18 guide strand hits and 12 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_015886 | PI15 | 868 | 886 | C | a | U | C | U | U | G | U | C | C | U | C | C | A | A | g | U | U | a | 57 | 3 | 13 | c | false | <90% | 6732 | ||
NM_017868 | TTC12 | 1146 | 1164 | C | C | U | C | U | U | G | U | C | C | U | C | C | A | A | g | g | U | c | 45 | 3 | 15 | c | false | <90% | 2330 | ||
XR_015839 | LOC729142 | 598 | 616 | a | g | c | C | U | U | G | U | C | C | U | C | C | A | c | U | U | U | G | 42 | 4 | 11 | c | false | <90% | 2012 | ||
XR_015795 | LOC731134 | 598 | 616 | a | g | c | C | U | U | G | U | C | C | U | C | C | A | c | U | U | U | G | 42 | 4 | 11 | c | false | <90% | 2012 | ||
NM_003247 | THBS2 | 4402 | 4420 | C | C | U | C | U | U | G | U | C | C | U | a | C | A | A | U | g | a | a | 35 | 4 | 11 | false | <90% | 5826 | |||
XR_015856 | LOC728797 | 1460 | 1478 | C | C | U | C | U | U | G | g | C | C | U | C | u | A | A | U | U | U | G | 27 | 2 | 7 | false | <90% | 1956 | |||
NM_001004321 | FLJ45445 | 2069 | 2087 | C | C | U | C | U | U | G | g | C | C | U | C | u | A | A | U | U | U | G | 27 | 2 | 7 | false | <90% | 2181 | |||
XR_015126 | LOC727755 | 1277 | 1295 | C | C | U | C | U | U | G | g | C | C | U | C | u | A | A | U | U | U | G | 27 | 2 | 7 | false | <90% | 2191 | |||
XR_015434 | LOC729033 | 925 | 943 | C | C | U | C | U | U | G | g | C | C | U | C | u | A | A | U | U | U | G | 27 | 2 | 7 | false | <90% | 2236 | |||
XR_015615 | LOC729660 | 1555 | 1573 | C | C | U | C | U | U | G | g | C | C | U | C | u | A | A | U | U | U | G | 27 | 2 | 7 | false | <90% | 2884 | |||
XR_017612 | LOC653340 | 1798 | 1816 | C | C | U | C | U | U | G | g | C | C | U | C | u | A | A | U | U | U | G | 27 | 2 | 7 | false | <90% | 3331 | |||
XR_015328 | LOC728105 | 1793 | 1811 | C | C | U | C | U | U | G | g | C | C | U | C | u | A | A | U | U | U | G | 27 | 2 | 7 | false | <90% | 3332 | |||
XR_015431 | LOC731275 | 4891 | 4909 | C | C | U | C | U | U | G | g | C | C | U | C | u | A | A | U | U | U | G | 27 | 2 | 7 | false | <90% | 6202 | |||
XR_015834 | LOC729021 | 5634 | 5652 | C | C | U | C | U | U | G | g | C | C | U | C | u | A | A | U | U | U | G | 27 | 2 | 7 | false | <90% | 6544 | |||
NM_001013685 | LOC401357 | 3260 | 3278 | C | C | U | C | U | U | G | g | C | C | U | C | u | A | A | U | U | U | u | 22 | 3 | 7 | false | <90% | 3354 | |||
NM_020384 | CLDN2 | 333 | 351 | u | C | U | C | U | U | G | g | C | C | U | C | C | A | A | c | U | U | G | 9 | 3 | 7 | c | false | <90% | 2959 | ||
NM_004458 | ACSL4 | 2697 | 2715 | C | C | U | C | U | U | G | U | C | u | U | C | C | u | A | U | U | U | c | -7 | 3 | 9 | c | false | <90% | 5043 | ||
NM_022977 | ACSL4 | 3009 | 3027 | C | C | U | C | U | U | G | U | C | u | U | C | C | u | A | U | U | U | c | -7 | 3 | 9 | c | false | <90% | 5356 |
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_017933 | PID1 | 2361 | 2379 | C | A | c | A | U | U | G | G | A | G | G | A | C | A | A | G | A | G | c | 75 | 2 | 15 | bc | false | <90% | 2745 | ||
NR_002305 | PDIA3P | 901 | 919 | C | A | A | g | U | U | G | G | A | G | G | A | C | A | A | G | A | c | u | 55 | 3 | 13 | c | false | <90% | 2099 | ||
NM_002845 | PTPRM | 1263 | 1281 | C | A | A | g | U | U | G | G | A | G | G | A | C | A | A | G | A | a | c | 55 | 3 | 13 | c | false | <90% | 5065 | ||
NM_001270 | CHD1 | 1564 | 1582 | u | A | u | A | U | U | G | G | A | G | G | A | C | A | u | G | A | G | G | 53 | 3 | 11 | c | false | <90% | 6457 | ||
NM_138780 | SYTL5 | 97 | 115 | a | A | A | A | g | U | G | G | A | G | G | A | C | A | A | G | A | G | a | 41 | 3 | 13 | bc | false | <90% | 2193 | ||
NM_000380 | XPA | 1171 | 1189 | C | A | A | A | U | U | u | G | A | G | G | A | C | A | A | G | A | u | a | 26 | 3 | 10 | c | false | <90% | 1439 | ||
NM_003273 | TM7SF2 | 413 | 431 | g | g | A | A | U | U | G | a | A | G | G | A | C | A | A | G | A | G | u | 19 | 4 | 10 | bc | false | <90% | 1599 | ||
NM_001010870 | TDRD6 | 1674 | 1692 | C | A | A | A | U | U | G | G | A | u | G | A | C | A | A | G | A | G | u | 12 | 2 | 9 | bc | false | <90% | 6817 | ||
XM_001125737 | LOC730275 | 79 | 97 | a | A | A | A | U | U | a | G | A | G | G | c | C | A | A | G | A | G | G | -2 | 3 | 7 | false | <90% | 3983 | |||
NM_153252 | BRWD3 | 5253 | 5271 | g | A | A | A | U | U | G | G | A | a | G | A | C | c | A | G | A | G | G | -4 | 3 | 8 | c | false | <90% | 6085 | ||
XM_001129327 | PKP3 | 1661 | 1679 | C | A | A | A | U | g | c | G | A | G | G | A | C | A | A | G | A | G | c | -34 | 3 | 11 | bc | false | <90% | 2798 | ||
NM_007183 | PKP3 | 1627 | 1645 | C | A | A | A | U | g | c | G | A | G | G | A | C | A | A | G | A | G | c | -34 | 3 | 11 | bc | false | <90% | 2845 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2738
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