Automatic recommendation
Not OK - siRNA is not specific
33 hits were found for GCAGCUGCCAAAUGUCAAA (16 guide strand hits and 17 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_006225 | PLCD1 | 2038 | 2056 | G | C | A | G | C | U | G | C | C | A | A | A | a | G | U | C | A | A | c | 84 | 2 | 12 | false | <90% | 2707 | |||
NM_181882 | PRX | 2318 | 2336 | G | C | A | G | C | U | G | C | C | A | A | A | a | G | U | C | u | c | A | 63 | 3 | 12 | false | <90% | 4884 | |||
NM_020956 | PRX | 2967 | 2985 | G | C | A | G | C | U | G | C | C | A | A | A | a | G | U | C | u | c | A | 63 | 3 | 12 | false | <90% | 5533 | |||
NM_001077711 | KRTAP27-1 | 199 | 217 | c | C | A | G | C | U | G | C | C | A | A | A | U | G | a | C | c | A | A | 49 | 3 | 13 | c | false | <90% | 682 | ||
NM_058191 | C21orf66 | 1277 | 1295 | u | C | A | G | a | U | G | C | C | A | A | A | U | c | U | C | A | A | A | 27 | 3 | 8 | c | false | <90% | 2530 | ||
NM_013329 | C21orf66 | 1277 | 1295 | u | C | A | G | a | U | G | C | C | A | A | A | U | c | U | C | A | A | A | 27 | 3 | 8 | c | false | <90% | 2836 | ||
NM_016631 | C21orf66 | 1277 | 1295 | u | C | A | G | a | U | G | C | C | A | A | A | U | c | U | C | A | A | A | 27 | 3 | 8 | c | false | <90% | 4011 | ||
NM_007227 | GPR45 | 1382 | 1400 | G | C | A | G | C | U | c | C | C | A | A | A | U | u | U | C | A | A | A | 14 | 2 | 6 | c | false | <90% | 1725 | ||
NM_001001549 | GRB10 | 2250 | 2268 | u | C | A | G | C | U | c | C | C | A | A | A | U | G | a | C | A | A | A | 6 | 3 | 7 | c | false | <90% | 4579 | ||
NM_005311 | GRB10 | 2388 | 2406 | u | C | A | G | C | U | c | C | C | A | A | A | U | G | a | C | A | A | A | 6 | 3 | 7 | c | false | <90% | 4717 | ||
NM_001001550 | GRB10 | 2468 | 2486 | u | C | A | G | C | U | c | C | C | A | A | A | U | G | a | C | A | A | A | 6 | 3 | 7 | c | false | <90% | 4797 | ||
NM_001001555 | GRB10 | 2714 | 2732 | u | C | A | G | C | U | c | C | C | A | A | A | U | G | a | C | A | A | A | 6 | 3 | 7 | c | false | <90% | 5043 | ||
NM_001751 | CARS | 1282 | 1300 | c | a | g | G | C | U | G | C | a | A | A | A | U | G | U | C | A | A | A | 6 | 4 | 10 | bc | false | <90% | 2528 | ||
NM_139273 | CARS | 1282 | 1300 | c | a | g | G | C | U | G | C | a | A | A | A | U | G | U | C | A | A | A | 6 | 4 | 10 | bc | false | <90% | 2536 | ||
NM_001014437 | CARS | 1531 | 1549 | c | a | g | G | C | U | G | C | a | A | A | A | U | G | U | C | A | A | A | 6 | 4 | 10 | bc | false | <90% | 2767 | ||
NM_001014438 | CARS | 1578 | 1596 | c | a | g | G | C | U | G | C | a | A | A | A | U | G | U | C | A | A | A | 6 | 4 | 10 | bc | false | <90% | 2814 |
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_152400 | C4orf32 | 477 | 495 | U | U | U | G | A | C | A | U | U | U | G | G | u | A | G | C | c | a | u | 58 | 4 | 12 | false | <90% | 2594 | |||
NM_000499 | CYP1A1 | 2078 | 2096 | U | U | U | G | A | C | A | a | U | U | G | G | g | A | G | C | U | G | C | 27 | 2 | 7 | false | <90% | 2602 | |||
NM_005689 | ABCB6 | 2735 | 2753 | g | c | U | G | A | C | A | U | g | U | G | G | C | A | G | C | U | G | C | 26 | 3 | 10 | bc | false | <90% | 2993 | ||
XM_934796 | LOC653566 | 280 | 298 | g | a | U | G | A | u | A | U | U | U | G | G | C | A | G | C | U | G | u | 18 | 4 | 12 | bc | false | <90% | 1202 | ||
XM_944485 | LOC653566 | 280 | 298 | g | a | U | G | A | u | A | U | U | U | G | G | C | A | G | C | U | G | u | 18 | 4 | 12 | bc | false | <90% | 1202 | ||
NM_014752 | SPCS2 | 460 | 478 | g | a | U | G | A | u | A | U | U | U | G | G | C | A | G | C | U | G | u | 18 | 4 | 12 | bc | false | <90% | 1370 | ||
XM_934797 | LOC653566 | 492 | 510 | g | a | U | G | A | u | A | U | U | U | G | G | C | A | G | C | U | G | u | 18 | 4 | 12 | bc | false | <90% | 1414 | ||
XM_944490 | LOC653566 | 492 | 510 | g | a | U | G | A | u | A | U | U | U | G | G | C | A | G | C | U | G | u | 18 | 4 | 12 | bc | false | <90% | 1414 | ||
NM_001080536 | LOC653566 | 509 | 527 | g | a | U | G | A | u | A | U | U | U | G | G | C | A | G | C | U | G | u | 18 | 4 | 12 | bc | false | <90% | 1431 | ||
XM_940181 | LOC653566 | 509 | 527 | g | a | U | G | A | u | A | U | U | U | G | G | C | A | G | C | U | G | u | 18 | 4 | 12 | bc | false | <90% | 1431 | ||
NM_021796 | PLAC1 | 143 | 161 | U | U | g | G | A | a | A | U | U | U | G | G | C | A | G | C | U | G | C | 17 | 2 | 13 | bc | false | <90% | 1126 | ||
XR_015856 | LOC728797 | 1172 | 1190 | U | U | U | G | A | C | u | U | U | U | G | G | C | A | G | C | c | u | C | 7 | 3 | 9 | c | false | <90% | 1956 | ||
NM_001004321 | FLJ45445 | 1783 | 1801 | U | U | U | G | A | C | u | U | U | U | G | G | C | A | G | C | c | u | C | 7 | 3 | 9 | c | false | <90% | 2181 | ||
XR_015615 | LOC729660 | 1275 | 1293 | U | U | U | G | A | C | u | U | U | U | G | G | C | A | G | C | c | u | C | 7 | 3 | 9 | c | false | <90% | 2884 | ||
XR_017612 | LOC653340 | 1512 | 1530 | U | U | U | G | A | C | u | U | U | U | G | G | C | A | G | C | c | u | C | 7 | 3 | 9 | c | false | <90% | 3331 | ||
XR_015328 | LOC728105 | 1507 | 1525 | U | U | U | G | A | C | u | U | U | U | G | G | C | A | G | C | c | u | C | 7 | 3 | 9 | c | false | <90% | 3332 | ||
NM_015055 | SWAP70 | 3764 | 3782 | U | U | U | G | A | a | A | U | U | U | G | a | C | A | G | C | U | G | a | -2 | 3 | 6 | false | <90% | 4848 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3470
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