Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
42 hits were found for UGGGAGUGCAGAUGCAGCG (25 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_016815 | GYPC | 405 | 423 | U | G | a | G | A | G | U | G | C | A | G | A | U | G | C | A | G | C | c | 75 | 2 | 15 | bc | false | <90% | 1019 | ||
NM_002101 | GYPC | 462 | 480 | U | G | a | G | A | G | U | G | C | A | G | A | U | G | C | A | G | C | c | 75 | 2 | 15 | bc | false | <90% | 1075 | ||
NM_003253 | TIAM1 | 4507 | 4525 | g | G | c | G | A | G | U | G | C | A | G | A | U | G | C | A | G | a | G | 75 | 3 | 14 | c | false | <90% | 7218 | ||
NM_020964 | KIAA1632 | 4850 | 4868 | U | u | G | G | A | G | U | G | C | A | G | A | g | G | C | A | G | C | a | 73 | 3 | 10 | false | <90% | 12715 | |||
NM_016111 | TELO2 | 2854 | 2872 | g | G | a | G | A | G | U | G | C | A | G | A | U | G | C | A | G | g | a | 70 | 4 | 14 | c | false | <90% | 3319 | ||
XM_001133738 | LOC731746 | 197 | 215 | U | G | G | G | A | G | U | G | C | A | G | A | g | G | C | A | a | C | G | 66 | 2 | 12 | false | <90% | 459 | |||
NM_145159 | JAG2 | 1182 | 1200 | g | G | G | G | A | G | U | G | C | A | G | g | U | G | C | A | G | C | u | 59 | 3 | 10 | false | <90% | 4963 | |||
NM_002226 | JAG2 | 1182 | 1200 | g | G | G | G | A | G | U | G | C | A | G | g | U | G | C | A | G | C | u | 59 | 3 | 10 | false | <90% | 5077 | |||
NM_014947 | FOXJ3 | 3100 | 3118 | U | G | G | G | A | G | U | G | C | A | G | g | U | G | C | A | c | a | c | 35 | 4 | 11 | false | <90% | 5246 | |||
NM_021216 | ZNF71 | 2089 | 2107 | c | u | G | G | A | G | U | c | C | A | G | A | U | G | C | A | G | C | u | 19 | 4 | 10 | bc | false | <90% | 3116 | ||
NM_001092 | ABR | 3998 | 4016 | U | a | G | G | A | G | a | G | C | A | G | A | U | G | C | A | G | C | u | 17 | 3 | 11 | bc | false | <90% | 5095 | ||
NM_021962 | ABR | 4203 | 4221 | U | a | G | G | A | G | a | G | C | A | G | A | U | G | C | A | G | C | u | 17 | 3 | 11 | bc | false | <90% | 5300 | ||
NM_019619 | PARD3 | 3596 | 3614 | U | G | G | a | g | G | U | G | C | A | G | A | U | G | C | A | G | C | G | 11 | 2 | 14 | bc | false | <90% | 4071 | ||
NM_000695 | ALDH3B2 | 149 | 167 | a | G | G | G | A | G | U | G | g | A | G | g | U | G | C | A | G | C | G | 4 | 3 | 7 | false | <90% | 2660 | |||
NM_183359 | BRD8 | 2539 | 2557 | U | G | G | c | A | G | U | G | g | A | G | A | U | G | C | A | G | C | G | 3 | 2 | 10 | bc | false | <90% | 3086 | ||
NM_006696 | BRD8 | 2661 | 2679 | U | G | G | c | A | G | U | G | g | A | G | A | U | G | C | A | G | C | G | 3 | 2 | 10 | bc | false | <90% | 3253 | ||
NM_139199 | BRD8 | 2442 | 2460 | U | G | G | c | A | G | U | G | g | A | G | A | U | G | C | A | G | C | G | 3 | 2 | 10 | bc | false | <90% | 4074 | ||
NM_133487 | RAD51 | 259 | 277 | U | G | G | c | A | a | U | G | C | A | G | A | U | G | C | A | G | C | u | -5 | 3 | 12 | bc | false | <90% | 1963 | ||
NM_002875 | RAD51 | 259 | 277 | U | G | G | c | A | a | U | G | C | A | G | A | U | G | C | A | G | C | u | -5 | 3 | 12 | bc | false | <90% | 2254 | ||
XM_053966 | LOC113230 | 608 | 626 | c | G | G | G | c | G | c | G | C | A | G | A | U | G | C | A | G | C | G | -19 | 3 | 12 | bc | false | <90% | 1425 | ||
XM_937316 | LOC113230 | 608 | 626 | c | G | G | G | c | G | c | G | C | A | G | A | U | G | C | A | G | C | G | -19 | 3 | 12 | bc | false | <90% | 1425 | ||
NM_145871 | GSTZ1 | 397 | 415 | U | G | G | G | A | G | a | G | g | A | G | A | U | G | C | A | G | C | u | -31 | 3 | 9 | bc | false | <90% | 1145 | ||
NM_145870 | GSTZ1 | 523 | 541 | U | G | G | G | A | G | a | G | g | A | G | A | U | G | C | A | G | C | u | -31 | 3 | 9 | bc | false | <90% | 1231 | ||
NM_001513 | GSTZ1 | 737 | 755 | U | G | G | G | A | G | a | G | g | A | G | A | U | G | C | A | G | C | u | -31 | 3 | 9 | bc | false | <90% | 1448 | ||
NM_018502 | TMCO6 | 1081 | 1099 | U | G | G | G | A | G | g | G | C | A | a | A | U | G | C | A | G | C | u | -32 | 3 | 7 | c | false | <90% | 1896 |
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 | |||||||||||||
XM_001130495 | LOC728429 | 2560 | 2578 | a | u | u | U | G | C | A | U | C | U | G | C | A | C | U | C | C | C | u | 62 | 4 | 15 | bc | false | <90% | 3784 | ||
NM_021035 | ZNFX1 | 7215 | 7233 | g | c | C | U | G | C | A | U | C | U | G | C | A | u | U | C | C | C | u | 62 | 4 | 11 | c | false | <90% | 7371 | ||
XM_001133349 | NOTCH2 | 1365 | 1383 | a | c | C | U | G | C | A | U | C | U | G | C | A | a | U | C | C | C | g | 62 | 4 | 11 | c | false | <90% | 10836 | ||
NM_024408 | NOTCH2 | 2032 | 2050 | a | c | C | U | G | C | A | U | C | U | G | C | A | a | U | C | C | C | g | 62 | 4 | 11 | c | false | <90% | 11433 | ||
XR_018080 | LOC642073 | 804 | 822 | C | c | C | U | G | C | A | U | C | U | G | u | A | C | U | C | C | C | c | 49 | 3 | 9 | false | <90% | 864 | |||
NM_080431 | ACTRT2 | 408 | 426 | C | c | C | U | G | C | A | g | C | U | G | C | A | C | U | C | C | C | c | 21 | 3 | 10 | bc | false | <90% | 1437 | ||
NM_024503 | HIVEP3 | 7451 | 7469 | a | c | C | U | G | C | c | U | C | U | G | C | A | C | U | C | C | C | A | 20 | 3 | 12 | bc | false | <90% | 8571 | ||
NM_032131 | ARMC2 | 1894 | 1912 | a | G | C | U | G | g | A | U | C | U | G | C | A | u | U | C | C | C | A | 15 | 3 | 7 | c | false | <90% | 3277 | ||
NM_001031710 | KLHL7 | 120 | 138 | C | G | C | U | G | C | A | g | C | U | G | C | A | C | U | g | C | C | g | 6 | 3 | 7 | c | false | <90% | 3137 | ||
NM_018846 | KLHL7 | 129 | 147 | C | G | C | U | G | C | A | g | C | U | G | C | A | C | U | g | C | C | g | 6 | 3 | 7 | c | false | <90% | 3140 | ||
NM_012410 | SEZ6L2 | 664 | 682 | g | G | C | U | G | C | u | U | C | U | G | C | A | C | U | u | C | C | A | 5 | 3 | 8 | c | false | <90% | 2855 | ||
NM_201575 | SEZ6L2 | 1024 | 1042 | g | G | C | U | G | C | u | U | C | U | G | C | A | C | U | u | C | C | A | 5 | 3 | 8 | c | false | <90% | 3162 | ||
NM_019899 | ABCC1 | 5090 | 5108 | g | G | C | a | G | C | c | U | C | U | G | C | A | C | U | C | C | C | A | -5 | 3 | 12 | bc | false | <90% | 6219 | ||
NM_019900 | ABCC1 | 5240 | 5258 | g | G | C | a | G | C | c | U | C | U | G | C | A | C | U | C | C | C | A | -5 | 3 | 12 | bc | false | <90% | 6369 | ||
NM_019862 | ABCC1 | 5258 | 5276 | g | G | C | a | G | C | c | U | C | U | G | C | A | C | U | C | C | C | A | -5 | 3 | 12 | bc | false | <90% | 6387 | ||
NM_019898 | ABCC1 | 5267 | 5285 | g | G | C | a | G | C | c | U | C | U | G | C | A | C | U | C | C | C | A | -5 | 3 | 12 | bc | false | <90% | 6396 | ||
NM_004996 | ABCC1 | 5435 | 5453 | g | G | C | a | G | C | c | U | C | U | G | C | A | C | U | C | C | C | A | -5 | 3 | 12 | bc | false | <90% | 6564 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2292
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