Automatic recommendation
Not OK - siRNA is not specific
60 hits were found for GGAAGGAAUUGCAAAGGAU (45 guide strand hits and 15 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_022132 | MCCC2 | 1344 | 1362 | u | G | A | A | G | G | A | A | U | U | G | C | c | A | A | G | G | A | U | 87 | 2 | 11 | false | <90% | 2329 | |||
NM_001010860 | C14orf174 | 252 | 270 | G | G | A | A | G | G | A | A | U | U | G | C | c | A | A | G | G | A | g | 84 | 2 | 12 | false | <90% | 2025 | |||
NM_015516 | TSKU | 1742 | 1760 | a | G | A | A | G | G | A | A | U | U | G | C | A | A | A | G | a | A | U | 74 | 2 | 15 | ac | false | <90% | 2725 | ||
NM_018717 | MAML3 | 4796 | 4814 | c | u | c | A | G | G | A | A | U | U | G | C | A | A | A | G | G | c | U | 64 | 4 | 14 | c | false | <90% | 7086 | ||
NM_016356 | DCDC2 | 2416 | 2434 | G | G | A | A | G | G | A | A | U | U | G | u | A | A | A | G | G | A | g | 61 | 2 | 11 | false | <90% | 4708 | |||
XR_019077 | LOC642741 | 1208 | 1226 | a | G | A | c | G | G | A | A | U | U | G | C | A | A | A | G | G | A | a | 56 | 3 | 14 | bc | false | <90% | 1310 | ||
XR_016455 | LOC642741 | 1208 | 1226 | a | G | A | c | G | G | A | A | U | U | G | C | A | A | A | G | G | A | a | 56 | 3 | 14 | bc | false | <90% | 1310 | ||
NM_152677 | ZSCAN4 | 872 | 890 | G | G | c | A | G | G | A | A | U | U | G | C | A | A | A | G | a | c | U | 54 | 3 | 13 | c | false | <90% | 2230 | ||
NM_007342 | NUPL2 | 570 | 588 | G | G | A | A | G | G | A | A | U | U | G | u | A | A | A | a | G | A | U | 40 | 2 | 11 | false | <90% | 1778 | |||
NM_021738 | SVIL | 786 | 804 | G | G | A | A | G | G | A | A | U | U | G | a | A | A | A | u | G | A | c | 35 | 3 | 11 | false | <90% | 8300 | |||
NM_012115 | CASP8AP2 | 388 | 406 | a | G | A | A | G | G | A | A | c | U | G | C | A | A | A | G | G | A | g | 32 | 3 | 9 | bc | false | <90% | 6782 | ||
NM_018202 | TMEM57 | 2204 | 2222 | G | G | A | A | G | G | c | A | U | U | G | C | A | A | A | G | G | A | g | 28 | 2 | 11 | bc | false | <90% | 3158 | ||
XR_015525 | LOC728333 | 1480 | 1498 | G | G | A | A | G | G | A | A | U | U | c | C | c | A | A | G | G | A | a | 23 | 3 | 10 | false | <90% | 1813 | |||
XR_015797 | LOC731279 | 1480 | 1498 | G | G | A | A | G | G | A | A | U | U | c | C | c | A | A | G | G | A | a | 23 | 3 | 10 | false | <90% | 1813 | |||
NM_022495 | C14orf135 | 2694 | 2712 | G | G | A | A | G | a | A | A | U | U | G | C | c | A | A | G | G | A | c | 21 | 3 | 6 | false | <90% | 3952 | |||
NM_017654 | SAMD9 | 6233 | 6251 | G | a | A | A | G | a | A | A | U | U | G | C | A | A | A | G | G | A | c | 20 | 3 | 12 | bc | false | <90% | 6853 | ||
XM_001126131 | LOC730505 | 404 | 422 | a | u | A | A | G | G | A | A | U | U | u | C | A | A | A | G | G | A | a | 20 | 4 | 8 | c | false | <90% | 441 | ||
XM_374461 | LOC392713 | 404 | 422 | a | u | A | A | G | G | A | A | U | U | u | C | A | A | A | G | G | A | a | 20 | 4 | 8 | c | false | <90% | 441 | ||
XM_001130226 | LOC729425 | 578 | 596 | a | u | A | A | G | G | A | A | U | U | u | C | A | A | A | G | G | A | a | 20 | 4 | 8 | c | false | <90% | 699 | ||
NM_174930 | PMS2L5 | 448 | 466 | a | u | A | A | G | G | A | A | U | U | u | C | A | A | A | G | G | A | a | 20 | 4 | 8 | c | false | <90% | 748 | ||
XM_001128073 | LOC730313 | 554 | 572 | a | u | A | A | G | G | A | A | U | U | u | C | A | A | A | G | G | A | a | 20 | 4 | 8 | c | false | <90% | 768 | ||
XM_001128562 | LOC730324 | 554 | 572 | a | u | A | A | G | G | A | A | U | U | u | C | A | A | A | G | G | A | a | 20 | 4 | 8 | c | false | <90% | 768 | ||
XM_001129884 | LOC729299 | 554 | 572 | a | u | A | A | G | G | A | A | U | U | u | C | A | A | A | G | G | A | a | 20 | 4 | 8 | c | false | <90% | 768 | ||
XM_001130276 | LOC441259 | 554 | 572 | a | u | A | A | G | G | A | A | U | U | u | C | A | A | A | G | G | A | a | 20 | 4 | 8 | c | false | <90% | 768 | ||
XM_001130281 | LOC729453 | 554 | 572 | a | u | A | A | G | G | A | A | U | U | u | C | A | A | A | G | G | A | a | 20 | 4 | 8 | c | false | <90% | 768 | ||
XM_001134451 | PMS2L2 | 114 | 132 | a | u | A | A | G | G | A | A | U | U | u | C | A | A | A | G | G | A | a | 20 | 4 | 8 | c | false | <90% | 1082 | ||
XM_001134451 | PMS2L2 | 725 | 743 | a | u | A | A | G | G | A | A | U | U | u | C | A | A | A | G | G | A | a | 20 | 4 | 8 | c | false | <90% | 1082 | ||
XM_001134437 | PMS2L2 | 114 | 132 | a | u | A | A | G | G | A | A | U | U | u | C | A | A | A | G | G | A | a | 20 | 4 | 8 | c | false | <90% | 1082 | ||
XM_001134437 | PMS2L2 | 725 | 743 | a | u | A | A | G | G | A | A | U | U | u | C | A | A | A | G | G | A | a | 20 | 4 | 8 | c | false | <90% | 1082 | ||
XM_001128484 | LOC441259 | 554 | 572 | a | u | A | A | G | G | A | A | U | U | u | C | A | A | A | G | G | A | a | 20 | 4 | 8 | c | false | <90% | 1214 | ||
XM_001128555 | LOC730323 | 554 | 572 | a | u | A | A | G | G | A | A | U | U | u | C | A | A | A | G | G | A | a | 20 | 4 | 8 | c | false | <90% | 1214 | ||
NM_005395 | PMS2L3 | 1175 | 1193 | a | u | A | A | G | G | A | A | U | U | u | C | A | A | A | G | G | A | a | 20 | 4 | 8 | c | false | <90% | 1329 | ||
NM_001003686 | PMS2L3 | 1180 | 1198 | a | u | A | A | G | G | A | A | U | U | u | C | A | A | A | G | G | A | a | 20 | 4 | 8 | c | false | <90% | 1334 | ||
XM_001126008 | PMS2 | 830 | 848 | a | u | A | A | G | G | A | A | U | U | u | C | A | A | A | G | G | A | a | 20 | 4 | 8 | c | false | <90% | 2499 | ||
NR_003085 | PMS2 | 591 | 609 | a | u | A | A | G | G | A | A | U | U | u | C | A | A | A | G | G | A | a | 20 | 4 | 8 | c | false | <90% | 2828 | ||
NM_000535 | PMS2 | 596 | 614 | a | u | A | A | G | G | A | A | U | U | u | C | A | A | A | G | G | A | a | 20 | 4 | 8 | c | false | <90% | 2836 | ||
NM_001003398 | BICD1 | 1532 | 1550 | a | G | A | A | G | G | A | g | U | U | G | C | A | A | A | a | G | A | U | 9 | 3 | 7 | c | false | <90% | 3285 | ||
NM_001714 | BICD1 | 1532 | 1550 | a | G | A | A | G | G | A | g | U | U | G | C | A | A | A | a | G | A | U | 9 | 3 | 7 | c | false | <90% | 3589 | ||
NM_018897 | DNAH7 | 3396 | 3414 | u | G | A | A | G | G | A | A | U | c | G | C | A | A | A | G | G | u | a | 7 | 4 | 8 | c | false | <90% | 12395 | ||
NM_012063 | DNM1L | 1379 | 1397 | a | u | g | A | G | G | A | A | a | U | G | C | A | A | A | G | G | A | U | 6 | 4 | 10 | bc | false | <90% | 2415 | ||
NM_005690 | DNM1L | 1379 | 1397 | a | u | g | A | G | G | A | A | a | U | G | C | A | A | A | G | G | A | U | 6 | 4 | 10 | bc | false | <90% | 2445 | ||
NM_012062 | DNM1L | 1379 | 1397 | a | u | g | A | G | G | A | A | a | U | G | C | A | A | A | G | G | A | U | 6 | 4 | 10 | bc | false | <90% | 3293 | ||
NM_005656 | TMPRSS2 | 2235 | 2253 | G | G | A | A | G | c | A | A | U | U | G | a | A | A | A | G | G | A | a | -2 | 3 | 6 | false | <90% | 3226 | |||
NM_012215 | MGEA5 | 3101 | 3119 | G | G | A | A | G | G | A | u | U | U | c | C | A | A | A | G | G | A | U | -23 | 2 | 8 | c | false | <90% | 5146 | ||
NM_016343 | CENPF | 3399 | 3417 | G | G | A | A | G | c | A | u | U | U | G | C | A | A | A | G | G | A | a | -30 | 3 | 10 | bc | false | <90% | 10316 |
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_153692 | HTRA4 | 1134 | 1152 | c | U | C | C | U | U | U | G | C | A | A | U | U | C | C | U | U | C | a | 93 | 2 | 17 | abc | false | <90% | 1544 | ||
XR_000668 | CXorf30 | 52 | 70 | u | U | C | C | U | U | U | G | C | A | A | U | U | u | C | U | U | C | C | 78 | 2 | 12 | c | false | <90% | 903 | ||
XR_017930 | LOC158730 | 52 | 70 | u | U | C | C | U | U | U | G | C | A | A | U | U | u | C | U | U | C | C | 78 | 2 | 12 | c | false | <90% | 903 | ||
NM_005967 | NAB2 | 2496 | 2514 | g | U | C | C | U | U | U | G | C | A | A | U | U | u | C | U | U | C | C | 78 | 2 | 12 | c | false | <90% | 2725 | ||
XM_931553 | LOC643449 | 278 | 296 | u | a | C | C | U | U | U | G | C | A | A | U | U | a | C | U | U | C | a | 62 | 4 | 11 | c | false | <90% | 539 | ||
XM_945026 | LOC643449 | 278 | 296 | u | a | C | C | U | U | U | G | C | A | A | U | U | a | C | U | U | C | a | 62 | 4 | 11 | c | false | <90% | 539 | ||
NM_176876 | P2RY12 | 1115 | 1133 | u | U | C | C | U | U | U | G | C | A | A | g | U | C | C | U | U | C | a | 59 | 3 | 10 | false | <90% | 1474 | |||
NM_022788 | P2RY12 | 1143 | 1161 | u | U | C | C | U | U | U | G | C | A | A | g | U | C | C | U | U | C | a | 59 | 3 | 10 | false | <90% | 1502 | |||
NM_016630 | SPG21 | 667 | 685 | A | U | C | C | U | c | U | G | C | A | A | U | U | C | C | U | U | C | a | 31 | 2 | 12 | bc | false | <90% | 1815 | ||
NM_031966 | CCNB1 | 1081 | 1099 | u | a | C | C | U | U | U | G | C | A | c | U | U | C | C | U | U | C | g | 20 | 4 | 8 | c | false | <90% | 2101 | ||
NR_001317 | HCG4P6 | 542 | 560 | c | U | g | C | U | U | U | c | C | A | A | U | U | C | C | U | U | C | C | 16 | 3 | 11 | bc | false | <90% | 1060 | ||
NM_002112 | HDC | 1296 | 1314 | u | U | C | C | U | U | U | G | a | A | A | U | U | C | C | U | g | C | C | 14 | 3 | 7 | c | false | <90% | 2410 | ||
NM_005831 | CALCOCO2 | 443 | 461 | u | U | C | C | U | U | U | c | C | A | A | U | U | C | C | g | U | C | C | 9 | 3 | 7 | c | false | <90% | 3299 | ||
NM_016224 | SNX9 | 2704 | 2722 | u | c | u | C | U | U | U | G | C | A | c | U | U | C | C | U | U | C | C | 5 | 4 | 8 | c | false | <90% | 4200 | ||
NM_022491 | SUDS3 | 1901 | 1919 | u | U | C | a | U | U | U | G | u | A | A | U | U | C | C | U | U | C | C | 1 | 3 | 10 | bc | false | <90% | 4728 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3668
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