Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
50 hits were found for GGAAGAGAAAGGAGUGUCU (19 guide strand hits and 31 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_206909 | PSD3 | 3020 | 3038 | G | G | A | A | G | A | G | A | A | A | G | G | A | G | U | G | a | a | a | 68 | 3 | 16 | ac | false | <90% | 10091 | ||
NM_015310 | PSD3 | 4616 | 4634 | G | G | A | A | G | A | G | A | A | A | G | G | A | G | U | G | a | a | a | 68 | 3 | 16 | ac | false | <90% | 11687 | ||
NM_001024843 | TNRC6B | 8124 | 8142 | a | a | u | A | G | A | G | A | A | A | G | G | g | G | U | G | U | C | U | 56 | 4 | 9 | false | <90% | 15976 | |||
NM_015088 | TNRC6B | 10095 | 10113 | a | a | u | A | G | A | G | A | A | A | G | G | g | G | U | G | U | C | U | 56 | 4 | 9 | false | <90% | 17947 | |||
XM_001133281 | LOC283663 | 945 | 963 | a | G | A | A | G | A | G | A | A | A | G | G | A | G | U | u | c | a | U | 45 | 4 | 14 | c | false | <90% | 1177 | ||
XM_001133132 | LOC283663 | 945 | 963 | a | G | A | A | G | A | G | A | A | A | G | G | A | G | U | u | c | a | U | 45 | 4 | 14 | c | false | <90% | 1177 | ||
NM_000916 | OXTR | 3120 | 3138 | a | a | u | A | G | A | G | A | A | A | G | G | A | G | a | G | U | C | U | 42 | 4 | 11 | c | false | <90% | 4361 | ||
NM_012338 | TSPAN12 | 165 | 183 | G | G | A | A | G | A | G | A | A | A | G | a | A | G | c | G | U | C | U | 41 | 2 | 11 | false | <90% | 2579 | |||
NM_022899 | ACTR8 | 2923 | 2941 | G | G | A | A | G | A | G | A | A | A | G | c | A | u | U | G | U | C | c | 41 | 3 | 11 | false | <90% | 3525 | |||
NM_004258 | IGSF2 | 1917 | 1935 | G | G | A | A | G | A | G | A | c | A | G | G | A | G | U | G | U | a | U | 37 | 2 | 8 | c | false | <90% | 3339 | ||
NM_006170 | NOL1 | 667 | 685 | G | G | A | A | G | A | G | A | A | A | G | a | A | G | U | G | a | C | c | 37 | 3 | 11 | false | <90% | 2661 | |||
NM_001033714 | NOL1 | 735 | 753 | G | G | A | A | G | A | G | A | A | A | G | a | A | G | U | G | a | C | c | 37 | 3 | 11 | false | <90% | 2729 | |||
NM_014699 | ZNF646 | 3026 | 3044 | G | G | A | A | G | A | G | g | A | A | G | G | A | G | U | G | g | C | a | 9 | 3 | 8 | c | false | <90% | 6207 | ||
NM_024316 | LENG1 | 265 | 283 | G | G | A | A | G | g | G | A | A | A | G | G | A | G | U | G | a | u | c | 5 | 4 | 10 | c | false | <90% | 906 | ||
NM_001690 | ATP6V1A | 1261 | 1279 | G | a | A | A | G | A | G | A | A | g | G | G | A | G | U | G | U | C | a | 0 | 3 | 8 | bc | false | <90% | 4567 | ||
NM_017794 | KIAA1797 | 5276 | 5294 | u | G | A | A | G | A | G | A | A | u | G | G | A | G | U | G | g | C | U | -8 | 3 | 8 | c | false | <90% | 6117 | ||
NM_001007546 | FLJ46838 | 267 | 285 | G | G | A | A | G | A | G | A | A | c | G | G | A | G | c | G | U | C | g | -12 | 3 | 9 | c | false | <90% | 2243 | ||
NM_080663 | EXOD1 | 22 | 40 | G | G | A | A | a | A | G | c | A | A | G | G | A | G | U | G | U | C | g | -18 | 3 | 10 | bc | false | <90% | 1503 | ||
NM_174934 | SCN4B | 736 | 754 | a | G | A | A | G | A | a | g | A | A | G | G | A | G | U | G | U | C | U | -30 | 3 | 11 | bc | false | <90% | 4485 |
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_130387 | ASB14 | 1329 | 1347 | c | c | A | C | A | C | U | C | C | U | U | U | C | c | C | U | U | C | C | 67 | 3 | 11 | c | false | <90% | 2218 | ||
NM_002545 | OPCML | 2025 | 2043 | u | a | A | C | A | C | U | C | C | U | U | U | C | U | a | U | U | C | u | 56 | 4 | 12 | c | false | <90% | 6300 | ||
NM_001012393 | OPCML | 2138 | 2156 | u | a | A | C | A | C | U | C | C | U | U | U | C | U | a | U | U | C | u | 56 | 4 | 12 | c | false | <90% | 6413 | ||
XR_017882 | C17orf73 | 1036 | 1054 | A | u | u | C | A | C | U | C | C | U | U | U | C | c | C | U | U | C | C | 49 | 3 | 10 | c | false | <90% | 2762 | ||
XR_017981 | C17orf73 | 1036 | 1054 | A | u | u | C | A | C | U | C | C | U | U | U | C | c | C | U | U | C | C | 49 | 3 | 10 | c | false | <90% | 2776 | ||
NM_024616 | C3orf52 | 801 | 819 | g | G | A | g | A | C | U | C | C | U | U | U | C | U | C | U | c | C | C | 37 | 3 | 12 | c | false | <90% | 2240 | ||
NM_002646 | PIK3C2B | 129 | 147 | A | u | u | C | A | C | U | C | C | U | U | c | C | U | C | U | U | C | C | 35 | 3 | 8 | false | <90% | 7618 | |||
NM_152826 | SNX1 | 369 | 387 | A | a | A | C | A | C | U | C | a | U | U | U | C | U | C | U | U | C | C | 28 | 2 | 10 | bc | false | <90% | 8077 | ||
NM_003099 | SNX1 | 369 | 387 | A | a | A | C | A | C | U | C | a | U | U | U | C | U | C | U | U | C | C | 28 | 2 | 10 | bc | false | <90% | 8221 | ||
XM_029101 | KIAA0947 | 4071 | 4089 | A | G | A | C | A | C | U | a | C | U | U | U | u | U | C | U | U | C | a | 22 | 3 | 7 | false | <90% | 8577 | |||
XM_940469 | KIAA0947 | 4380 | 4398 | A | G | A | C | A | C | U | a | C | U | U | U | u | U | C | U | U | C | a | 22 | 3 | 7 | false | <90% | 8886 | |||
NM_183425 | RBM38 | 1799 | 1817 | u | G | A | C | A | C | U | C | C | U | c | U | C | c | C | U | U | C | C | 17 | 3 | 9 | c | false | <90% | 2346 | ||
NM_017495 | RBM38 | 1854 | 1872 | u | G | A | C | A | C | U | C | C | U | c | U | C | c | C | U | U | C | C | 17 | 3 | 9 | c | false | <90% | 2401 | ||
NM_018154 | ASF1B | 1179 | 1197 | u | G | u | C | A | u | U | C | C | U | U | U | C | U | C | U | U | C | C | 15 | 3 | 13 | bc | false | <90% | 1746 | ||
NM_001001693 | FLJ46257 | 1369 | 1387 | c | u | u | C | c | C | U | C | C | U | U | U | C | U | C | U | U | C | C | 15 | 4 | 14 | bc | false | <90% | 4182 | ||
NM_032836 | FIZ1 | 2372 | 2390 | g | G | A | C | A | C | U | C | C | U | c | U | C | U | u | U | U | C | C | 11 | 3 | 9 | c | false | <90% | 2651 | ||
NM_138923 | TAF1 | 5253 | 5271 | A | G | A | C | A | a | U | C | C | U | U | U | C | U | C | U | g | C | u | 8 | 3 | 10 | c | false | <90% | 6074 | ||
NM_004606 | TAF1 | 5316 | 5334 | A | G | A | C | A | a | U | C | C | U | U | U | C | U | C | U | g | C | u | 8 | 3 | 10 | c | false | <90% | 6137 | ||
NM_153809 | TAF1L | 5436 | 5454 | A | G | A | C | A | a | U | C | C | U | U | U | C | U | C | U | g | C | u | 8 | 3 | 10 | c | false | <90% | 6216 | ||
NM_006055 | LANCL1 | 1200 | 1218 | A | G | A | C | A | C | c | C | C | U | U | U | C | U | C | U | c | u | C | 7 | 3 | 9 | c | false | <90% | 4544 | ||
NM_014676 | PUM1 | 2541 | 2559 | c | a | g | C | A | C | U | C | u | U | U | U | C | U | C | U | U | C | C | 6 | 4 | 10 | bc | false | <90% | 5410 | ||
NM_001020658 | PUM1 | 2541 | 2559 | c | a | g | C | A | C | U | C | u | U | U | U | C | U | C | U | U | C | C | 6 | 4 | 10 | bc | false | <90% | 5416 | ||
NR_003017 | SNORA71C | 100 | 118 | g | u | c | C | A | C | U | C | C | U | g | U | C | U | C | U | U | C | C | 5 | 4 | 8 | c | false | <90% | 138 | ||
NM_172314 | IL25 | 918 | 936 | c | a | c | C | A | C | U | C | C | U | g | U | C | U | C | U | U | C | C | 5 | 4 | 8 | c | false | <90% | 1187 | ||
NM_022789 | IL25 | 1118 | 1136 | c | a | c | C | A | C | U | C | C | U | g | U | C | U | C | U | U | C | C | 5 | 4 | 8 | c | false | <90% | 1387 | ||
NM_017454 | STAU1 | 2331 | 2349 | c | a | c | C | A | C | U | g | C | U | U | U | C | U | C | U | U | C | C | 4 | 4 | 11 | bc | false | <90% | 3324 | ||
NM_017452 | STAU1 | 2406 | 2424 | c | a | c | C | A | C | U | g | C | U | U | U | C | U | C | U | U | C | C | 4 | 4 | 11 | bc | false | <90% | 3399 | ||
NM_004602 | STAU1 | 2529 | 2547 | c | a | c | C | A | C | U | g | C | U | U | U | C | U | C | U | U | C | C | 4 | 4 | 11 | bc | false | <90% | 3522 | ||
NM_001037328 | STAU1 | 2547 | 2565 | c | a | c | C | A | C | U | g | C | U | U | U | C | U | C | U | U | C | C | 4 | 4 | 11 | bc | false | <90% | 3540 | ||
NM_017453 | STAU1 | 2695 | 2713 | c | a | c | C | A | C | U | g | C | U | U | U | C | U | C | U | U | C | C | 4 | 4 | 11 | bc | false | <90% | 3688 | ||
NM_000306 | POU1F1 | 1040 | 1058 | u | u | u | C | A | u | U | C | C | U | U | U | C | U | C | U | U | C | C | 3 | 4 | 13 | bc | false | <90% | 1262 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3576
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