Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
39 hits were found for CAUCCCCUGCUGCAUUCAA (15 guide strand hits and 24 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_147158 | OPRS1 | 1483 | 1501 | C | A | g | C | C | C | C | U | G | C | U | G | C | A | U | U | C | u | c | 72 | 3 | 14 | c | false | <90% | 1547 | ||
NM_147157 | OPRS1 | 1498 | 1516 | C | A | g | C | C | C | C | U | G | C | U | G | C | A | U | U | C | u | c | 72 | 3 | 14 | c | false | <90% | 1580 | ||
NM_005866 | OPRS1 | 1591 | 1609 | C | A | g | C | C | C | C | U | G | C | U | G | C | A | U | U | C | u | c | 72 | 3 | 14 | c | false | <90% | 1655 | ||
NM_014587 | SOX8 | 2958 | 2976 | a | c | U | C | C | C | C | U | G | C | U | G | C | c | U | U | C | A | c | 62 | 4 | 11 | c | false | <90% | 3069 | ||
NM_178136 | POLDIP3 | 476 | 494 | g | u | U | C | C | C | C | U | G | C | U | G | C | c | U | U | C | A | u | 62 | 4 | 11 | c | false | <90% | 3348 | ||
NM_032311 | POLDIP3 | 476 | 494 | g | u | U | C | C | C | C | U | G | C | U | G | C | c | U | U | C | A | u | 62 | 4 | 11 | c | false | <90% | 3435 | ||
NM_007118 | TRIO | 450 | 468 | C | u | U | C | C | C | C | U | G | C | U | G | C | A | U | c | C | A | u | 57 | 3 | 13 | c | false | <90% | 10244 | ||
NM_022749 | RAI16 | 412 | 430 | C | A | c | C | C | C | C | U | G | C | U | G | C | A | U | U | a | c | c | 49 | 4 | 13 | c | false | <90% | 3759 | ||
XR_017088 | LOC441774 | 242 | 260 | C | A | U | a | C | C | C | U | G | C | U | G | g | A | U | U | C | A | c | 47 | 3 | 8 | false | <90% | 803 | |||
XR_018247 | LOC441774 | 242 | 260 | C | A | U | a | C | C | C | U | G | C | U | G | g | A | U | U | C | A | c | 47 | 3 | 8 | false | <90% | 803 | |||
NM_001039567 | RPS4Y2 | 338 | 356 | C | A | U | a | C | C | C | U | G | C | U | G | g | A | U | U | C | A | u | 47 | 3 | 8 | false | <90% | 888 | |||
NM_001008 | RPS4Y1 | 285 | 303 | C | A | U | a | C | C | C | U | G | C | U | G | g | A | U | U | C | A | u | 47 | 3 | 8 | false | <90% | 910 | |||
NM_015568 | PPP1R16B | 3277 | 3295 | u | A | U | C | C | C | C | U | c | C | U | G | C | A | U | U | C | A | g | 32 | 3 | 9 | bc | false | <90% | 6251 | ||
NM_033056 | PCDH15 | 4547 | 4565 | C | A | U | C | C | u | C | U | G | C | U | G | C | A | U | U | C | c | u | 29 | 3 | 11 | c | false | <90% | 7021 | ||
NM_014705 | DOCK4 | 2459 | 2477 | g | u | U | C | C | g | C | U | G | C | U | G | C | A | U | U | C | A | g | 18 | 4 | 12 | bc | false | <90% | 8343 |
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_004787 | SLIT2 | 4512 | 4530 | g | U | G | A | A | U | G | C | A | G | C | A | G | u | G | G | A | U | a | 73 | 3 | 12 | c | false | <90% | 4950 | ||
NM_004603 | STX1A | 1899 | 1917 | g | U | G | c | A | U | G | C | A | G | C | A | G | G | G | G | A | U | G | 61 | 2 | 15 | bc | false | <90% | 2117 | ||
NM_178312 | GGTLA4 | 8 | 26 | U | U | G | A | A | U | G | C | A | G | C | A | a | G | G | G | u | c | u | 58 | 4 | 12 | false | <90% | 977 | |||
NM_080920 | GGTLA4 | 8 | 26 | U | U | G | A | A | U | G | C | A | G | C | A | a | G | G | G | u | c | u | 58 | 4 | 12 | false | <90% | 1108 | |||
NM_001649 | SHROOM2 | 2040 | 2058 | c | U | G | A | c | U | G | C | A | G | C | A | G | G | G | G | A | g | G | 43 | 3 | 12 | c | false | <90% | 7445 | ||
XR_015520 | LOC729353 | 78 | 96 | c | U | G | g | A | U | G | C | A | G | C | A | G | G | a | G | A | U | G | 36 | 3 | 10 | c | false | <90% | 3045 | ||
NM_001029840 | C3orf23 | 1272 | 1290 | c | U | G | u | A | U | G | C | A | G | C | A | G | G | G | c | A | U | G | 35 | 3 | 11 | c | false | <90% | 1992 | ||
NM_001029839 | C3orf23 | 1396 | 1414 | c | U | G | u | A | U | G | C | A | G | C | A | G | G | G | c | A | U | G | 35 | 3 | 11 | c | false | <90% | 2123 | ||
NM_005491 | CXorf6 | 1641 | 1659 | g | a | u | c | A | U | G | C | A | G | C | A | G | G | G | G | A | U | G | 30 | 4 | 15 | bc | false | <90% | 4636 | ||
NM_182936 | SLC8A3 | 455 | 473 | g | U | c | A | g | U | G | C | A | G | C | A | G | G | G | G | A | U | G | 26 | 3 | 14 | bc | false | <90% | 2845 | ||
NM_182932 | SLC8A3 | 2860 | 2878 | g | U | c | A | g | U | G | C | A | G | C | A | G | G | G | G | A | U | G | 26 | 3 | 14 | bc | false | <90% | 5250 | ||
NM_058240 | SLC8A3 | 2869 | 2887 | g | U | c | A | g | U | G | C | A | G | C | A | G | G | G | G | A | U | G | 26 | 3 | 14 | bc | false | <90% | 5259 | ||
NM_033262 | SLC8A3 | 2872 | 2890 | g | U | c | A | g | U | G | C | A | G | C | A | G | G | G | G | A | U | G | 26 | 3 | 14 | bc | false | <90% | 5262 | ||
NM_183002 | SLC8A3 | 2878 | 2896 | g | U | c | A | g | U | G | C | A | G | C | A | G | G | G | G | A | U | G | 26 | 3 | 14 | bc | false | <90% | 5268 | ||
NM_020298 | ABCC9 | 2459 | 2477 | U | U | u | A | A | U | G | C | A | G | g | A | G | G | G | G | A | U | u | 14 | 3 | 7 | c | false | <90% | 4562 | ||
NM_005691 | ABCC9 | 2567 | 2585 | U | U | u | A | A | U | G | C | A | G | g | A | G | G | G | G | A | U | u | 14 | 3 | 7 | c | false | <90% | 4670 | ||
NM_020297 | ABCC9 | 2567 | 2585 | U | U | u | A | A | U | G | C | A | G | g | A | G | G | G | G | A | U | u | 14 | 3 | 7 | c | false | <90% | 8325 | ||
NM_005541 | INPP5D | 4840 | 4858 | g | U | G | A | A | U | G | C | A | G | a | A | G | G | G | a | A | U | G | 10 | 3 | 9 | c | false | <90% | 4925 | ||
NM_001017915 | INPP5D | 4843 | 4861 | g | U | G | A | A | U | G | C | A | G | a | A | G | G | G | a | A | U | G | 10 | 3 | 9 | c | false | <90% | 4928 | ||
NM_033393 | KIAA1727 | 990 | 1008 | a | U | G | A | A | U | G | C | A | G | g | A | G | G | G | u | A | U | G | 10 | 3 | 9 | c | false | <90% | 6480 | ||
NM_004543 | NEB | 1316 | 1334 | c | U | G | A | A | g | G | C | A | G | C | A | G | G | a | G | A | U | G | 9 | 3 | 8 | c | false | <90% | 20632 | ||
XM_934286 | LOC647070 | 277 | 295 | U | U | G | A | A | a | G | C | A | G | C | A | G | G | G | G | c | c | u | 5 | 4 | 10 | c | false | <90% | 1019 | ||
XM_944562 | LOC647070 | 277 | 295 | U | U | G | A | A | a | G | C | A | G | C | A | G | G | G | G | c | c | u | 5 | 4 | 10 | c | false | <90% | 1019 | ||
NM_017908 | ZNF446 | 1552 | 1570 | c | U | G | g | A | g | G | C | A | G | C | A | G | G | G | G | A | U | G | -2 | 3 | 13 | bc | false | <90% | 1995 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2341
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