Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
35 hits were found for CCUCCUGUCCUCCAACUUG (14 guide strand hits and 21 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_182527 | CABP7 | 1728 | 1746 | C | C | U | C | C | U | G | U | C | C | U | C | C | c | A | C | U | U | c | 75 | 2 | 13 | c | false | <90% | 3044 | ||
NM_018037 | RALGPS2 | 1134 | 1152 | u | g | U | C | C | U | G | U | C | C | U | C | C | A | c | C | U | U | u | 56 | 4 | 12 | c | false | <90% | 1894 | ||
XM_001125940 | LOC727847 | 397 | 415 | C | C | U | C | C | U | G | U | C | C | U | C | C | u | c | C | U | U | G | 55 | 2 | 13 | c | false | <90% | 522 | ||
XM_001125923 | LOC730458 | 397 | 415 | C | C | U | C | C | U | G | U | C | C | U | C | C | u | c | C | U | U | G | 55 | 2 | 13 | c | false | <90% | 522 | ||
NM_016192 | TMEFF2 | 99 | 117 | C | C | U | C | C | U | G | U | C | C | U | C | C | g | g | C | U | U | c | 50 | 3 | 13 | c | false | <90% | 1814 | ||
NM_025002 | C6orf208 | 558 | 576 | u | g | U | u | C | U | G | U | C | C | U | C | C | A | A | C | U | U | G | 49 | 3 | 15 | bc | false | <90% | 2318 | ||
NM_152463 | EME1 | 234 | 252 | C | C | U | C | C | U | G | U | C | C | U | C | C | A | g | C | a | c | c | 44 | 4 | 14 | c | false | <90% | 2304 | ||
NM_031272 | TEX14 | 2507 | 2525 | C | C | U | C | C | U | G | U | C | C | U | a | C | A | g | C | U | U | u | 36 | 3 | 11 | false | <90% | 4825 | |||
NM_198393 | TEX14 | 2507 | 2525 | C | C | U | C | C | U | G | U | C | C | U | a | C | A | g | C | U | U | u | 36 | 3 | 11 | false | <90% | 4945 | |||
XM_929878 | LOC646915 | 1099 | 1117 | a | C | U | C | C | a | G | U | C | C | U | C | C | u | A | C | U | U | G | 15 | 3 | 7 | c | false | <90% | 2942 | ||
NM_017789 | SEMA4C | 1864 | 1882 | C | C | a | C | C | U | c | U | C | C | U | C | C | A | A | C | U | U | G | 14 | 2 | 12 | bc | false | <90% | 3537 | ||
NM_006194 | PAX9 | 1502 | 1520 | C | C | U | C | C | U | G | c | C | C | U | C | C | A | A | C | c | c | u | 6 | 4 | 8 | c | false | <90% | 1630 | ||
NM_016464 | TMEM138 | 276 | 294 | a | C | U | C | C | U | G | U | C | a | U | C | C | A | g | C | U | U | G | -9 | 3 | 8 | c | false | <90% | 1192 | ||
NM_020384 | CLDN2 | 333 | 351 | u | C | U | C | u | U | G | g | C | C | U | C | C | A | A | C | U | U | G | -15 | 3 | 11 | bc | false | <90% | 2959 |
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_025047 | ARL14 | 378 | 396 | g | A | u | G | U | U | G | G | A | G | G | A | C | A | G | G | A | a | a | 70 | 4 | 14 | c | false | <90% | 1306 | ||
NR_002305 | PDIA3P | 901 | 919 | C | A | A | G | U | U | G | G | A | G | G | A | C | A | a | G | A | c | u | 67 | 3 | 14 | c | false | <90% | 2099 | ||
NM_002845 | PTPRM | 1263 | 1281 | C | A | A | G | U | U | G | G | A | G | G | A | C | A | a | G | A | a | c | 67 | 3 | 14 | c | false | <90% | 5065 | ||
NM_006948 | STCH | 826 | 844 | a | A | A | c | U | U | G | G | A | G | G | A | C | A | G | G | A | c | u | 53 | 4 | 13 | c | false | <90% | 4001 | ||
NM_019041 | MTRF1L | 436 | 454 | g | g | A | G | U | U | G | G | A | G | G | u | C | A | G | G | A | G | G | 52 | 3 | 9 | false | <90% | 2549 | |||
XM_938267 | LOC649201 | 1691 | 1709 | C | A | g | G | U | U | G | G | A | G | G | c | C | A | G | G | A | G | G | 46 | 2 | 8 | false | <90% | 1818 | |||
XM_001127211 | LOC649201 | 1691 | 1709 | C | A | g | G | U | U | G | G | A | G | G | c | C | A | G | G | A | G | G | 46 | 2 | 8 | false | <90% | 1818 | |||
NM_018090 | NECAP2 | 196 | 214 | C | A | A | G | c | U | G | G | A | G | G | A | C | A | G | G | A | c | G | 45 | 2 | 12 | c | false | <90% | 2037 | ||
NM_006155 | SEPT2 | 90 | 108 | C | u | u | c | U | U | G | G | A | G | G | A | C | A | G | G | A | G | G | 32 | 3 | 15 | bc | false | <90% | 3497 | ||
NM_001008491 | SEPT2 | 90 | 108 | C | u | u | c | U | U | G | G | A | G | G | A | C | A | G | G | A | G | G | 32 | 3 | 15 | bc | false | <90% | 3598 | ||
NM_018237 | CCAR1 | 126 | 144 | C | A | A | u | U | U | G | G | A | G | G | A | C | A | G | a | A | G | a | 32 | 3 | 11 | c | false | <90% | 3858 | ||
XM_928187 | KIAA0960 | 2873 | 2891 | C | A | A | G | a | U | G | G | A | G | G | A | C | A | G | G | c | u | G | 22 | 3 | 11 | c | false | <90% | 6385 | ||
XM_937164 | KIAA0960 | 2873 | 2891 | C | A | A | G | a | U | G | G | A | G | G | A | C | A | G | G | c | u | G | 22 | 3 | 11 | c | false | <90% | 6385 | ||
XM_935904 | KIAA0960 | 2873 | 2891 | C | A | A | G | a | U | G | G | A | G | G | A | C | A | G | G | c | u | G | 22 | 3 | 11 | c | false | <90% | 6385 | ||
NM_032288 | FYTTD1 | 1877 | 1895 | C | A | A | G | U | U | G | a | A | G | G | A | C | A | G | G | u | a | G | 11 | 3 | 8 | c | false | <90% | 3542 | ||
NM_001011537 | FYTTD1 | 2050 | 2068 | C | A | A | G | U | U | G | a | A | G | G | A | C | A | G | G | u | a | G | 11 | 3 | 8 | c | false | <90% | 3715 | ||
NM_005366 | MAGEA11 | 312 | 330 | C | A | A | c | c | U | G | G | A | G | G | A | C | A | G | G | A | G | u | 6 | 3 | 13 | bc | false | <90% | 1892 | ||
NM_001011544 | MAGEA11 | 313 | 331 | C | A | A | c | c | U | G | G | A | G | G | A | C | A | G | G | A | G | u | 6 | 3 | 13 | bc | false | <90% | 1893 | ||
NM_001039799 | FLJ41484 | 988 | 1006 | u | g | c | G | U | U | G | a | A | G | G | A | C | A | G | G | A | G | G | 4 | 4 | 11 | bc | false | <90% | 3249 | ||
XM_001127437 | LOC730839 | 389 | 407 | C | A | A | G | U | U | G | G | A | G | u | g | C | A | G | G | A | G | a | 0 | 3 | 10 | false | <90% | 6652 | |||
NM_001009931 | HRNR | 465 | 483 | C | A | A | G | U | U | G | G | A | G | u | g | C | A | G | G | A | G | a | 0 | 3 | 10 | false | <90% | 9623 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 4945
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