Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
58 hits were found for GCCUUCAGCACCAGACACA (25 guide strand hits and 33 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_152475 | ZNF417 | 857 | 875 | G | C | C | U | U | C | A | G | C | A | C | C | A | a | A | C | A | C | u | 75 | 2 | 13 | c | false | <90% | 4703 | ||
NM_032828 | ZNF587 | 796 | 814 | G | C | C | U | U | C | A | G | C | A | C | C | A | a | A | C | A | C | u | 75 | 2 | 13 | c | false | <90% | 6845 | ||
NM_170706 | NMNAT2 | 1717 | 1735 | u | u | C | U | U | C | A | G | C | A | C | C | A | c | A | C | A | C | A | 67 | 3 | 11 | c | false | <90% | 5465 | ||
NM_015039 | NMNAT2 | 1932 | 1950 | u | u | C | U | U | C | A | G | C | A | C | C | A | c | A | C | A | C | A | 67 | 3 | 11 | c | false | <90% | 5680 | ||
NM_207313 | TMEM132E | 614 | 632 | c | C | C | U | U | C | A | G | C | A | C | C | A | G | c | C | A | g | g | 65 | 4 | 13 | c | false | <90% | 4369 | ||
NM_001011666 | CREB5 | 463 | 481 | c | g | C | a | U | C | A | G | C | A | C | C | A | G | A | C | A | C | u | 44 | 4 | 14 | bc | false | <90% | 7772 | ||
NM_182899 | CREB5 | 879 | 897 | c | g | C | a | U | C | A | G | C | A | C | C | A | G | A | C | A | C | u | 44 | 4 | 14 | bc | false | <90% | 8188 | ||
NM_004904 | CREB5 | 904 | 922 | c | g | C | a | U | C | A | G | C | A | C | C | A | G | A | C | A | C | u | 44 | 4 | 14 | bc | false | <90% | 8213 | ||
NM_182898 | CREB5 | 1223 | 1241 | c | g | C | a | U | C | A | G | C | A | C | C | A | G | A | C | A | C | u | 44 | 4 | 14 | bc | false | <90% | 8532 | ||
NM_000092 | COL4A4 | 5643 | 5661 | u | g | C | U | c | C | A | G | C | A | C | C | A | G | A | C | A | C | c | 30 | 4 | 13 | bc | false | <90% | 10341 | ||
NM_004783 | TAOK2 | 2903 | 2921 | G | C | C | U | g | C | A | G | C | A | C | C | A | G | A | C | g | g | A | 22 | 3 | 11 | c | false | <90% | 4625 | ||
NM_016151 | TAOK2 | 2903 | 2921 | G | C | C | U | g | C | A | G | C | A | C | C | A | G | A | C | g | g | A | 22 | 3 | 11 | c | false | <90% | 4920 | ||
NM_003215 | TEC | 562 | 580 | a | C | C | U | c | C | A | G | C | A | C | C | A | G | A | a | A | C | A | 20 | 3 | 10 | c | false | <90% | 3620 | ||
NM_003274 | TMEM1 | 2999 | 3017 | c | C | C | U | U | C | A | G | g | A | C | C | A | c | A | C | A | C | A | 18 | 3 | 7 | c | false | <90% | 6982 | ||
NM_001045546 | LOC402715 | 620 | 638 | G | C | C | U | U | C | A | G | g | A | C | C | A | G | A | u | A | C | A | 13 | 2 | 8 | c | false | <90% | 1101 | ||
XR_016682 | LOC653435 | 1481 | 1499 | G | C | C | U | U | C | u | G | C | A | C | C | A | G | c | C | A | C | u | 4 | 3 | 7 | c | false | <90% | 2056 | ||
XR_018628 | LOC654048 | 1481 | 1499 | G | C | C | U | U | C | u | G | C | A | C | C | A | G | c | C | A | C | u | 4 | 3 | 7 | c | false | <90% | 2266 | ||
XM_001134336 | PRAMEF2 | 230 | 248 | G | C | C | U | U | C | A | G | C | A | g | g | A | G | A | C | A | C | u | 0 | 3 | 10 | false | <90% | 973 | |||
XR_017927 | PRAMEF20 | 205 | 223 | G | C | C | U | U | C | A | G | C | A | g | g | A | G | A | C | A | C | u | 0 | 3 | 10 | false | <90% | 1506 | |||
NM_023013 | PRAMEF1 | 230 | 248 | G | C | C | U | U | C | A | G | C | A | g | g | A | G | A | C | A | C | u | 0 | 3 | 10 | false | <90% | 1606 | |||
NM_023014 | PRAMEF2 | 214 | 232 | G | C | C | U | U | C | A | G | C | A | g | g | A | G | A | C | A | C | u | 0 | 3 | 10 | false | <90% | 1642 | |||
XM_937753 | PRDM6 | 2344 | 2362 | a | C | C | U | U | C | A | G | C | c | C | C | A | G | A | C | g | C | A | -8 | 3 | 8 | c | false | <90% | 2668 | ||
XM_927647 | PRDM6 | 2350 | 2368 | a | C | C | U | U | C | A | G | C | c | C | C | A | G | A | C | g | C | A | -8 | 3 | 8 | c | false | <90% | 2674 | ||
NM_138368 | DKFZp761E198 | 280 | 298 | G | C | C | U | U | C | A | G | C | c | C | C | A | G | g | C | A | C | c | -12 | 3 | 9 | c | false | <90% | 4181 | ||
NM_015239 | AGTPBP1 | 181 | 199 | G | C | C | U | U | C | A | G | a | A | u | C | A | G | A | C | A | C | u | -26 | 3 | 8 | c | false | <90% | 4220 |
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_025252 | RAPH1 | 1779 | 1797 | a | u | U | G | U | C | U | G | G | U | G | C | U | G | A | A | G | c | a | 78 | 4 | 15 | ac | false | <90% | 2394 | ||
NM_203365 | RAPH1 | 1779 | 1797 | a | u | U | G | U | C | U | G | G | U | G | C | U | G | A | A | G | c | a | 78 | 4 | 15 | ac | false | <90% | 2782 | ||
NM_213589 | RAPH1 | 1623 | 1641 | a | u | U | G | U | C | U | G | G | U | G | C | U | G | A | A | G | c | a | 78 | 4 | 15 | ac | false | <90% | 9615 | ||
NM_007184 | NISCH | 2467 | 2485 | U | G | U | G | U | C | U | G | G | U | G | C | U | c | A | A | G | G | u | 75 | 2 | 13 | c | false | <90% | 5252 | ||
NM_012260 | HACL1 | 201 | 219 | g | G | U | G | U | C | U | G | G | U | G | C | U | a | A | A | G | u | C | 75 | 3 | 12 | c | false | <90% | 2037 | ||
NM_207645 | LOC399947 | 1845 | 1863 | c | a | g | G | U | C | U | G | G | U | G | C | U | G | A | A | G | u | C | 64 | 4 | 14 | c | false | <90% | 2353 | ||
NM_014780 | CUL7 | 5070 | 5088 | U | c | U | G | U | C | U | G | G | U | G | C | U | G | g | A | G | G | C | 63 | 2 | 12 | c | false | <90% | 5491 | ||
NM_015089 | PARC | 5757 | 5775 | U | u | U | G | U | C | U | G | G | U | G | C | U | G | g | A | G | G | C | 63 | 2 | 12 | c | false | <90% | 7771 | ||
NM_004093 | EFNB2 | 3629 | 3647 | U | G | U | G | U | C | U | G | G | U | G | C | a | G | A | A | u | a | u | 58 | 4 | 12 | false | <90% | 4335 | |||
NM_153461 | IL17RC | 437 | 455 | U | c | U | G | U | C | U | G | G | U | G | C | U | G | A | u | G | G | u | 57 | 3 | 13 | c | false | <90% | 2691 | ||
NM_001012279 | C6orf174 | 447 | 465 | U | G | U | G | g | C | U | G | G | U | G | C | U | G | A | A | G | c | g | 40 | 3 | 12 | c | false | <90% | 3556 | ||
NM_001087 | AAMP | 1409 | 1427 | U | G | U | G | U | C | U | G | G | U | G | u | U | G | A | g | G | G | g | 35 | 3 | 11 | false | <90% | 1859 | |||
NM_014309 | RBM9 | 1869 | 1887 | U | G | U | a | U | C | U | G | G | U | G | C | U | G | A | A | u | G | a | 34 | 3 | 12 | c | false | <90% | 6948 | ||
NM_001082579 | RBM9 | 1875 | 1893 | U | G | U | a | U | C | U | G | G | U | G | C | U | G | A | A | u | G | a | 34 | 3 | 12 | c | false | <90% | 6954 | ||
NM_001082577 | RBM9 | 1878 | 1896 | U | G | U | a | U | C | U | G | G | U | G | C | U | G | A | A | u | G | a | 34 | 3 | 12 | c | false | <90% | 6957 | ||
NM_001082578 | RBM9 | 1878 | 1896 | U | G | U | a | U | C | U | G | G | U | G | C | U | G | A | A | u | G | a | 34 | 3 | 12 | c | false | <90% | 6957 | ||
NM_001082576 | RBM9 | 1906 | 1924 | U | G | U | a | U | C | U | G | G | U | G | C | U | G | A | A | u | G | a | 34 | 3 | 12 | c | false | <90% | 6985 | ||
NM_001031695 | RBM9 | 1918 | 1936 | U | G | U | a | U | C | U | G | G | U | G | C | U | G | A | A | u | G | a | 34 | 3 | 12 | c | false | <90% | 6997 | ||
NM_173492 | PIP5KL1 | 318 | 336 | U | u | g | u | U | C | U | G | G | U | G | C | U | G | A | A | G | G | a | 27 | 4 | 14 | bc | false | <90% | 1131 | ||
NM_004811 | LPXN | 821 | 839 | g | G | U | G | U | u | U | G | G | U | G | C | a | G | A | A | G | G | C | 24 | 3 | 6 | false | <90% | 1875 | |||
NM_053013 | ENO3 | 1081 | 1099 | a | c | U | G | U | C | U | G | c | U | G | C | U | G | A | A | G | G | u | 21 | 4 | 9 | bc | false | <90% | 1452 | ||
NM_001976 | ENO3 | 1123 | 1141 | a | c | U | G | U | C | U | G | c | U | G | C | U | G | A | A | G | G | u | 21 | 4 | 9 | bc | false | <90% | 1494 | ||
NM_001040653 | ZXDC | 4381 | 4399 | U | G | U | G | c | C | U | G | G | U | G | C | U | G | A | A | u | G | g | 20 | 3 | 11 | c | false | <90% | 4888 | ||
NM_002353 | TACSTD2 | 832 | 850 | a | G | U | G | U | C | U | G | c | U | G | C | U | c | A | A | G | G | C | 18 | 3 | 7 | c | false | <90% | 2805 | ||
XM_063871 | LOC123855 | 2080 | 2098 | g | G | U | G | U | C | U | G | G | g | G | C | U | G | A | A | G | u | C | 12 | 3 | 8 | c | false | <90% | 3259 | ||
XM_937998 | LOC123855 | 2080 | 2098 | g | G | U | G | U | C | U | G | G | g | G | C | U | G | A | A | G | u | C | 12 | 3 | 8 | c | false | <90% | 3259 | ||
NM_012291 | ESPL1 | 3177 | 3195 | U | G | U | u | c | C | U | G | G | U | G | C | U | G | A | A | G | G | g | 6 | 3 | 13 | bc | false | <90% | 6641 | ||
NM_003181 | T | 705 | 723 | U | G | U | u | U | C | c | G | G | U | G | C | U | G | A | A | G | G | u | -8 | 3 | 11 | bc | false | <90% | 2518 | ||
NM_024979 | MCF2L | 205 | 223 | U | G | U | G | g | C | U | G | c | U | G | C | U | G | A | A | G | G | C | -11 | 2 | 10 | bc | false | <90% | 3463 | ||
NM_005181 | CA3 | 1303 | 1321 | U | G | U | G | g | C | U | G | c | U | G | C | U | G | A | A | G | G | a | -16 | 3 | 9 | bc | false | <90% | 2357 | ||
NM_001040458 | ARTS-1 | 1019 | 1037 | U | G | U | G | a | C | U | G | u | U | G | C | U | G | A | A | G | G | a | -16 | 3 | 9 | bc | false | <90% | 5085 | ||
NM_016442 | ARTS-1 | 1019 | 1037 | U | G | U | G | a | C | U | G | u | U | G | C | U | G | A | A | G | G | a | -16 | 3 | 9 | bc | false | <90% | 5584 | ||
NM_020440 | PTGFRN | 995 | 1013 | U | G | U | G | U | C | U | G | u | g | G | C | U | G | A | A | G | G | a | -47 | 3 | 8 | bc | false | <90% | 6160 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2361
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)
Motif found in sense strand
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