Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
43 hits were found for CUUCAAGGGAUUCACCUAA (22 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_001003690 | MAD2L1BP | 303 | 321 | g | U | U | C | A | A | G | G | G | A | U | U | C | u | C | C | U | g | c | 70 | 4 | 12 | c | false | <90% | 1550 | ||
NM_001745 | CAMLG | 1822 | 1840 | g | U | U | C | A | A | G | G | G | A | U | U | C | u | C | C | U | g | c | 70 | 4 | 12 | c | false | <90% | 2203 | ||
NM_004696 | SLC16A4 | 1864 | 1882 | g | U | U | C | A | A | G | G | G | A | U | U | C | u | C | C | U | g | c | 70 | 4 | 12 | c | false | <90% | 2529 | ||
NM_001652 | AQP6 | 1845 | 1863 | g | U | U | C | A | A | G | G | G | A | U | U | C | u | C | C | U | g | c | 70 | 4 | 12 | c | false | <90% | 2654 | ||
XM_929714 | LOC646762 | 1139 | 1157 | a | U | U | C | A | A | G | G | G | A | U | U | C | u | C | C | U | g | c | 70 | 4 | 12 | c | false | <90% | 4090 | ||
XM_938418 | LOC646762 | 1139 | 1157 | a | U | U | C | A | A | G | G | G | A | U | U | C | u | C | C | U | g | c | 70 | 4 | 12 | c | false | <90% | 4090 | ||
XM_935722 | LOC646762 | 1139 | 1157 | a | U | U | C | A | A | G | G | G | A | U | U | C | u | C | C | U | g | c | 70 | 4 | 12 | c | false | <90% | 4090 | ||
NM_022753 | S100PBP | 2829 | 2847 | g | U | U | C | A | A | G | G | G | A | U | U | C | u | C | C | U | g | u | 70 | 4 | 12 | c | false | <90% | 4317 | ||
NM_138572 | TBN | 3885 | 3903 | g | U | U | C | A | A | G | G | G | A | U | U | C | u | C | C | U | g | c | 70 | 4 | 12 | c | false | <90% | 4323 | ||
NM_006873 | STON1 | 3861 | 3879 | g | U | U | C | A | A | G | G | G | A | U | U | C | u | C | C | U | g | c | 70 | 4 | 12 | c | false | <90% | 5822 | ||
NM_007054 | KIF3A | 4985 | 5003 | g | U | U | C | A | A | G | G | G | A | U | U | C | u | C | C | U | g | c | 70 | 4 | 12 | c | false | <90% | 6257 | ||
XM_001127140 | LOC728005 | 3921 | 3939 | g | U | U | C | A | A | G | G | G | A | U | U | C | u | C | C | U | g | c | 70 | 4 | 12 | c | false | <90% | 7115 | ||
NM_138764 | BAX | 489 | 507 | g | U | U | C | A | A | G | c | G | A | U | U | C | A | C | C | U | g | c | 28 | 4 | 9 | c | false | <90% | 986 | ||
XR_017973 | C12orf47 | 1622 | 1640 | g | U | U | C | A | A | G | u | G | A | U | U | C | A | C | C | U | c | c | 28 | 4 | 9 | c | false | <90% | 2285 | ||
XR_017874 | C12orf47 | 1622 | 1640 | g | U | U | C | A | A | G | u | G | A | U | U | C | A | C | C | U | c | c | 28 | 4 | 9 | c | false | <90% | 2285 | ||
NM_198460 | GBP6 | 2156 | 2174 | g | U | U | C | A | A | G | a | G | A | U | U | C | A | C | C | U | g | c | 28 | 4 | 9 | c | false | <90% | 3047 | ||
NM_014033 | METTL7A | 1552 | 1570 | g | U | U | C | A | A | G | u | G | A | U | U | C | A | C | C | U | g | c | 28 | 4 | 9 | c | false | <90% | 3390 | ||
NM_022896 | LPIN3 | 3012 | 3030 | g | U | U | C | A | A | G | c | G | A | U | U | C | A | C | C | U | g | c | 28 | 4 | 9 | c | false | <90% | 4464 | ||
NR_003130 | HSP90B3P | 3303 | 3321 | g | U | U | C | A | A | G | c | G | A | U | U | C | A | C | C | U | g | c | 28 | 4 | 9 | c | false | <90% | 8768 | ||
XR_017604 | LOC390218 | 222 | 240 | C | U | U | C | A | A | G | G | c | A | U | U | C | g | C | C | U | A | c | 15 | 3 | 8 | c | false | <90% | 456 | ||
XR_019460 | LOC390218 | 222 | 240 | C | U | U | C | A | A | G | G | c | A | U | U | C | g | C | C | U | A | c | 15 | 3 | 8 | c | false | <90% | 456 | ||
NM_002834 | PTPN11 | 6029 | 6047 | u | U | U | C | A | A | G | a | G | A | U | U | C | A | C | u | U | A | A | 9 | 3 | 7 | c | false | <90% | 6300 |
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_020724 | RNF150 | 3089 | 3107 | U | U | A | G | G | U | G | A | A | U | C | C | C | U | a | G | c | A | G | 51 | 2 | 14 | c | false | <90% | 4661 | ||
NM_000807 | GABRA2 | 1973 | 1991 | c | U | A | G | a | U | G | A | A | U | C | C | u | U | U | G | A | A | G | 36 | 3 | 7 | false | <90% | 2189 | |||
NM_018448 | CAND1 | 1094 | 1112 | a | U | A | G | G | U | G | A | A | U | a | C | C | U | U | G | A | g | a | 29 | 4 | 9 | c | false | <90% | 5387 | ||
NM_012463 | ATP6V0A2 | 869 | 887 | c | U | g | G | a | U | G | A | A | U | C | C | C | U | U | G | A | A | G | 26 | 3 | 14 | bc | false | <90% | 4681 | ||
NM_001040025 | ARL16 | 1088 | 1106 | a | c | A | G | G | a | G | A | A | U | C | C | C | U | U | G | A | A | c | 18 | 4 | 12 | bc | false | <90% | 1207 | ||
XM_001130512 | LOC729518 | 1585 | 1603 | g | c | A | G | G | a | G | A | A | U | C | C | C | U | U | G | A | A | c | 18 | 4 | 12 | bc | false | <90% | 1883 | ||
XM_945225 | LOC144817 | 1374 | 1392 | g | c | A | G | G | a | G | A | A | U | C | C | C | U | U | G | A | A | c | 18 | 4 | 12 | bc | false | <90% | 2036 | ||
XM_934287 | LOC144817 | 1374 | 1392 | g | c | A | G | G | a | G | A | A | U | C | C | C | U | U | G | A | A | c | 18 | 4 | 12 | bc | false | <90% | 2036 | ||
NM_001039145 | WBSCR23 | 2218 | 2236 | g | g | A | G | G | a | G | A | A | U | C | C | C | U | U | G | A | A | c | 18 | 4 | 12 | bc | false | <90% | 2630 | ||
NM_016264 | ZNF44 | 2352 | 2370 | g | c | A | G | G | a | G | A | A | U | C | C | C | U | U | G | A | A | c | 18 | 4 | 12 | bc | false | <90% | 2674 | ||
NM_001001789 | C21orf24 | 3499 | 3517 | a | c | A | G | G | a | G | A | A | U | C | C | C | U | U | G | A | A | c | 18 | 4 | 12 | bc | false | <90% | 3620 | ||
NM_015138 | RTF1 | 3430 | 3448 | a | c | A | G | G | a | G | A | A | U | C | C | C | U | U | G | A | A | c | 18 | 4 | 12 | bc | false | <90% | 5014 | ||
NM_003123 | SPN | 6146 | 6164 | g | c | A | G | G | a | G | A | A | U | C | C | C | U | U | G | A | A | c | 18 | 4 | 12 | bc | false | <90% | 6871 | ||
NM_021615 | CHST6 | 4052 | 4070 | g | c | A | G | G | a | G | A | A | U | C | C | C | U | U | G | A | A | u | 18 | 4 | 12 | bc | false | <90% | 6885 | ||
NM_001030288 | SPN | 6190 | 6208 | g | c | A | G | G | a | G | A | A | U | C | C | C | U | U | G | A | A | c | 18 | 4 | 12 | bc | false | <90% | 6915 | ||
NM_181265 | WDR17 | 5038 | 5056 | g | c | A | G | G | a | G | A | A | U | C | C | C | U | U | G | A | A | c | 18 | 4 | 12 | bc | false | <90% | 7255 | ||
NM_170710 | WDR17 | 5161 | 5179 | g | c | A | G | G | a | G | A | A | U | C | C | C | U | U | G | A | A | c | 18 | 4 | 12 | bc | false | <90% | 7378 | ||
NM_005393 | PLXNB3 | 5393 | 5411 | c | U | g | G | G | U | G | A | A | U | g | C | C | U | U | G | A | A | G | 17 | 3 | 8 | c | false | <90% | 6145 | ||
NM_002737 | PRKCA | 3461 | 3479 | U | U | A | G | c | U | G | A | A | U | C | C | C | U | U | G | c | u | u | 17 | 4 | 11 | c | false | <90% | 8787 | ||
NM_032268 | ZNRF1 | 4163 | 4181 | a | U | A | G | G | U | G | A | A | U | g | C | C | U | U | c | A | A | G | 10 | 3 | 9 | c | false | <90% | 4633 | ||
NM_001010860 | C14orf174 | 663 | 681 | c | U | A | G | G | a | G | A | A | U | C | a | C | U | U | G | A | A | G | 0 | 3 | 7 | false | <90% | 2025 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2129
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