Automatic recommendation
Not OK - siRNA is not specific
36 hits were found for CUGCUAUGCCUCAUCUUCU (14 guide strand hits and 22 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_194286 | KIAA1853 | 7267 | 7285 | a | a | G | C | U | A | U | G | C | C | U | C | A | U | C | U | U | C | U | 86 | 2 | 17 | abc | false | <90% | 8382 | ||
NM_005546 | ITK | 2785 | 2803 | u | g | a | C | U | A | U | G | C | C | U | C | c | U | C | U | U | C | U | 56 | 4 | 9 | false | <90% | 4366 | |||
NM_007256 | SLCO2B1 | 1615 | 1633 | C | U | G | C | U | g | U | G | C | C | U | C | u | U | C | U | U | C | a | 21 | 3 | 6 | false | <90% | 4108 | |||
NM_015999 | ADIPOR1 | 734 | 752 | g | U | G | C | U | c | U | G | C | C | U | C | A | g | C | U | U | C | U | 15 | 3 | 7 | c | false | <90% | 2108 | ||
NM_014849 | SV2A | 1103 | 1121 | a | U | G | C | U | A | g | G | C | C | U | C | A | U | C | g | U | C | U | 5 | 3 | 8 | c | false | <90% | 4066 | ||
NM_001082618 | CD33 | 479 | 497 | u | g | u | C | U | c | U | G | C | C | U | C | A | U | C | U | U | C | U | 3 | 4 | 13 | bc | false | <90% | 1085 | ||
NM_001772 | CD33 | 860 | 878 | u | g | u | C | U | c | U | G | C | C | U | C | A | U | C | U | U | C | U | 3 | 4 | 13 | bc | false | <90% | 1466 | ||
NM_003830 | SIGLEC5 | 1499 | 1517 | u | g | u | C | U | g | U | G | C | C | U | C | A | U | C | U | U | C | U | 3 | 4 | 13 | bc | false | <90% | 2130 | ||
NM_181798 | KCNQ1 | 275 | 293 | C | U | G | g | U | c | U | G | C | C | U | C | A | U | C | U | U | C | a | -5 | 3 | 12 | bc | false | <90% | 3029 | ||
NM_000218 | KCNQ1 | 508 | 526 | C | U | G | g | U | c | U | G | C | C | U | C | A | U | C | U | U | C | a | -5 | 3 | 12 | bc | false | <90% | 3262 | ||
NM_052970 | HSPA12B | 1190 | 1208 | C | U | G | C | U | g | U | G | C | C | g | C | A | U | C | U | U | C | g | -29 | 3 | 7 | c | false | <90% | 3109 | ||
NM_000873 | ICAM2 | 783 | 801 | C | U | G | C | U | c | U | G | C | u | U | C | A | U | C | U | U | C | g | -51 | 3 | 8 | bc | false | <90% | 1035 | ||
NM_005116 | SLC23A2 | 1348 | 1366 | C | U | G | C | U | c | U | G | C | u | U | C | A | U | C | U | U | C | a | -51 | 3 | 8 | bc | false | <90% | 6953 | ||
NM_203327 | SLC23A2 | 1366 | 1384 | C | U | G | C | U | c | U | G | C | u | U | C | A | U | C | U | U | C | a | -51 | 3 | 8 | bc | false | <90% | 6971 |
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_006354 | TADA3L | 1088 | 1106 | A | G | A | A | G | A | U | G | A | G | G | C | u | g | A | G | C | A | u | 65 | 3 | 12 | false | <90% | 2245 | |||
NM_133480 | TADA3L | 1088 | 1106 | A | G | A | A | G | A | U | G | A | G | G | C | u | g | A | G | C | A | u | 65 | 3 | 12 | false | <90% | 2571 | |||
XR_015396 | LOC728853 | 317 | 335 | A | G | A | A | G | A | U | G | A | G | G | C | u | U | c | G | C | A | u | 59 | 3 | 12 | false | <90% | 3334 | |||
XR_015633 | LOC731867 | 317 | 335 | A | G | A | A | G | A | U | G | A | G | G | C | u | U | c | G | C | A | u | 59 | 3 | 12 | false | <90% | 3334 | |||
NM_020850 | RANBP10 | 4926 | 4944 | A | G | A | A | G | A | U | G | A | G | G | C | A | g | A | G | a | A | u | 51 | 3 | 13 | c | false | <90% | 5305 | ||
NM_199296 | THSD3 | 892 | 910 | g | G | A | A | G | A | U | G | A | G | G | a | A | g | A | G | C | A | G | 44 | 3 | 10 | false | <90% | 2942 | |||
NM_199265 | THSD3 | 997 | 1015 | g | G | A | A | G | A | U | G | A | G | G | a | A | g | A | G | C | A | G | 44 | 3 | 10 | false | <90% | 3047 | |||
NM_015250 | BICD2 | 4454 | 4472 | A | G | A | A | a | A | U | G | A | G | G | C | A | g | A | G | C | A | u | 24 | 3 | 8 | c | false | <90% | 4625 | ||
NM_001003800 | BICD2 | 6245 | 6263 | A | G | A | A | a | A | U | G | A | G | G | C | A | g | A | G | C | A | u | 24 | 3 | 8 | c | false | <90% | 6433 | ||
XR_019066 | LOC645901 | 1448 | 1466 | u | G | A | A | G | A | U | G | g | G | G | C | A | U | u | G | C | A | G | 13 | 3 | 7 | c | false | <90% | 1865 | ||
XR_015621 | LOC729668 | 1625 | 1643 | u | G | A | A | G | A | U | G | g | G | G | C | A | U | u | G | C | A | G | 13 | 3 | 7 | c | false | <90% | 2026 | ||
NM_138554 | TLR4 | 422 | 440 | u | G | A | A | G | A | U | G | g | G | G | C | A | U | A | u | C | A | G | 11 | 3 | 7 | c | false | <90% | 5503 | ||
NM_000648 | CCR2 | 1062 | 1080 | A | G | A | A | G | A | a | G | A | G | G | C | A | U | A | G | g | g | c | 2 | 4 | 9 | c | false | <90% | 2492 | ||
NM_000647 | CCR2 | 1062 | 1080 | A | G | A | A | G | A | a | G | A | G | G | C | A | U | A | G | g | g | c | 2 | 4 | 9 | c | false | <90% | 2562 | ||
XM_001133430 | LOC729230 | 1068 | 1086 | A | G | A | A | G | A | a | G | A | G | G | C | A | U | A | G | g | g | c | 2 | 4 | 9 | c | false | <90% | 2568 | ||
XM_001133431 | LOC729230 | 1068 | 1086 | A | G | A | A | G | A | a | G | A | G | G | C | A | U | A | G | g | g | c | 2 | 4 | 9 | c | false | <90% | 2669 | ||
NM_001080435 | WHDC1 | 1177 | 1195 | g | G | A | A | G | A | U | G | A | a | G | C | A | U | A | c | C | A | G | -10 | 3 | 8 | c | false | <90% | 4261 | ||
XM_939866 | WHDC1 | 1177 | 1195 | g | G | A | A | G | A | U | G | A | a | G | C | A | U | A | c | C | A | G | -10 | 3 | 8 | c | false | <90% | 4261 | ||
NM_006603 | STAG2 | 2290 | 2308 | u | G | A | A | G | A | U | G | A | u | G | C | A | U | A | u | C | A | G | -10 | 3 | 8 | c | false | <90% | 6010 | ||
NM_001042751 | STAG2 | 2355 | 2373 | u | G | A | A | G | A | U | G | A | u | G | C | A | U | A | u | C | A | G | -10 | 3 | 8 | c | false | <90% | 6075 | ||
NM_001042750 | STAG2 | 2355 | 2373 | u | G | A | A | G | A | U | G | A | u | G | C | A | U | A | u | C | A | G | -10 | 3 | 8 | c | false | <90% | 6186 | ||
NM_001042749 | STAG2 | 2446 | 2464 | u | G | A | A | G | A | U | G | A | u | G | C | A | U | A | u | C | A | G | -10 | 3 | 8 | c | false | <90% | 6277 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1704
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