Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
21 hits were found for GCAAAGACAUCUGGACAAA (12 guide strand hits and 9 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_144694 | ZNF570 | 631 | 649 | u | C | A | A | A | G | A | C | A | U | C | U | G | u | A | C | A | g | u | 70 | 4 | 12 | c | false | <90% | 2247 | ||
NM_001543 | NDST1 | 2159 | 2177 | a | C | A | A | A | G | A | C | A | U | C | U | G | G | u | C | c | A | A | 49 | 3 | 13 | c | false | <90% | 7913 | ||
NM_001022 | RPS19 | 753 | 771 | a | C | A | A | A | G | A | g | A | U | C | U | G | G | A | C | A | g | A | 33 | 3 | 9 | c | false | <90% | 872 | ||
NM_014743 | KIAA0232 | 2929 | 2947 | u | u | A | A | A | G | A | C | A | U | u | U | G | G | A | C | A | A | A | 25 | 3 | 8 | c | false | <90% | 7840 | ||
NM_005707 | PDCD7 | 1476 | 1494 | G | C | A | A | c | G | A | C | A | U | C | U | G | G | g | C | A | A | c | 18 | 3 | 9 | c | false | <90% | 2866 | ||
NM_001040274 | NO145 | 2037 | 2055 | c | C | A | A | A | G | A | C | u | U | C | U | G | a | A | C | A | A | A | 18 | 3 | 7 | c | false | <90% | 3139 | ||
XM_001127465 | LOC730845 | 160 | 178 | c | C | A | A | A | a | A | C | A | U | C | U | G | a | A | C | A | A | A | 15 | 3 | 7 | c | false | <90% | 426 | ||
NM_030647 | JHDM1D | 445 | 463 | a | C | A | A | A | G | A | u | A | U | C | U | G | G | A | g | A | A | A | 9 | 3 | 7 | c | false | <90% | 9178 | ||
NM_004460 | FAP | 191 | 209 | u | C | A | A | A | a | A | C | A | U | C | U | G | G | A | a | A | A | A | 8 | 3 | 9 | c | false | <90% | 2788 | ||
NM_001039896 | LOC643079 | 2456 | 2474 | u | g | g | A | A | G | A | C | A | U | u | U | G | G | A | C | A | A | A | 5 | 4 | 8 | c | false | <90% | 3029 | ||
NM_199175 | C21orf123 | 845 | 863 | G | C | A | A | A | G | c | C | A | U | C | U | G | G | c | C | A | A | g | 4 | 3 | 7 | c | false | <90% | 2341 | ||
NM_001047 | SRD5A1 | 1561 | 1579 | G | C | A | A | A | G | g | C | A | U | C | U | G | G | A | C | u | u | g | 2 | 4 | 9 | c | false | <90% | 2285 |
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_000935 | PLOD2 | 2189 | 2207 | c | c | U | G | U | C | C | A | G | A | U | G | U | C | U | U | U | u | g | 78 | 4 | 15 | ac | false | <90% | 4009 | ||
NM_182943 | PLOD2 | 2252 | 2270 | c | c | U | G | U | C | C | A | G | A | U | G | U | C | U | U | U | u | g | 78 | 4 | 15 | ac | false | <90% | 4072 | ||
NM_001004752 | OR51F1 | 300 | 318 | a | U | U | G | U | C | C | A | G | A | U | G | U | u | U | U | U | u | C | 75 | 3 | 12 | c | false | <90% | 939 | ||
NM_130847 | AMOTL1 | 1460 | 1478 | U | U | g | G | U | C | C | A | G | A | U | G | c | C | U | U | U | G | C | 70 | 2 | 9 | false | <90% | 8999 | |||
NM_016603 | C5orf5 | 981 | 999 | U | U | g | G | U | C | C | A | G | A | U | G | U | C | U | U | c | c | a | 49 | 4 | 13 | c | false | <90% | 5470 | ||
NM_001010874 | SRD5A2L2 | 1099 | 1117 | a | g | U | a | U | C | C | A | G | A | U | G | U | C | U | U | U | G | u | 44 | 4 | 14 | bc | false | <90% | 3595 | ||
NM_001604 | PAX6 | 1177 | 1195 | a | U | U | a | U | C | C | A | G | A | U | G | U | g | U | U | U | G | C | 41 | 3 | 9 | c | false | <90% | 2781 | ||
NM_000280 | PAX6 | 1212 | 1230 | a | U | U | a | U | C | C | A | G | A | U | G | U | g | U | U | U | G | C | 41 | 3 | 9 | c | false | <90% | 2816 | ||
NM_014109 | ATAD2 | 1430 | 1448 | U | U | U | a | U | C | C | A | G | A | a | G | U | C | U | U | U | G | a | -3 | 3 | 7 | c | false | <90% | 4916 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2144
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