Automatic recommendation
Not OK - siRNA is not specific
32 hits were found for GGGCAGUUCUGGGUGAAGU (19 guide strand hits and 13 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_153013 | C5orf33 | 1725 | 1743 | c | a | G | C | A | G | U | U | C | U | G | G | G | U | G | A | A | a | U | 83 | 3 | 15 | ac | false | <90% | 3659 | ||
NM_016321 | RHCG | 443 | 461 | G | G | G | C | A | G | U | U | C | U | G | G | G | U | a | A | A | G | U | 75 | 1 | 14 | c | false | <90% | 1952 | ||
XM_001130634 | LOC651746 | 2146 | 2164 | G | a | G | C | A | G | U | U | C | U | G | G | G | a | G | A | A | G | U | 69 | 2 | 11 | c | false | <90% | 2874 | ||
XM_940961 | LOC651746 | 2293 | 2311 | G | a | G | C | A | G | U | U | C | U | G | G | G | a | G | A | A | G | U | 69 | 2 | 11 | c | false | <90% | 3021 | ||
NM_207412 | FLJ43582 | 907 | 925 | G | a | a | C | A | G | U | U | C | U | G | G | a | U | G | A | A | G | U | 58 | 3 | 9 | false | <90% | 2250 | |||
NM_014738 | KIAA0195 | 4881 | 4899 | c | c | c | C | A | G | U | U | C | U | G | G | G | a | G | A | A | G | U | 47 | 4 | 10 | c | false | <90% | 5001 | ||
NM_004459 | BPTF | 936 | 954 | a | a | G | C | A | G | U | U | C | U | G | c | G | U | G | A | A | G | a | 47 | 4 | 9 | false | <90% | 10863 | |||
NM_182641 | BPTF | 936 | 954 | a | a | G | C | A | G | U | U | C | U | G | c | G | U | G | A | A | G | a | 47 | 4 | 9 | false | <90% | 10914 | |||
NM_173628 | DNAHL1 | 1248 | 1266 | u | G | G | C | A | G | U | U | C | U | G | a | G | a | G | A | A | G | U | 44 | 3 | 10 | false | <90% | 1846 | |||
NM_023085 | CAPN10 | 1079 | 1097 | G | G | G | g | A | G | U | U | C | U | G | G | G | U | G | g | A | G | g | 32 | 3 | 11 | c | false | <90% | 2161 | ||
NM_023083 | CAPN10 | 1079 | 1097 | G | G | G | g | A | G | U | U | C | U | G | G | G | U | G | g | A | G | g | 32 | 3 | 11 | c | false | <90% | 2626 | ||
NM_032872 | SYTL1 | 1401 | 1419 | c | u | G | C | A | c | U | U | C | U | G | G | G | U | G | A | A | G | g | 18 | 4 | 12 | bc | false | <90% | 1898 | ||
NM_024095 | ASB8 | 1064 | 1082 | a | G | G | C | A | G | c | U | C | U | G | G | G | U | G | A | g | G | U | 8 | 3 | 9 | c | false | <90% | 2629 | ||
NM_014759 | PHYHIP | 2386 | 2404 | G | G | G | g | A | G | U | U | C | U | u | G | G | U | G | A | A | G | U | 1 | 2 | 8 | c | false | <90% | 2964 | ||
XM_927433 | LOC644253 | 829 | 847 | G | a | c | C | A | G | U | U | C | c | G | G | G | U | G | A | A | G | U | -13 | 3 | 9 | bc | false | <90% | 1272 | ||
XM_927372 | LOC644172 | 859 | 877 | G | a | c | C | A | G | U | U | C | c | G | G | G | U | G | A | A | G | U | -13 | 3 | 9 | bc | false | <90% | 1302 | ||
NM_005456 | MAPK8IP1 | 1863 | 1881 | G | a | c | C | A | G | U | U | C | c | G | G | G | U | G | A | A | G | U | -13 | 3 | 9 | bc | false | <90% | 3079 | ||
NM_058229 | FBXO32 | 226 | 244 | G | G | G | C | A | G | a | a | C | U | G | G | G | U | G | A | A | G | a | -33 | 3 | 10 | bc | false | <90% | 1530 | ||
NM_005422 | TECTA | 3799 | 3817 | G | G | G | C | A | G | a | g | C | U | G | G | G | U | G | A | A | G | a | -33 | 3 | 10 | bc | false | <90% | 6468 |
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_003280 | TNNC1 | 522 | 540 | c | C | U | U | C | A | C | C | C | A | G | A | g | C | U | G | C | C | u | 82 | 3 | 11 | false | <90% | 686 | |||
NM_172364 | CACNA2D4 | 2255 | 2273 | g | C | U | U | C | A | C | C | C | A | G | A | c | C | U | G | g | C | C | 64 | 3 | 11 | false | <90% | 5343 | |||
XM_166571 | KIAA0363 | 983 | 1001 | c | u | g | U | C | A | C | C | C | A | G | A | g | C | U | G | C | C | C | 56 | 4 | 9 | false | <90% | 5351 | |||
XM_001133202 | KIAA0363 | 1172 | 1190 | c | u | g | U | C | A | C | C | C | A | G | A | g | C | U | G | C | C | C | 56 | 4 | 9 | false | <90% | 5420 | |||
XM_001126176 | KIAA0363 | 1172 | 1190 | c | u | g | U | C | A | C | C | C | A | G | A | g | C | U | G | C | C | C | 56 | 4 | 9 | false | <90% | 5420 | |||
NM_017871 | CPSF3L | 207 | 225 | A | C | a | U | C | A | C | C | C | A | G | A | A | C | g | G | C | C | g | 50 | 3 | 11 | c | false | <90% | 2147 | ||
NM_005817 | M6PRBP1 | 2211 | 2229 | A | C | U | U | C | A | C | C | C | A | c | A | A | C | U | G | C | a | u | 31 | 3 | 10 | c | false | <90% | 2241 | ||
NM_152437 | ZNF664 | 3424 | 3442 | u | C | U | U | C | A | u | C | C | A | G | A | A | u | U | G | C | C | C | 12 | 3 | 6 | c | false | <90% | 5125 | ||
NM_018071 | FLJ10357 | 630 | 648 | A | C | U | g | C | c | C | C | C | A | G | A | A | C | U | G | C | C | C | 0 | 2 | 13 | bc | false | <90% | 5458 | ||
NM_000915 | OXT | 97 | 115 | g | C | U | a | C | A | u | C | C | A | G | A | A | C | U | G | C | C | C | -5 | 3 | 12 | bc | false | <90% | 512 | ||
NM_000347 | SPTB | 3887 | 3905 | A | C | U | U | C | c | u | C | C | A | G | A | A | C | U | G | C | C | a | -34 | 3 | 11 | bc | false | <90% | 6695 | ||
NM_001024858 | SPTB | 3887 | 3905 | A | C | U | U | C | c | u | C | C | A | G | A | A | C | U | G | C | C | a | -34 | 3 | 11 | bc | false | <90% | 10064 | ||
NM_173687 | C8orf31 | 256 | 274 | c | C | U | U | C | A | a | C | C | u | G | A | A | C | U | G | C | C | C | -51 | 3 | 9 | bc | false | <90% | 1875 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2043
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