Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
14 hits were found for GUCACCCAAAGCAAGUGAG (8 guide strand hits and 6 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_139045 | SMARCA2 | 1929 | 1947 | a | g | C | A | C | C | C | A | A | A | G | C | A | A | G | U | c | A | G | 63 | 3 | 14 | ac | false | <90% | 5703 | ||
NM_003070 | SMARCA2 | 1929 | 1947 | a | g | C | A | C | C | C | A | A | A | G | C | A | A | G | U | c | A | G | 63 | 3 | 14 | ac | false | <90% | 5758 | ||
NM_194286 | KIAA1853 | 5497 | 5515 | c | U | a | A | C | C | C | A | A | A | G | C | A | A | G | g | G | A | G | 52 | 3 | 12 | c | false | <90% | 8382 | ||
XR_018199 | LOC648160 | 1095 | 1113 | a | U | C | A | C | C | C | A | c | A | G | C | A | A | G | U | G | c | u | 30 | 4 | 8 | c | false | <90% | 1118 | ||
XR_016844 | LOC643309 | 1095 | 1113 | a | U | C | A | C | C | C | A | c | A | G | C | A | A | G | U | G | c | u | 30 | 4 | 8 | c | false | <90% | 1118 | ||
NM_004687 | MTMR4 | 3025 | 3043 | G | U | C | A | u | C | C | A | A | A | G | C | A | A | G | U | c | u | c | 17 | 4 | 11 | c | false | <90% | 5840 | ||
NM_003955 | SOCS3 | 420 | 438 | G | U | C | A | C | C | C | A | c | A | G | C | A | A | G | U | u | u | c | 8 | 4 | 8 | c | false | <90% | 2746 | ||
NM_002663 | PLD2 | 1379 | 1397 | G | U | C | A | C | C | C | A | g | A | c | C | A | A | G | U | G | A | c | -26 | 3 | 8 | c | false | <90% | 3475 |
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_153035 | C1orf83 | 2765 | 2783 | C | U | C | A | C | U | U | G | C | U | U | U | a | G | G | U | c | u | C | 63 | 3 | 12 | false | <90% | 4097 | |||
NM_005828 | WDR68 | 5777 | 5795 | C | U | C | A | C | U | U | G | C | U | U | U | G | G | u | U | c | c | u | 44 | 4 | 14 | c | false | <90% | 6369 | ||
NM_016201 | AMOTL2 | 3211 | 3229 | C | U | C | A | C | U | U | G | C | U | g | U | G | G | G | U | G | A | g | 33 | 2 | 10 | c | false | <90% | 4984 | ||
NM_003326 | TNFSF4 | 2751 | 2769 | C | U | C | A | C | U | c | G | C | U | U | U | G | G | G | U | G | c | a | 26 | 3 | 10 | c | false | <90% | 3510 | ||
NM_000350 | ABCA4 | 989 | 1007 | a | g | g | A | C | U | U | G | C | U | g | U | G | G | G | U | G | A | C | 5 | 4 | 8 | c | false | <90% | 7326 | ||
NM_013255 | MKLN1 | 6162 | 6180 | C | U | C | A | u | U | U | G | u | U | U | U | G | G | G | U | G | A | g | -16 | 3 | 9 | bc | false | <90% | 11157 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1822
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