Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
17 hits were found for CCAAGUGUUUGCUGACGCA (6 guide strand hits and 11 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_147233 | NCOA1 | 4425 | 4443 | u | C | A | g | G | U | G | U | U | U | G | C | U | G | A | C | G | u | c | 53 | 4 | 13 | c | false | <90% | 6892 | ||
NM_003743 | NCOA1 | 4428 | 4446 | u | C | A | g | G | U | G | U | U | U | G | C | U | G | A | C | G | u | c | 53 | 4 | 13 | c | false | <90% | 6895 | ||
NM_147223 | NCOA1 | 4485 | 4503 | u | C | A | g | G | U | G | U | U | U | G | C | U | G | A | C | G | u | c | 53 | 4 | 13 | c | false | <90% | 6952 | ||
NM_001858 | COL19A1 | 7676 | 7694 | a | C | A | A | G | U | G | U | U | U | a | C | U | G | u | C | G | C | A | 11 | 3 | 9 | c | false | <90% | 8725 | ||
NM_023915 | GPR87 | 311 | 329 | C | C | A | A | G | U | G | U | U | U | c | C | U | G | A | C | a | C | g | 10 | 3 | 10 | c | false | <90% | 1498 | ||
NM_014709 | USP34 | 9760 | 9778 | u | C | A | A | G | U | G | U | U | U | u | C | U | G | A | a | G | C | A | 10 | 3 | 9 | c | false | <90% | 11326 |
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_023927 | GRAMD3 | 1802 | 1820 | g | G | C | G | U | C | A | G | C | A | A | A | C | A | C | U | c | c | a | 66 | 4 | 15 | ac | false | <90% | 2912 | ||
NM_001012642 | GRAMD2 | 1351 | 1369 | a | G | C | u | U | C | A | G | C | A | A | A | C | A | C | U | U | a | G | 58 | 3 | 13 | c | false | <90% | 3280 | ||
XR_018074 | LOC442192 | 556 | 574 | c | a | g | G | U | C | A | G | C | A | A | A | C | A | C | a | U | G | G | 40 | 4 | 12 | c | false | <90% | 1436 | ||
XR_019261 | LOC442192 | 556 | 574 | c | a | g | G | U | C | A | G | C | A | A | A | C | A | C | a | U | G | G | 40 | 4 | 12 | c | false | <90% | 1436 | ||
XR_017267 | LOC442192 | 556 | 574 | c | a | g | G | U | C | A | G | C | A | A | A | C | A | C | a | U | G | G | 40 | 4 | 12 | c | false | <90% | 1436 | ||
NM_020365 | EIF2B3 | 1167 | 1185 | a | u | u | G | U | C | A | G | C | A | A | A | C | A | C | c | U | G | G | 40 | 4 | 12 | c | false | <90% | 1659 | ||
NM_004397 | DDX6 | 893 | 911 | c | a | g | G | U | C | A | G | C | A | A | A | C | A | C | a | U | G | G | 40 | 4 | 12 | c | false | <90% | 4180 | ||
NM_152795 | HIF3A | 367 | 385 | a | a | u | G | U | C | A | G | C | A | A | A | C | A | C | c | U | G | G | 40 | 4 | 12 | c | false | <90% | 5850 | ||
NM_152794 | HIF3A | 381 | 399 | a | a | u | G | U | C | A | G | C | A | A | A | C | A | C | c | U | G | G | 40 | 4 | 12 | c | false | <90% | 5864 | ||
NM_022462 | HIF3A | 425 | 443 | a | a | u | G | U | C | A | G | C | A | A | A | C | A | C | c | U | G | G | 40 | 4 | 12 | c | false | <90% | 5908 | ||
NR_002807 | TMED10P | 537 | 555 | U | G | a | G | U | C | A | a | C | A | A | A | C | A | C | U | U | G | G | 18 | 2 | 11 | bc | false | <90% | 1295 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2257
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