Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
29 hits were found for GACUGAUGAAGCUCAGCCU (11 guide strand hits and 18 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_015914 | TXNDC11 | 1942 | 1960 | c | A | C | U | G | A | U | G | A | A | G | C | U | C | A | c | C | C | U | 71 | 2 | 14 | c | false | <90% | 3047 | ||
NM_173642 | FAM80A | 549 | 567 | G | A | u | U | G | A | U | G | A | A | G | C | U | g | A | G | C | C | c | 55 | 3 | 10 | c | false | <90% | 1525 | ||
NM_139289 | AKAP4 | 2205 | 2223 | c | u | g | U | G | A | U | G | A | A | G | C | U | C | u | G | C | C | U | 42 | 4 | 11 | c | false | <90% | 2867 | ||
NM_003886 | AKAP4 | 2232 | 2250 | c | u | g | U | G | A | U | G | A | A | G | C | U | C | u | G | C | C | U | 42 | 4 | 11 | c | false | <90% | 2881 | ||
NM_005778 | RBM5 | 1426 | 1444 | G | A | C | U | G | A | g | G | A | A | G | C | a | C | A | G | C | C | U | 23 | 2 | 6 | false | <90% | 3135 | |||
NM_173549 | C8orf47 | 583 | 601 | a | A | a | U | G | c | U | G | A | A | G | C | U | C | A | G | C | C | U | 15 | 3 | 13 | bc | false | <90% | 1550 | ||
XR_017070 | LOC646083 | 379 | 397 | G | A | C | U | G | A | U | G | u | A | G | C | U | C | A | G | g | g | g | 8 | 4 | 8 | c | false | <90% | 1894 | ||
XR_018644 | LOC646083 | 379 | 397 | G | A | C | U | G | A | U | G | u | A | G | C | U | C | A | G | g | g | g | 8 | 4 | 8 | c | false | <90% | 2002 | ||
XM_001132454 | SLCO3A1 | 1228 | 1246 | u | g | g | U | G | A | a | G | A | A | G | C | U | C | A | G | C | C | U | 0 | 4 | 12 | bc | false | <90% | 2522 | ||
NM_013272 | SLCO3A1 | 1419 | 1437 | u | g | g | U | G | A | a | G | A | A | G | C | U | C | A | G | C | C | U | 0 | 4 | 12 | bc | false | <90% | 2740 | ||
XM_001132480 | SLCO3A1 | 1151 | 1169 | u | g | g | U | G | A | a | G | A | A | G | C | U | C | A | G | C | C | U | 0 | 4 | 12 | bc | false | <90% | 4829 |
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_153045 | C9orf91 | 1091 | 1109 | A | G | a | C | U | G | A | G | C | U | U | C | A | U | C | A | G | c | u | 72 | 3 | 14 | c | false | <90% | 3699 | ||
NM_014858 | TMCC2 | 2159 | 2177 | u | G | a | C | U | G | A | G | C | U | U | C | A | U | C | A | G | a | a | 70 | 4 | 14 | c | false | <90% | 3792 | ||
NM_001045 | SLC6A4 | 516 | 534 | u | G | G | C | U | G | A | G | C | U | U | C | A | U | C | A | a | g | g | 66 | 4 | 15 | ac | false | <90% | 2775 | ||
NM_018943 | TUBA8 | 1591 | 1609 | A | c | a | C | U | G | A | G | C | U | U | C | A | U | C | A | G | g | C | 66 | 3 | 14 | c | false | <90% | 2018 | ||
XM_001132853 | C3orf49 | 867 | 885 | A | u | G | C | U | G | A | G | C | U | U | C | A | a | C | A | G | U | g | 64 | 3 | 11 | c | false | <90% | 1045 | ||
XM_001132201 | C3orf49 | 867 | 885 | A | u | G | C | U | G | A | G | C | U | U | C | A | a | C | A | G | U | g | 64 | 3 | 11 | c | false | <90% | 1045 | ||
NM_024805 | C18orf22 | 709 | 727 | u | a | G | C | U | G | A | G | C | U | U | g | A | U | C | A | G | U | u | 47 | 4 | 9 | false | <90% | 1419 | |||
XM_934796 | LOC653566 | 335 | 353 | A | a | G | C | U | G | A | c | C | U | U | C | A | U | C | A | G | U | g | 21 | 3 | 10 | bc | false | <90% | 1202 | ||
XM_944485 | LOC653566 | 335 | 353 | A | a | G | C | U | G | A | c | C | U | U | C | A | U | C | A | G | U | g | 21 | 3 | 10 | bc | false | <90% | 1202 | ||
NM_014752 | SPCS2 | 515 | 533 | A | a | G | C | U | G | A | c | C | U | U | C | A | U | C | A | G | U | g | 21 | 3 | 10 | bc | false | <90% | 1370 | ||
XM_934797 | LOC653566 | 547 | 565 | A | a | G | C | U | G | A | c | C | U | U | C | A | U | C | A | G | U | g | 21 | 3 | 10 | bc | false | <90% | 1414 | ||
XM_944490 | LOC653566 | 547 | 565 | A | a | G | C | U | G | A | c | C | U | U | C | A | U | C | A | G | U | g | 21 | 3 | 10 | bc | false | <90% | 1414 | ||
NM_001080536 | LOC653566 | 564 | 582 | A | a | G | C | U | G | A | c | C | U | U | C | A | U | C | A | G | U | g | 21 | 3 | 10 | bc | false | <90% | 1431 | ||
XM_940181 | LOC653566 | 564 | 582 | A | a | G | C | U | G | A | c | C | U | U | C | A | U | C | A | G | U | g | 21 | 3 | 10 | bc | false | <90% | 1431 | ||
NM_001040432 | ZCWPW2 | 384 | 402 | A | G | u | C | U | c | A | G | C | U | U | C | A | U | C | A | G | U | g | 12 | 3 | 12 | bc | false | <90% | 1752 | ||
XM_001127975 | FAM66C | 642 | 660 | A | G | G | a | U | G | A | a | C | U | U | C | A | U | C | A | G | U | a | -3 | 3 | 10 | bc | false | <90% | 914 | ||
NM_024993 | LRRTM4 | 39 | 57 | g | c | u | C | U | G | A | G | C | a | U | C | A | U | C | A | G | U | C | -15 | 4 | 9 | bc | false | <90% | 3616 | ||
NM_014747 | RIMS3 | 418 | 436 | A | G | G | C | U | c | A | G | a | U | U | C | A | U | C | A | G | U | u | -28 | 3 | 9 | bc | false | <90% | 7233 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1431
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