Automatic recommendation
Not OK - siRNA is not specific
45 hits were found for UCACAGAUGCUGUUGAUUG (36 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_017943 | FBXO34 | 1470 | 1488 | c | C | A | C | A | G | A | U | G | C | U | G | U | U | G | A | U | U | G | 98 | 1 | 18 | abc | false | <90% | 3423 | ||
NM_001903 | CTNNA1 | 1588 | 1606 | U | C | A | C | A | G | A | U | G | C | U | G | U | c | G | A | U | g | a | 72 | 3 | 13 | c | false | <90% | 3778 | ||
NM_000866 | HTR1F | 527 | 545 | U | C | A | C | A | G | A | U | G | C | U | G | U | U | G | A | g | U | a | 71 | 2 | 16 | ac | false | <90% | 2716 | ||
XR_016108 | LOC441768 | 557 | 575 | c | C | A | C | A | G | A | U | G | C | U | G | U | U | G | A | x | x | x | 66 | 4 | 15 | ac | false | <90% | 572 | ||
XR_019199 | LOC441768 | 557 | 575 | c | C | A | C | A | G | A | U | G | C | U | G | U | U | G | A | x | x | x | 66 | 4 | 15 | ac | false | <90% | 572 | ||
NM_001039547 | GK5 | 1186 | 1204 | U | C | A | C | A | G | A | U | G | C | U | G | c | U | G | A | g | a | c | 58 | 4 | 12 | false | <90% | 9834 | |||
NM_016249 | MAGEC2 | 841 | 859 | g | C | A | g | A | G | A | U | G | C | U | G | a | U | G | A | U | U | G | 50 | 3 | 8 | false | <90% | 2021 | |||
NM_004332 | BPHL | 514 | 532 | c | a | A | a | A | G | A | U | G | C | U | G | U | U | G | A | U | U | u | 44 | 4 | 14 | bc | false | <90% | 1521 | ||
NM_002425 | MMP10 | 396 | 414 | c | a | A | g | A | G | A | U | G | C | U | G | U | U | G | A | U | U | c | 44 | 4 | 14 | bc | false | <90% | 1743 | ||
NM_002422 | MMP3 | 442 | 460 | c | a | A | a | A | G | A | U | G | C | U | G | U | U | G | A | U | U | c | 44 | 4 | 14 | bc | false | <90% | 1828 | ||
NM_153189 | SPAM1 | 1754 | 1772 | a | C | A | C | u | G | A | U | G | C | U | G | U | U | G | A | U | g | u | 38 | 4 | 12 | c | false | <90% | 2009 | ||
NM_003117 | SPAM1 | 1748 | 1766 | a | C | A | C | u | G | A | U | G | C | U | G | U | U | G | A | U | g | u | 38 | 4 | 12 | c | false | <90% | 2395 | ||
NM_152609 | C1orf71 | 645 | 663 | U | C | A | C | A | u | A | U | G | C | U | G | U | U | G | A | U | g | a | 29 | 3 | 11 | c | false | <90% | 3608 | ||
NM_031458 | PARP9 | 611 | 629 | c | C | A | C | A | c | A | U | G | C | U | G | U | U | G | A | U | g | c | 27 | 4 | 11 | c | false | <90% | 3243 | ||
NM_199354 | PRB1 | 32 | 50 | U | g | c | a | A | G | A | U | G | C | U | G | U | U | G | A | U | U | c | 27 | 4 | 14 | bc | false | <90% | 714 | ||
NM_199353 | PRB1 | 32 | 50 | U | g | c | a | A | G | A | U | G | C | U | G | U | U | G | A | U | U | c | 27 | 4 | 14 | bc | false | <90% | 774 | ||
NM_005039 | PRB1 | 32 | 50 | U | g | c | a | A | G | A | U | G | C | U | G | U | U | G | A | U | U | c | 27 | 4 | 14 | bc | false | <90% | 1173 | ||
XM_932567 | LOC653247 | 67 | 85 | U | g | c | a | A | G | A | U | G | C | U | G | U | U | G | A | U | U | c | 27 | 4 | 14 | bc | false | <90% | 1260 | ||
XM_001128835 | LOC653247 | 67 | 85 | U | g | c | a | A | G | A | U | G | C | U | G | U | U | G | A | U | U | c | 27 | 4 | 14 | bc | false | <90% | 1260 | ||
XM_933614 | LOC646434 | 336 | 354 | U | a | c | C | A | c | A | U | G | C | U | G | U | U | G | A | U | U | G | 5 | 3 | 13 | bc | false | <90% | 2018 | ||
XR_015330 | LOC728170 | 1272 | 1290 | g | C | A | a | A | c | A | U | G | C | U | G | U | U | G | A | U | U | G | -2 | 3 | 13 | bc | false | <90% | 1336 | ||
XR_016058 | LOC732014 | 1274 | 1292 | g | C | A | a | A | c | A | U | G | C | U | G | U | U | G | A | U | U | G | -2 | 3 | 13 | bc | false | <90% | 1336 | ||
XR_016080 | LOC732259 | 1252 | 1270 | g | C | A | C | c | c | A | U | G | C | U | G | U | U | G | A | U | U | G | -16 | 3 | 13 | bc | false | <90% | 1311 | ||
XR_016093 | LOC730246 | 1252 | 1270 | g | C | A | C | c | c | A | U | G | C | U | G | U | U | G | A | U | U | G | -16 | 3 | 13 | bc | false | <90% | 1311 | ||
XR_016373 | LOC642817 | 1282 | 1300 | g | C | A | C | c | c | A | U | G | C | U | G | U | U | G | A | U | U | G | -16 | 3 | 13 | bc | false | <90% | 1348 | ||
XR_018564 | LOC642817 | 1282 | 1300 | g | C | A | C | c | c | A | U | G | C | U | G | U | U | G | A | U | U | G | -16 | 3 | 13 | bc | false | <90% | 1349 | ||
XM_939887 | HNRPA1P4 | 1125 | 1143 | g | C | A | C | c | c | A | U | G | C | U | G | U | U | G | A | U | U | G | -16 | 3 | 13 | bc | false | <90% | 1574 | ||
XM_372050 | HNRPA1P4 | 1125 | 1143 | g | C | A | C | c | c | A | U | G | C | U | G | U | U | G | A | U | U | G | -16 | 3 | 13 | bc | false | <90% | 1574 | ||
XR_015537 | LOC729423 | 1513 | 1531 | g | C | A | C | c | c | A | U | G | C | U | G | U | U | G | A | U | U | G | -16 | 3 | 13 | bc | false | <90% | 1579 | ||
XR_015853 | LOC732365 | 1513 | 1531 | g | C | A | C | c | c | A | U | G | C | U | G | U | U | G | A | U | U | G | -16 | 3 | 13 | bc | false | <90% | 1579 | ||
XM_928701 | LOC645691 | 1227 | 1245 | g | C | A | C | c | c | A | U | G | C | U | G | U | U | G | A | U | U | G | -16 | 3 | 13 | bc | false | <90% | 1679 | ||
XM_936790 | LOC645691 | 1227 | 1245 | g | C | A | C | c | c | A | U | G | C | U | G | U | U | G | A | U | U | G | -16 | 3 | 13 | bc | false | <90% | 1679 | ||
XR_018923 | LOC648210 | 1299 | 1317 | g | C | A | C | c | u | A | U | G | C | U | G | U | U | G | A | U | U | G | -16 | 3 | 13 | bc | false | <90% | 1753 | ||
XR_017337 | LOC644037 | 1299 | 1317 | g | C | A | C | c | u | A | U | G | C | U | G | U | U | G | A | U | U | G | -16 | 3 | 13 | bc | false | <90% | 1753 | ||
NM_001011725 | LOC144983 | 2164 | 2182 | g | C | A | C | c | c | A | U | G | C | U | G | U | U | G | A | U | U | G | -16 | 3 | 13 | bc | false | <90% | 2224 | ||
NM_001011724 | LOC144983 | 2305 | 2323 | g | C | A | C | c | c | A | U | G | C | U | G | U | U | G | A | U | U | G | -16 | 3 | 13 | bc | false | <90% | 2365 |
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_033518 | SLC38A5 | 1570 | 1588 | g | A | c | U | C | A | A | C | A | G | C | A | g | C | U | G | U | G | A | 68 | 3 | 9 | false | <90% | 2667 | |||
NM_152632 | CXorf22 | 1607 | 1625 | C | u | u | U | C | A | A | C | A | G | C | A | U | C | U | G | U | a | A | 66 | 3 | 14 | c | false | <90% | 3660 | ||
NM_018227 | UBE1L2 | 118 | 136 | a | u | g | U | C | A | A | C | A | G | C | A | U | C | U | G | U | G | g | 62 | 4 | 15 | bc | false | <90% | 5385 | ||
NM_001004754 | OR51I2 | 580 | 598 | g | u | A | U | C | A | A | C | A | G | C | A | U | C | U | a | U | G | g | 55 | 4 | 13 | c | false | <90% | 939 | ||
NM_173452 | FCN3 | 692 | 710 | C | A | A | g | C | A | A | C | A | G | C | A | a | C | U | G | U | G | c | 47 | 3 | 8 | false | <90% | 1026 | |||
NM_003665 | FCN3 | 725 | 743 | C | A | A | g | C | A | A | C | A | G | C | A | a | C | U | G | U | G | c | 47 | 3 | 8 | false | <90% | 1059 | |||
NM_006493 | CLN5 | 2546 | 2564 | C | A | A | U | C | A | c | C | A | G | C | A | U | C | U | G | U | u | u | 26 | 3 | 10 | c | false | <90% | 4080 | ||
NM_012291 | ESPL1 | 1903 | 1921 | g | c | u | U | C | A | A | C | A | u | C | A | U | C | U | G | U | G | A | -15 | 4 | 9 | bc | false | <90% | 6641 | ||
NM_001975 | ENO2 | 1826 | 1844 | g | A | A | U | g | A | u | C | A | G | C | A | U | C | U | G | U | G | A | -19 | 3 | 12 | bc | false | <90% | 2423 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2762
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