Automatic recommendation
Not OK - siRNA is not specific
54 hits were found for UCCUGCUGCUAUGCCUCAU (26 guide strand hits and 28 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_003711 | PPAP2A | 1381 | 1399 | U | g | C | U | G | C | U | G | C | U | A | U | G | C | C | U | C | u | U | 85 | 2 | 15 | ac | false | <90% | 1638 | ||
NM_176895 | PPAP2A | 1384 | 1402 | U | g | C | U | G | C | U | G | C | U | A | U | G | C | C | U | C | u | U | 85 | 2 | 15 | ac | false | <90% | 1641 | ||
NM_005823 | MSLN | 413 | 431 | a | C | C | U | G | C | U | G | C | U | A | U | u | C | C | U | C | A | a | 82 | 3 | 11 | false | <90% | 2052 | |||
NM_013404 | MSLN | 413 | 431 | a | C | C | U | G | C | U | G | C | U | A | U | u | C | C | U | C | A | a | 82 | 3 | 11 | false | <90% | 2076 | |||
NM_006702 | PNPLA6 | 4343 | 4361 | U | C | C | U | G | C | U | G | C | U | A | U | G | C | C | U | g | u | g | 68 | 3 | 16 | ac | false | <90% | 4466 | ||
NM_016306 | DNAJB11 | 252 | 270 | U | g | u | U | G | C | U | G | C | U | A | U | a | C | C | U | C | A | U | 58 | 3 | 9 | false | <90% | 1723 | |||
NM_198578 | LRRK2 | 3612 | 3630 | U | C | u | U | G | C | U | G | C | U | A | U | G | C | C | U | u | u | c | 49 | 4 | 13 | c | false | <90% | 9234 | ||
NM_181340 | WDR21A | 797 | 815 | a | C | a | U | u | C | U | G | C | U | A | U | G | C | C | U | C | A | U | 26 | 3 | 14 | bc | false | <90% | 2461 | ||
NM_015604 | WDR21A | 897 | 915 | a | C | a | U | u | C | U | G | C | U | A | U | G | C | C | U | C | A | U | 26 | 3 | 14 | bc | false | <90% | 2563 | ||
NM_020468 | SNX14 | 291 | 309 | U | C | C | U | G | C | U | G | C | U | c | U | G | u | C | U | C | A | g | 14 | 3 | 10 | c | false | <90% | 3350 | ||
NM_153816 | SNX14 | 291 | 309 | U | C | C | U | G | C | U | G | C | U | c | U | G | u | C | U | C | A | g | 14 | 3 | 10 | c | false | <90% | 3509 | ||
NM_012129 | CLDN12 | 490 | 508 | c | C | C | U | G | C | U | G | C | U | c | U | G | C | C | U | g | A | U | 13 | 3 | 9 | c | false | <90% | 3493 | ||
NM_001042559 | EIF4G2 | 1431 | 1449 | U | C | C | U | G | C | U | c | C | U | A | U | G | g | C | U | C | A | a | 13 | 3 | 7 | c | false | <90% | 3797 | ||
NM_001418 | EIF4G2 | 1431 | 1449 | U | C | C | U | G | C | U | c | C | U | A | U | G | g | C | U | C | A | a | 13 | 3 | 7 | c | false | <90% | 3911 | ||
NM_002858 | ABCD3 | 83 | 101 | U | C | C | U | G | C | U | G | C | U | c | U | G | C | C | U | g | c | U | 12 | 3 | 10 | c | false | <90% | 3423 | ||
XM_941211 | NBEAL2 | 753 | 771 | U | C | C | U | G | C | U | G | C | U | u | U | G | C | C | c | C | A | g | 7 | 3 | 10 | c | false | <90% | 8887 | ||
XM_291064 | NBEAL2 | 753 | 771 | U | C | C | U | G | C | U | G | C | U | u | U | G | C | C | c | C | A | g | 7 | 3 | 10 | c | false | <90% | 8887 | ||
NM_023038 | ADAM19 | 1388 | 1406 | c | C | C | U | G | C | U | G | C | a | A | U | G | C | C | U | C | u | a | 7 | 4 | 8 | c | false | <90% | 3127 | ||
NM_033274 | ADAM19 | 1385 | 1403 | c | C | C | U | G | C | U | G | C | a | A | U | G | C | C | U | C | u | a | 7 | 4 | 8 | c | false | <90% | 6466 | ||
NM_175734 | C17orf74 | 156 | 174 | U | C | C | U | G | C | U | G | C | U | g | g | G | C | C | U | C | A | U | 4 | 2 | 10 | false | <90% | 1662 | |||
NM_012447 | STAG3 | 2935 | 2953 | U | C | C | U | G | C | U | G | C | U | g | a | G | C | C | U | C | A | a | 0 | 3 | 10 | false | <90% | 4285 | |||
NM_174936 | PCSK9 | 2086 | 2104 | U | C | C | U | G | C | U | G | C | c | A | U | G | C | C | c | C | A | g | -13 | 3 | 9 | c | false | <90% | 3636 | ||
NM_001013646 | C20orf107 | 122 | 140 | U | C | C | U | G | C | U | u | C | U | g | U | G | C | C | U | C | A | c | -28 | 3 | 7 | c | false | <90% | 694 | ||
NM_001012971 | C20orf106 | 343 | 361 | U | C | C | U | G | C | U | u | C | U | g | U | G | C | C | U | C | A | c | -28 | 3 | 7 | c | false | <90% | 905 | ||
NM_005443 | PAPSS1 | 1653 | 1671 | c | C | C | U | G | C | U | G | g | c | A | U | G | C | C | U | C | A | U | -44 | 3 | 9 | bc | false | <90% | 2558 | ||
NM_001991 | EZH1 | 1233 | 1251 | U | C | C | U | G | C | U | c | C | a | A | U | G | C | C | U | C | A | g | -49 | 3 | 8 | bc | false | <90% | 4640 |
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_138572 | TBN | 1637 | 1655 | g | U | G | g | G | G | C | A | U | A | G | C | A | G | C | A | G | c | c | 53 | 4 | 13 | c | false | <90% | 4323 | ||
NM_002283 | KRT85 | 1224 | 1242 | c | U | G | A | G | G | C | A | g | A | G | C | A | G | C | A | G | G | g | 32 | 3 | 9 | bc | false | <90% | 2491 | ||
NM_033033 | KRT82 | 1210 | 1228 | c | U | G | A | G | G | C | A | g | A | G | C | A | G | C | A | G | G | g | 32 | 3 | 9 | bc | false | <90% | 2681 | ||
NM_014728 | FRMPD4 | 4714 | 4732 | c | U | G | A | G | a | C | A | U | A | G | C | A | G | C | A | G | u | A | 32 | 3 | 11 | c | false | <90% | 6352 | ||
NM_033020 | TRIM33 | 5509 | 5527 | g | U | G | A | G | G | a | A | U | A | G | C | A | G | C | A | G | u | A | 29 | 3 | 10 | c | false | <90% | 8288 | ||
NM_015906 | TRIM33 | 5560 | 5578 | g | U | G | A | G | G | a | A | U | A | G | C | A | G | C | A | G | u | A | 29 | 3 | 10 | c | false | <90% | 8339 | ||
NM_012109 | TMEM59L | 425 | 443 | A | g | G | A | G | G | C | A | g | A | G | C | A | G | C | A | G | G | c | 23 | 3 | 9 | bc | false | <90% | 1712 | ||
NM_133452 | RAVER1 | 958 | 976 | A | g | G | A | G | G | C | A | c | A | G | C | A | G | C | A | G | G | c | 23 | 3 | 9 | bc | false | <90% | 3606 | ||
NM_032498 | PEPP-2 | 347 | 365 | g | c | a | A | G | G | C | A | c | A | G | C | A | G | C | A | G | G | A | 6 | 4 | 10 | bc | false | <90% | 1297 | ||
XM_001126279 | LOC727940 | 347 | 365 | g | c | a | A | G | G | C | A | c | A | G | C | A | G | C | A | G | G | A | 6 | 4 | 10 | bc | false | <90% | 1309 | ||
NM_006778 | TRIM10 | 57 | 75 | g | g | a | A | G | c | C | A | U | A | G | C | A | G | C | A | G | G | A | 3 | 4 | 13 | bc | false | <90% | 2004 | ||
NM_052828 | TRIM10 | 57 | 75 | g | g | a | A | G | c | C | A | U | A | G | C | A | G | C | A | G | G | A | 3 | 4 | 13 | bc | false | <90% | 3033 | ||
NM_007372 | DDX42 | 158 | 176 | u | g | c | A | G | c | C | A | U | A | G | C | A | G | C | A | G | G | A | 3 | 4 | 13 | bc | false | <90% | 4014 | ||
XM_001129865 | LOC729294 | 1975 | 1993 | g | U | G | u | G | G | C | A | c | A | G | C | A | G | C | A | G | G | A | 1 | 3 | 10 | bc | false | <90% | 2469 | ||
XM_001129875 | LOC729297 | 1858 | 1876 | g | U | G | u | G | G | C | A | c | A | G | C | A | G | C | A | G | G | A | 1 | 3 | 10 | bc | false | <90% | 2718 | ||
XM_001127087 | FLJ43950 | 3774 | 3792 | g | U | G | u | G | G | C | A | c | A | G | C | A | G | C | A | G | G | A | 1 | 3 | 10 | bc | false | <90% | 4762 | ||
XM_294521 | FLJ43950 | 3853 | 3871 | g | U | G | u | G | G | C | A | c | A | G | C | A | G | C | A | G | G | A | 1 | 3 | 10 | bc | false | <90% | 4789 | ||
XR_015253 | FLJ43859 | 3880 | 3898 | g | U | G | u | G | G | C | A | c | A | G | C | A | G | C | A | G | G | A | 1 | 3 | 10 | bc | false | <90% | 4871 | ||
NM_020986 | CHAT | 1181 | 1199 | g | U | G | A | c | G | C | A | g | A | G | C | A | G | C | A | G | G | A | -13 | 3 | 10 | bc | false | <90% | 2103 | ||
NM_020984 | CHAT | 1202 | 1220 | g | U | G | A | c | G | C | A | g | A | G | C | A | G | C | A | G | G | A | -13 | 3 | 10 | bc | false | <90% | 2124 | ||
NM_020985 | CHAT | 1364 | 1382 | g | U | G | A | c | G | C | A | g | A | G | C | A | G | C | A | G | G | A | -13 | 3 | 10 | bc | false | <90% | 2286 | ||
NM_020549 | CHAT | 1563 | 1581 | g | U | G | A | c | G | C | A | g | A | G | C | A | G | C | A | G | G | A | -13 | 3 | 10 | bc | false | <90% | 2485 | ||
NM_014426 | SNX5 | 1104 | 1122 | c | U | G | A | G | G | C | A | c | A | c | C | A | G | C | A | G | G | A | -23 | 3 | 8 | c | false | <90% | 2058 | ||
NM_152227 | SNX5 | 1198 | 1216 | c | U | G | A | G | G | C | A | c | A | c | C | A | G | C | A | G | G | A | -23 | 3 | 8 | c | false | <90% | 2154 | ||
XM_938203 | C1orf167 | 3359 | 3377 | A | U | G | A | G | G | C | c | c | A | G | C | A | G | C | A | G | G | c | -27 | 3 | 9 | bc | false | <90% | 5515 | ||
XM_209234 | C1orf167 | 3359 | 3377 | A | U | G | A | G | G | C | c | c | A | G | C | A | G | C | A | G | G | c | -27 | 3 | 9 | bc | false | <90% | 5515 | ||
NM_152753 | SCUBE3 | 3672 | 3690 | A | U | G | A | G | G | a | A | g | A | G | C | A | G | C | A | G | G | c | -31 | 3 | 9 | bc | false | <90% | 5115 | ||
NM_005895 | GOLGA3 | 2696 | 2714 | u | U | G | A | G | G | C | u | U | u | G | C | A | G | C | A | G | G | A | -46 | 3 | 9 | bc | false | <90% | 9252 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3711
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