Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
60 hits were found for GGGAAAUGCAGAGAUAAAA (40 guide strand hits and 20 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_004745 | DLGAP2 | 8163 | 8181 | u | G | G | A | A | A | U | G | C | A | G | A | a | A | U | A | A | c | u | 79 | 4 | 11 | false | <90% | 10101 | |||
XM_939082 | LOC338805 | 261 | 279 | u | G | a | A | A | A | U | G | C | A | G | A | G | A | U | A | A | c | A | 75 | 3 | 14 | c | false | <90% | 387 | ||
XM_927967 | LOC338805 | 261 | 279 | u | G | a | A | A | A | U | G | C | A | G | A | G | A | U | A | A | c | A | 75 | 3 | 14 | c | false | <90% | 387 | ||
XR_016561 | LOC399950 | 303 | 321 | u | G | a | A | A | A | U | G | C | A | G | A | G | A | U | A | A | c | A | 75 | 3 | 14 | c | false | <90% | 1082 | ||
XR_018475 | LOC649058 | 303 | 321 | u | G | a | A | A | A | U | G | C | A | G | A | G | A | U | A | A | c | A | 75 | 3 | 14 | c | false | <90% | 1087 | ||
XR_017370 | LOC344328 | 302 | 320 | u | G | a | A | A | A | U | G | C | A | G | A | G | A | U | A | A | c | A | 75 | 3 | 14 | c | false | <90% | 1109 | ||
XR_019373 | LOC344328 | 302 | 320 | u | G | a | A | A | A | U | G | C | A | G | A | G | A | U | A | A | c | A | 75 | 3 | 14 | c | false | <90% | 1109 | ||
XR_015215 | LOC728162 | 288 | 306 | u | G | a | A | A | A | U | G | C | A | G | A | G | A | U | A | A | c | A | 75 | 3 | 14 | c | false | <90% | 1470 | ||
XR_018201 | LOC390244 | 288 | 306 | u | G | a | A | A | A | U | G | C | A | G | A | G | A | U | A | A | c | A | 75 | 3 | 14 | c | false | <90% | 1787 | ||
XR_018600 | LOC442621 | 389 | 407 | u | G | a | A | A | A | U | G | C | A | G | A | G | A | U | A | A | c | g | 70 | 4 | 14 | c | false | <90% | 974 | ||
XR_016071 | LOC729992 | 394 | 412 | u | G | a | A | A | A | U | G | C | A | G | A | G | A | U | A | A | c | g | 70 | 4 | 14 | c | false | <90% | 979 | ||
NM_005385 | NKTR | 1247 | 1265 | a | G | G | A | A | A | U | G | C | A | G | A | G | A | U | u | A | A | g | 66 | 3 | 14 | c | false | <90% | 7312 | ||
NM_017941 | C17orf80 | 1044 | 1062 | a | G | G | A | A | A | U | G | C | A | G | A | G | A | a | A | A | g | u | 65 | 4 | 13 | c | false | <90% | 2144 | ||
NM_001080450 | KIAA1553 | 3976 | 3994 | u | u | a | A | A | A | U | G | C | A | G | A | G | A | U | A | A | c | A | 64 | 4 | 14 | c | false | <90% | 6010 | ||
XM_939663 | KIAA1553 | 3976 | 3994 | u | u | a | A | A | A | U | G | C | A | G | A | G | A | U | A | A | c | A | 64 | 4 | 14 | c | false | <90% | 6011 | ||
XR_018116 | LOC642218 | 859 | 877 | a | a | G | A | A | A | U | G | C | A | G | A | G | A | U | g | A | A | A | 60 | 3 | 13 | c | false | <90% | 916 | ||
NM_001987 | ETV6 | 3748 | 3766 | c | u | G | A | A | A | U | G | C | A | G | A | G | A | U | u | A | A | g | 55 | 4 | 13 | c | false | <90% | 5992 | ||
NM_001024855 | ZNF197 | 1732 | 1750 | G | G | G | A | A | A | U | G | C | A | G | A | G | u | a | A | A | A | u | 50 | 3 | 13 | c | false | <90% | 2965 | ||
NM_033401 | CNTNAP4 | 3302 | 3320 | G | G | G | A | A | A | U | G | C | A | G | A | G | A | a | A | g | A | c | 46 | 3 | 14 | c | false | <90% | 4867 | ||
NM_000230 | LEP | 2744 | 2762 | u | G | G | A | g | A | U | G | C | A | G | A | G | g | U | A | A | A | A | 27 | 3 | 8 | c | false | <90% | 3426 | ||
NR_003255 | TSIX | 13310 | 13328 | G | G | G | A | A | A | U | G | g | A | G | A | a | A | U | A | A | A | g | 24 | 3 | 8 | false | <90% | 36861 | |||
XM_001132801 | LOC728741 | 76 | 94 | G | G | G | A | A | g | U | G | C | A | G | A | c | A | U | A | A | A | g | 21 | 3 | 6 | false | <90% | 1899 | |||
XM_001134445 | LOC339047 | 1937 | 1955 | G | G | G | A | A | g | U | G | C | A | G | A | c | A | U | A | A | A | g | 21 | 3 | 6 | false | <90% | 3655 | |||
XR_016512 | LOC642778 | 1950 | 1968 | G | G | G | A | A | g | U | G | C | A | G | A | c | A | U | A | A | A | g | 21 | 3 | 6 | false | <90% | 3666 | |||
XR_016550 | LOC642799 | 1950 | 1968 | G | G | G | A | A | g | U | G | C | A | G | A | c | A | U | A | A | A | g | 21 | 3 | 6 | false | <90% | 3666 | |||
XM_933869 | LOC23117 | 2240 | 2258 | G | G | G | A | A | g | U | G | C | A | G | A | c | A | U | A | A | A | g | 21 | 3 | 6 | false | <90% | 4880 | |||
XR_015889 | LOC728888 | 2239 | 2257 | G | G | G | A | A | g | U | G | C | A | G | A | c | A | U | A | A | A | g | 21 | 3 | 6 | false | <90% | 6489 | |||
XM_001128059 | LOC653355 | 70 | 88 | G | G | G | A | g | A | U | G | C | A | G | A | G | A | g | A | A | A | c | 18 | 3 | 9 | c | false | <90% | 1164 | ||
XM_001128489 | LOC728577 | 3149 | 3167 | G | G | G | A | g | A | U | G | C | A | G | A | G | A | g | A | A | A | c | 18 | 3 | 9 | c | false | <90% | 5222 | ||
NM_033655 | CNTNAP3 | 3156 | 3174 | G | G | G | A | g | A | U | G | C | A | G | A | G | A | g | A | A | A | c | 18 | 3 | 9 | c | false | <90% | 5229 | ||
NM_012113 | CA14 | 166 | 184 | a | a | G | A | A | A | a | G | C | A | G | A | G | A | U | A | A | A | u | 15 | 4 | 11 | bc | false | <90% | 1757 | ||
NM_022487 | DCLRE1C | 1842 | 1860 | u | u | G | A | A | A | a | G | C | A | G | A | G | A | U | A | A | A | g | 15 | 4 | 11 | bc | false | <90% | 3645 | ||
NM_001033855 | DCLRE1C | 1898 | 1916 | u | u | G | A | A | A | a | G | C | A | G | A | G | A | U | A | A | A | g | 15 | 4 | 11 | bc | false | <90% | 3701 | ||
NM_001033857 | DCLRE1C | 1983 | 2001 | u | u | G | A | A | A | a | G | C | A | G | A | G | A | U | A | A | A | g | 15 | 4 | 11 | bc | false | <90% | 3786 | ||
NM_001033858 | DCLRE1C | 2305 | 2323 | u | u | G | A | A | A | a | G | C | A | G | A | G | A | U | A | A | A | g | 15 | 4 | 11 | bc | false | <90% | 4108 | ||
NM_181706 | DPH4 | 323 | 341 | a | G | G | A | A | A | U | G | a | A | G | A | G | A | c | A | A | A | A | 13 | 3 | 7 | c | false | <90% | 3000 | ||
NR_001575 | RNF138P1 | 5002 | 5020 | a | G | G | A | A | A | U | a | C | A | G | A | G | A | g | A | A | A | A | 11 | 3 | 6 | c | false | <90% | 5701 | ||
NM_173538 | CNBD1 | 939 | 957 | G | G | G | A | u | A | U | G | C | A | a | A | G | A | U | A | A | A | g | -17 | 3 | 7 | c | false | <90% | 1593 | ||
NM_004847 | AIF1 | 202 | 220 | a | G | G | A | A | c | a | G | C | A | G | A | G | A | U | A | A | A | A | -31 | 3 | 12 | bc | false | <90% | 1363 | ||
NM_017637 | BNC2 | 5300 | 5318 | G | G | G | A | A | A | a | G | a | A | G | A | G | A | U | A | A | A | c | -31 | 3 | 9 | bc | false | <90% | 12926 |
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_182948 | PRKACB | 2785 | 2803 | U | U | U | U | A | U | C | U | C | U | G | C | g | U | U | U | C | a | g | 81 | 3 | 12 | false | <90% | 4499 | |||
NM_002731 | PRKACB | 2815 | 2833 | U | U | U | U | A | U | C | U | C | U | G | C | g | U | U | U | C | a | g | 81 | 3 | 12 | false | <90% | 4529 | |||
NM_006011 | ST8SIA2 | 3063 | 3081 | a | U | a | U | A | U | C | U | C | U | G | C | A | U | U | U | u | C | C | 54 | 3 | 13 | c | false | <90% | 5626 | ||
NM_014955 | KIAA0859 | 489 | 507 | c | g | c | U | A | U | C | U | C | U | G | C | A | U | c | U | C | C | C | 42 | 4 | 11 | c | false | <90% | 3096 | ||
NM_015935 | KIAA0859 | 814 | 832 | c | g | c | U | A | U | C | U | C | U | G | C | A | U | c | U | C | C | C | 42 | 4 | 11 | c | false | <90% | 3421 | ||
NM_024875 | SYNPO2L | 2503 | 2521 | c | U | U | U | g | U | C | U | C | U | G | C | A | U | U | U | C | C | u | 41 | 3 | 13 | bc | false | <90% | 3470 | ||
NM_183004 | EIF5 | 2296 | 2314 | U | U | U | U | A | U | C | U | C | U | G | u | A | g | U | U | C | C | u | 41 | 3 | 11 | false | <90% | 5782 | |||
NM_001969 | EIF5 | 2323 | 2341 | U | U | U | U | A | U | C | U | C | U | G | u | A | g | U | U | C | C | u | 41 | 3 | 11 | false | <90% | 5809 | |||
NM_174902 | LDLRAD3 | 1205 | 1223 | a | a | c | U | A | U | C | U | C | U | G | C | A | U | U | c | C | C | C | 40 | 4 | 12 | c | false | <90% | 2969 | ||
NM_133629 | RAD51L3 | 1332 | 1350 | U | U | U | U | g | U | C | U | C | U | G | C | c | U | U | U | C | C | a | 33 | 3 | 7 | false | <90% | 1477 | |||
NM_002878 | RAD51L3 | 1668 | 1686 | U | U | U | U | g | U | C | U | C | U | G | C | c | U | U | U | C | C | a | 33 | 3 | 7 | false | <90% | 1849 | |||
NM_001039580 | MAP9 | 3143 | 3161 | U | U | U | g | A | U | C | U | C | U | G | C | A | U | g | U | C | C | u | 33 | 3 | 10 | c | false | <90% | 7333 | ||
XM_937430 | LOC648377 | 1275 | 1293 | U | U | U | g | A | U | C | U | C | U | G | C | A | U | U | U | u | a | u | 32 | 4 | 12 | c | false | <90% | 2850 | ||
XM_929253 | LOC646316 | 1275 | 1293 | U | U | U | g | A | U | C | U | C | U | G | C | A | U | U | U | u | a | u | 32 | 4 | 12 | c | false | <90% | 2850 | ||
NM_199452 | ZNF365 | 1725 | 1743 | U | c | U | U | A | U | g | U | C | U | G | C | A | U | U | U | C | C | C | 22 | 2 | 12 | bc | false | <90% | 2695 | ||
NM_199451 | ZNF365 | 2406 | 2424 | U | c | U | U | A | U | g | U | C | U | G | C | A | U | U | U | C | C | C | 22 | 2 | 12 | bc | false | <90% | 3376 | ||
NR_003127 | ZNF542 | 725 | 743 | c | c | U | U | A | g | C | U | C | U | G | C | A | U | U | U | C | C | a | 18 | 4 | 12 | bc | false | <90% | 11390 | ||
NM_002427 | MMP13 | 2487 | 2505 | U | U | U | U | u | U | C | U | C | U | G | C | A | U | U | U | a | a | a | 17 | 4 | 11 | c | false | <90% | 2722 | ||
NM_003762 | VAMP4 | 1572 | 1590 | U | U | a | U | A | U | C | U | u | U | G | C | A | U | U | U | C | C | u | 15 | 3 | 9 | bc | false | <90% | 2126 | ||
NM_003590 | CUL3 | 4295 | 4313 | c | U | U | U | A | U | C | U | C | U | a | C | A | U | U | U | u | C | C | 13 | 3 | 9 | c | false | <90% | 6787 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2774
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