Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
57 hits were found for GAACAAAAACAGCAGGGAU (28 guide strand hits and 29 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_033394 | TANC1 | 4547 | 4565 | c | A | g | C | A | A | A | A | A | C | A | G | C | A | G | G | G | c | c | 70 | 4 | 14 | c | false | <90% | 7644 | ||
NM_138357 | CCDC109A | 1196 | 1214 | a | A | A | C | A | A | A | A | A | C | A | G | a | A | a | G | G | A | U | 62 | 3 | 11 | false | <90% | 2978 | |||
NM_033303 | ADRA1A | 2079 | 2097 | a | A | A | g | A | A | A | A | A | C | A | G | C | A | G | G | G | c | U | 58 | 3 | 13 | c | false | <90% | 2304 | ||
NR_003135 | CEP170L | 35121 | 35139 | c | A | A | a | A | A | A | A | A | C | A | G | C | A | G | G | G | c | a | 53 | 4 | 13 | c | false | <90% | 90477 | ||
NM_145058 | MGC7036 | 1161 | 1179 | c | A | A | g | A | A | A | A | A | C | A | G | a | A | G | G | G | A | U | 50 | 3 | 8 | false | <90% | 1435 | |||
XM_371949 | LOC442721 | 1084 | 1102 | G | A | g | C | A | A | A | A | A | C | A | G | C | A | G | G | a | g | g | 49 | 4 | 13 | c | false | <90% | 1626 | ||
XM_937717 | LOC442721 | 1084 | 1102 | G | A | g | C | A | A | A | A | A | C | A | G | C | A | G | G | a | g | g | 49 | 4 | 13 | c | false | <90% | 1626 | ||
XM_499467 | LOC442721 | 1084 | 1102 | G | A | g | C | A | A | A | A | A | C | A | G | C | A | G | G | a | g | g | 49 | 4 | 13 | c | false | <90% | 1626 | ||
NM_006088 | TUBB2C | 1104 | 1122 | a | A | A | C | A | A | A | A | A | C | A | G | C | A | G | c | u | A | U | 48 | 3 | 14 | c | false | <90% | 1591 | ||
NM_174981 | ANKRD21 | 896 | 914 | G | A | A | C | A | A | A | A | A | C | A | G | C | A | a | G | u | g | g | 44 | 4 | 14 | c | false | <90% | 1826 | ||
NM_207355 | POTE15 | 1211 | 1229 | G | A | A | C | A | A | A | A | A | C | A | G | C | A | a | G | u | g | g | 44 | 4 | 14 | c | false | <90% | 2132 | ||
XM_496269 | DKFZp686J0529 | 1298 | 1316 | G | A | A | C | A | A | A | A | A | C | A | G | C | A | a | G | u | g | g | 44 | 4 | 14 | c | false | <90% | 2236 | ||
XR_017296 | LOC442210 | 993 | 1011 | a | A | A | C | A | A | A | A | A | C | A | G | C | A | G | c | u | A | c | 43 | 4 | 14 | c | false | <90% | 1199 | ||
XR_019230 | LOC442210 | 993 | 1011 | a | A | A | C | A | A | A | A | A | C | A | G | C | A | G | c | u | A | c | 43 | 4 | 14 | c | false | <90% | 1199 | ||
NM_002848 | PTPRO | 879 | 897 | G | A | A | C | A | A | A | A | A | C | A | a | C | u | G | G | G | A | a | 41 | 3 | 11 | false | <90% | 5069 | |||
NM_030667 | PTPRO | 879 | 897 | G | A | A | C | A | A | A | A | A | C | A | a | C | u | G | G | G | A | a | 41 | 3 | 11 | false | <90% | 5153 | |||
NM_182635 | C9orf164 | 1342 | 1360 | G | A | A | C | u | A | A | A | A | C | A | G | C | A | G | G | G | u | g | 40 | 3 | 12 | c | false | <90% | 1837 | ||
NM_003079 | SMARCE1 | 2174 | 2192 | G | A | A | g | A | A | A | A | A | C | A | G | C | u | G | G | G | A | a | 38 | 3 | 9 | c | false | <90% | 2425 | ||
NM_033266 | ERN2 | 596 | 614 | a | c | c | C | A | A | A | A | A | C | A | a | C | A | G | G | G | A | U | 33 | 4 | 8 | false | <90% | 3634 | |||
NM_017915 | C12orf48 | 1090 | 1108 | a | g | g | C | c | A | A | A | A | C | A | G | C | A | G | G | G | A | U | 15 | 4 | 14 | bc | false | <90% | 3189 | ||
NM_147150 | PALM2-AKAP2 | 2643 | 2661 | G | u | c | C | A | A | A | A | c | C | A | G | C | A | G | G | G | A | U | 8 | 3 | 10 | bc | false | <90% | 5180 | ||
NM_001004065 | AKAP2 | 2041 | 2059 | G | u | c | C | A | A | A | A | c | C | A | G | C | A | G | G | G | A | U | 8 | 3 | 10 | bc | false | <90% | 6866 | ||
NM_007203 | PALM2-AKAP2 | 2643 | 2661 | G | u | c | C | A | A | A | A | c | C | A | G | C | A | G | G | G | A | U | 8 | 3 | 10 | bc | false | <90% | 7522 | ||
NM_001003828 | PARVB | 108 | 126 | G | A | A | C | A | A | A | A | A | C | u | G | C | A | G | G | a | g | g | 7 | 4 | 10 | c | false | <90% | 1808 | ||
NM_014916 | LMTK2 | 1586 | 1604 | G | A | A | C | A | c | A | A | A | C | A | G | C | A | G | a | G | A | c | 5 | 3 | 9 | c | false | <90% | 5602 | ||
NM_175728 | IL5RA | 1600 | 1618 | u | A | A | a | A | A | c | A | A | C | A | G | C | A | G | G | G | A | U | -5 | 3 | 12 | bc | false | <90% | 1626 | ||
NM_175725 | IL5RA | 1668 | 1686 | u | A | A | a | A | A | c | A | A | C | A | G | C | A | G | G | G | A | U | -5 | 3 | 12 | bc | false | <90% | 1694 | ||
NM_001763 | CD1A | 124 | 142 | G | A | u | C | A | A | A | A | A | g | A | G | C | A | G | G | G | A | c | -7 | 3 | 8 | bc | false | <90% | 2111 |
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_138327 | TAAR1 | 447 | 465 | g | U | C | C | C | U | G | C | U | G | U | U | U | U | U | G | c | a | u | 66 | 4 | 15 | ac | false | <90% | 1020 | ||
NM_172210 | CSF1 | 242 | 260 | c | U | C | C | C | U | G | C | U | G | U | U | g | U | U | G | g | U | C | 64 | 3 | 11 | false | <90% | 1519 | |||
NM_172211 | CSF1 | 242 | 260 | c | U | C | C | C | U | G | C | U | G | U | U | g | U | U | G | g | U | C | 64 | 3 | 11 | false | <90% | 1855 | |||
NM_172212 | CSF1 | 242 | 260 | c | U | C | C | C | U | G | C | U | G | U | U | g | U | U | G | g | U | C | 64 | 3 | 11 | false | <90% | 2545 | |||
NM_000757 | CSF1 | 242 | 260 | c | U | C | C | C | U | G | C | U | G | U | U | g | U | U | G | g | U | C | 64 | 3 | 11 | false | <90% | 2749 | |||
XM_001131225 | LOC731909 | 356 | 374 | u | c | u | C | C | U | G | C | U | G | U | U | g | U | U | G | U | U | C | 56 | 4 | 9 | false | <90% | 1224 | |||
XM_371534 | LOC389000 | 437 | 455 | u | c | u | C | C | U | G | C | U | G | U | U | g | U | U | G | U | U | C | 56 | 4 | 9 | false | <90% | 1495 | |||
NM_173491 | LSM11 | 2373 | 2391 | u | c | C | C | C | U | G | C | U | G | U | a | U | U | U | G | U | U | g | 47 | 4 | 9 | false | <90% | 2561 | |||
NM_032098 | PCDHGB4 | 59 | 77 | c | U | u | C | C | U | G | C | U | G | U | c | U | U | U | G | U | U | C | 44 | 3 | 8 | false | <90% | 2412 | |||
NM_032095 | PCDHGB1 | 53 | 71 | c | U | u | C | C | U | G | C | U | G | U | c | U | U | U | G | U | U | C | 44 | 3 | 8 | false | <90% | 2433 | |||
NM_032099 | PCDHGB5 | 59 | 77 | c | U | u | C | C | U | G | C | U | G | U | c | U | U | U | G | U | U | C | 44 | 3 | 8 | false | <90% | 2457 | |||
NM_018925 | PCDHGB5 | 59 | 77 | c | U | u | C | C | U | G | C | U | G | U | c | U | U | U | G | U | U | C | 44 | 3 | 8 | false | <90% | 4578 | |||
NM_003736 | PCDHGB4 | 59 | 77 | c | U | u | C | C | U | G | C | U | G | U | c | U | U | U | G | U | U | C | 44 | 3 | 8 | false | <90% | 4578 | |||
NM_018922 | PCDHGB1 | 53 | 71 | c | U | u | C | C | U | G | C | U | G | U | c | U | U | U | G | U | U | C | 44 | 3 | 8 | false | <90% | 4590 | |||
XR_016885 | LOC645163 | 367 | 385 | A | U | C | C | C | U | G | C | U | G | U | U | U | U | g | G | c | c | a | 44 | 4 | 14 | c | false | <90% | 1291 | ||
XR_018802 | LOC650032 | 367 | 385 | A | U | C | C | C | U | G | C | U | G | U | U | U | U | g | G | c | c | a | 44 | 4 | 14 | c | false | <90% | 1291 | ||
NM_024692 | CLIP4 | 894 | 912 | A | U | C | C | C | U | G | C | U | G | a | U | g | U | U | G | U | U | C | 28 | 2 | 10 | false | <90% | 4307 | |||
XM_941973 | DKFZp313A2432 | 1752 | 1770 | A | U | u | C | g | U | G | C | U | G | U | U | U | U | U | G | U | U | C | 28 | 2 | 14 | bc | false | <90% | 4541 | ||
XM_930226 | DKFZp313A2432 | 1752 | 1770 | A | U | u | C | g | U | G | C | U | G | U | U | U | U | U | G | U | U | C | 28 | 2 | 14 | bc | false | <90% | 4541 | ||
XM_945597 | DKFZp313A2432 | 2088 | 2106 | A | U | u | C | g | U | G | C | U | G | U | U | U | U | U | G | U | U | C | 28 | 2 | 14 | bc | false | <90% | 4877 | ||
XM_934482 | DKFZp313A2432 | 2088 | 2106 | A | U | u | C | g | U | G | C | U | G | U | U | U | U | U | G | U | U | C | 28 | 2 | 14 | bc | false | <90% | 4877 | ||
NM_152737 | RNF182 | 2384 | 2402 | A | U | C | C | C | U | G | u | U | G | U | U | U | U | U | G | a | g | u | 6 | 4 | 8 | c | false | <90% | 3317 | ||
XM_001128421 | LOC728069 | 2058 | 2076 | A | U | C | C | C | U | u | C | U | G | U | U | U | U | U | c | U | U | g | 2 | 3 | 8 | c | false | <90% | 2334 | ||
XM_001134379 | LOC732350 | 2058 | 2076 | A | U | C | C | C | U | u | C | U | G | U | U | U | U | U | c | U | U | g | 2 | 3 | 8 | c | false | <90% | 2334 | ||
NM_001079906 | ZNF331 | 2648 | 2666 | A | U | C | a | C | U | G | u | U | G | U | U | U | U | U | G | U | U | u | -3 | 3 | 10 | bc | false | <90% | 4151 | ||
NM_001079907 | ZNF331 | 2668 | 2686 | A | U | C | a | C | U | G | u | U | G | U | U | U | U | U | G | U | U | u | -3 | 3 | 10 | bc | false | <90% | 4171 | ||
NM_018555 | ZNF331 | 3660 | 3678 | A | U | C | a | C | U | G | u | U | G | U | U | U | U | U | G | U | U | u | -3 | 3 | 10 | bc | false | <90% | 5163 | ||
NM_005239 | ETS2 | 2319 | 2337 | A | U | C | C | C | U | G | C | U | u | U | U | U | g | U | G | U | U | u | -7 | 3 | 9 | c | false | <90% | 3672 | ||
NM_003639 | IKBKG | 1741 | 1759 | c | U | C | g | C | U | G | C | U | c | U | U | U | U | U | G | U | U | C | -21 | 3 | 9 | bc | false | <90% | 2120 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2859
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