Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
40 hits were found for GUGGACAGAGAAGGUCUCU (22 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_020145 | SH3GLB2 | 299 | 317 | c | U | G | G | A | C | A | G | A | G | A | A | G | a | U | C | U | u | g | 70 | 4 | 12 | c | false | <90% | 2039 | ||
NM_079421 | CDKN2D | 751 | 769 | u | U | G | G | A | C | A | G | A | G | A | A | G | G | g | C | U | C | c | 68 | 3 | 13 | c | false | <90% | 1162 | ||
NM_001800 | CDKN2D | 1005 | 1023 | u | U | G | G | A | C | A | G | A | G | A | A | G | G | g | C | U | C | c | 68 | 3 | 13 | c | false | <90% | 1416 | ||
XM_291020 | LOC339809 | 4721 | 4739 | c | a | a | G | A | C | A | G | A | G | A | A | G | G | U | C | U | C | U | 67 | 3 | 16 | bc | false | <90% | 5135 | ||
XM_936940 | LOC339809 | 4725 | 4743 | c | a | a | G | A | C | A | G | A | G | A | A | G | G | U | C | U | C | U | 67 | 3 | 16 | bc | false | <90% | 5139 | ||
NM_014732 | KIAA0513 | 3813 | 3831 | G | c | u | G | A | C | A | G | A | G | A | A | G | G | U | C | U | C | c | 64 | 3 | 15 | bc | false | <90% | 7361 | ||
XR_017421 | LOC400129 | 467 | 485 | G | U | G | G | A | C | A | G | A | G | A | c | a | G | U | C | U | C | g | 50 | 3 | 11 | false | <90% | 1300 | |||
XR_019239 | LOC400129 | 467 | 485 | G | U | G | G | A | C | A | G | A | G | A | c | a | G | U | C | U | C | g | 50 | 3 | 11 | false | <90% | 1300 | |||
NM_032264 | NBPF3 | 3389 | 3407 | G | U | G | G | g | C | A | G | A | G | A | A | G | G | U | C | U | a | g | 40 | 3 | 12 | c | false | <90% | 3783 | ||
XM_927442 | LOC644264 | 1136 | 1154 | c | U | G | G | A | C | A | G | A | G | A | u | G | G | c | C | U | C | U | 39 | 3 | 10 | false | <90% | 1556 | |||
NM_000045 | ARG1 | 815 | 833 | a | c | a | u | A | C | A | G | A | G | A | A | G | G | U | C | U | C | U | 30 | 4 | 15 | bc | false | <90% | 1447 | ||
NM_022452 | FBRS | 2256 | 2274 | G | U | G | G | c | C | A | G | A | G | A | A | G | G | U | C | a | C | c | 20 | 3 | 11 | c | false | <90% | 2510 | ||
NM_152831 | ACE | 2501 | 2519 | G | U | G | G | A | C | A | G | g | G | A | A | G | G | c | C | U | C | U | 15 | 2 | 8 | c | false | <90% | 4863 | ||
XM_001127452 | LOC728433 | 43 | 61 | G | U | G | G | A | C | A | a | A | G | A | A | G | c | U | C | U | C | a | 13 | 3 | 7 | c | false | <90% | 393 | ||
NM_022169 | ABCG4 | 2769 | 2787 | a | U | G | G | A | C | A | G | g | G | A | A | G | G | a | C | U | C | U | 13 | 3 | 7 | c | false | <90% | 3874 | ||
XM_001132522 | LOC728689 | 412 | 430 | G | U | G | G | A | C | A | a | A | G | A | A | G | G | U | g | U | C | c | 6 | 3 | 7 | c | false | <90% | 2610 | ||
XM_001132482 | LOC728689 | 378 | 396 | G | U | G | G | A | C | A | a | A | G | A | A | G | G | U | g | U | C | c | 6 | 3 | 7 | c | false | <90% | 3053 | ||
NM_003752 | EIF3S8 | 377 | 395 | G | U | G | G | A | C | A | a | A | G | A | A | G | G | U | g | U | C | c | 6 | 3 | 7 | c | false | <90% | 3063 | ||
XM_001132506 | LOC728689 | 426 | 444 | G | U | G | G | A | C | A | a | A | G | A | A | G | G | U | g | U | C | c | 6 | 3 | 7 | c | false | <90% | 3101 | ||
NM_001037808 | EIF3S8 | 426 | 444 | G | U | G | G | A | C | A | a | A | G | A | A | G | G | U | g | U | C | c | 6 | 3 | 7 | c | false | <90% | 3111 | ||
XM_001132509 | LOC728689 | 502 | 520 | G | U | G | G | A | C | A | a | A | G | A | A | G | G | U | g | U | C | c | 6 | 3 | 7 | c | false | <90% | 3177 | ||
XM_001132505 | LOC728689 | 585 | 603 | G | U | G | G | A | C | A | a | A | G | A | A | G | G | U | g | U | C | c | 6 | 3 | 7 | c | false | <90% | 3260 |
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_138457 | FOXP4 | 3627 | 3645 | c | a | A | G | A | C | C | U | U | C | U | C | U | c | U | C | C | A | C | 67 | 3 | 11 | c | false | <90% | 5926 | ||
NM_001012427 | FOXP4 | 3660 | 3678 | c | a | A | G | A | C | C | U | U | C | U | C | U | c | U | C | C | A | C | 67 | 3 | 11 | c | false | <90% | 5959 | ||
NM_001012426 | FOXP4 | 3666 | 3684 | c | a | A | G | A | C | C | U | U | C | U | C | U | c | U | C | C | A | C | 67 | 3 | 11 | c | false | <90% | 5965 | ||
NM_016446 | C9orf127 | 1234 | 1252 | g | G | A | c | A | C | C | U | U | C | U | C | U | G | U | C | C | A | C | 61 | 2 | 15 | bc | false | <90% | 2173 | ||
NM_001042589 | C9orf127 | 1155 | 1173 | g | G | A | c | A | C | C | U | U | C | U | C | U | G | U | C | C | A | C | 61 | 2 | 15 | bc | false | <90% | 3474 | ||
NM_001042590 | C9orf127 | 1428 | 1446 | g | G | A | c | A | C | C | U | U | C | U | C | U | G | U | C | C | A | C | 61 | 2 | 15 | bc | false | <90% | 3747 | ||
XR_017955 | LOC221442 | 1329 | 1347 | g | G | u | u | A | C | C | U | U | C | U | C | U | G | U | C | C | A | C | 41 | 3 | 15 | bc | false | <90% | 3037 | ||
XR_017852 | LOC221442 | 1329 | 1347 | g | G | u | u | A | C | C | U | U | C | U | C | U | G | U | C | C | A | C | 41 | 3 | 15 | bc | false | <90% | 3037 | ||
NM_173515 | CNKSR3 | 705 | 723 | g | u | g | G | A | C | C | U | U | C | U | C | U | G | U | g | C | A | C | 40 | 4 | 12 | c | false | <90% | 3277 | ||
NM_001031685 | TP53BP2 | 2596 | 2614 | g | G | A | G | A | C | C | a | U | C | U | C | U | G | U | C | C | c | a | 28 | 4 | 9 | c | false | <90% | 4670 | ||
NM_005426 | TP53BP2 | 2728 | 2746 | g | G | A | G | A | C | C | a | U | C | U | C | U | G | U | C | C | c | a | 28 | 4 | 9 | c | false | <90% | 4802 | ||
NM_024923 | NUP210 | 4288 | 4306 | c | G | u | G | A | C | C | U | U | C | a | C | U | G | U | C | C | A | C | 17 | 3 | 8 | c | false | <90% | 7191 | ||
NM_001042646 | TRAK1 | 3176 | 3194 | u | c | u | G | c | C | C | U | U | C | U | C | U | G | U | C | C | A | C | 15 | 4 | 14 | bc | false | <90% | 5123 | ||
NM_147233 | NCOA1 | 3002 | 3020 | g | a | u | G | A | g | C | U | U | C | U | C | U | G | U | C | C | A | C | 3 | 4 | 13 | bc | false | <90% | 6892 | ||
NM_003743 | NCOA1 | 3002 | 3020 | g | a | u | G | A | g | C | U | U | C | U | C | U | G | U | C | C | A | C | 3 | 4 | 13 | bc | false | <90% | 6895 | ||
NM_147223 | NCOA1 | 3002 | 3020 | g | a | u | G | A | g | C | U | U | C | U | C | U | G | U | C | C | A | C | 3 | 4 | 13 | bc | false | <90% | 6952 | ||
XM_001133864 | LOXL1 | 294 | 312 | u | G | A | G | A | g | C | c | U | C | U | C | U | G | U | C | C | A | C | -27 | 3 | 11 | bc | false | <90% | 2353 | ||
NM_005576 | LOXL1 | 297 | 315 | u | G | A | G | A | g | C | c | U | C | U | C | U | G | U | C | C | A | C | -27 | 3 | 11 | bc | false | <90% | 2361 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2000
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