Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
25 hits were found for GGUGGAUGUUGUAGACAUG (12 guide strand hits and 13 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_152490 | B3GALNT2 | 1195 | 1213 | u | G | U | G | G | A | U | G | U | U | G | U | c | G | A | C | A | c | u | 79 | 4 | 11 | false | <90% | 2022 | |||
NM_033647 | HELB | 1273 | 1291 | u | G | U | G | G | A | U | G | U | U | G | U | g | G | A | C | A | c | a | 79 | 4 | 11 | false | <90% | 3368 | |||
NM_170672 | RASGRP3 | 2616 | 2634 | u | G | U | G | G | A | U | G | U | U | G | U | A | G | A | C | c | g | G | 71 | 3 | 15 | ac | false | <90% | 4670 | ||
NM_020746 | VISA | 197 | 215 | u | G | U | G | G | A | U | G | U | U | G | U | A | G | A | g | A | U | u | 66 | 3 | 14 | c | false | <90% | 2936 | ||
XM_375931 | LOC400858 | 229 | 247 | u | G | U | a | G | A | U | G | U | U | G | U | A | G | A | a | A | U | G | 35 | 3 | 11 | c | false | <90% | 510 | ||
NM_018036 | C14orf103 | 7162 | 7180 | a | G | U | G | a | A | U | G | U | U | G | c | A | G | A | C | A | U | G | 12 | 3 | 7 | false | <90% | 11099 | |||
NM_024855 | ACTR5 | 1174 | 1192 | G | G | U | G | G | A | U | G | U | g | G | U | A | G | A | C | A | g | c | 9 | 3 | 9 | c | false | <90% | 2247 | ||
XM_937807 | DYNC2H1 | 10926 | 10944 | u | G | U | G | G | u | U | G | U | U | G | g | A | G | A | C | A | U | G | 0 | 3 | 7 | false | <90% | 13436 | |||
XM_931085 | DYNC2H1 | 10926 | 10944 | u | G | U | G | G | u | U | G | U | U | G | g | A | G | A | C | A | U | G | 0 | 3 | 7 | false | <90% | 13436 | |||
NM_001080463 | DYNC2H1 | 10947 | 10965 | u | G | U | G | G | u | U | G | U | U | G | g | A | G | A | C | A | U | G | 0 | 3 | 7 | false | <90% | 13699 | |||
NM_004875 | POLR1C | 207 | 225 | u | G | U | G | G | A | U | G | U | a | G | U | A | c | A | C | A | U | G | -4 | 3 | 8 | c | false | <90% | 1138 | ||
NM_203290 | POLR1C | 207 | 225 | u | G | U | G | G | A | U | G | U | a | G | U | A | c | A | C | A | U | G | -4 | 3 | 8 | c | false | <90% | 1322 |
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 | |||||||||||||
XR_017103 | LOC441630 | 165 | 183 | a | g | g | G | U | C | U | A | C | A | A | C | A | U | C | C | A | C | a | 62 | 4 | 15 | bc | false | <90% | 378 | ||
XR_019372 | LOC441630 | 165 | 183 | a | g | g | G | U | C | U | A | C | A | A | C | A | U | C | C | A | C | a | 62 | 4 | 15 | bc | false | <90% | 378 | ||
XR_016066 | LOC730010 | 166 | 184 | a | g | g | G | U | C | U | A | C | A | A | C | A | U | C | C | A | C | a | 62 | 4 | 15 | bc | false | <90% | 675 | ||
XR_015539 | LOC730832 | 166 | 184 | a | g | g | G | U | C | U | A | C | A | A | C | A | U | C | C | A | C | a | 62 | 4 | 15 | bc | false | <90% | 675 | ||
NM_015379 | BRI3 | 287 | 305 | a | g | g | G | U | C | U | A | C | A | A | C | A | U | C | C | A | C | a | 62 | 4 | 15 | bc | false | <90% | 798 | ||
NM_153837 | GPR114 | 1556 | 1574 | C | g | U | G | U | C | U | A | C | A | A | C | A | U | C | u | A | C | a | 57 | 3 | 13 | c | false | <90% | 3848 | ||
NM_018964 | SLC37A1 | 855 | 873 | u | A | U | u | U | C | U | A | C | A | A | C | A | U | C | C | A | C | a | 56 | 3 | 14 | bc | false | <90% | 3098 | ||
NM_031461 | CRISPLD1 | 2933 | 2951 | g | A | U | G | U | C | U | A | C | A | A | a | A | U | C | g | A | C | C | 38 | 3 | 10 | false | <90% | 4073 | |||
XM_001134446 | PTPRQ | 2174 | 2192 | a | A | U | u | U | C | U | A | C | A | A | C | A | U | a | C | A | C | C | 36 | 3 | 10 | c | false | <90% | 10103 | ||
XM_940335 | PTPRQ | 2174 | 2192 | a | A | U | u | U | C | U | A | C | A | A | C | A | U | a | C | A | C | C | 36 | 3 | 10 | c | false | <90% | 10103 | ||
NM_002765 | PRPS2 | 278 | 296 | g | A | U | G | U | C | U | A | C | A | u | C | A | U | C | C | A | g | a | 29 | 4 | 9 | c | false | <90% | 2509 | ||
NM_001039091 | PRPS2 | 278 | 296 | g | A | U | G | U | C | U | A | C | A | u | C | A | U | C | C | A | g | a | 29 | 4 | 9 | c | false | <90% | 2518 | ||
NM_181701 | QSOX2 | 432 | 450 | C | A | U | G | a | C | U | A | C | g | A | C | A | U | C | C | A | C | u | -39 | 3 | 8 | bc | false | <90% | 4549 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1949
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