Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
31 hits were found for GGUCCCCUAGAAGAAGAAC (25 guide strand hits and 6 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_024861 | FLJ22671 | 1380 | 1398 | u | u | U | C | C | C | C | U | A | G | A | A | G | u | A | G | A | A | a | 62 | 4 | 11 | c | false | <90% | 1975 | ||
NM_018120 | ARMC1 | 1669 | 1687 | a | G | U | C | C | C | C | U | A | G | A | A | a | A | A | c | A | A | C | 61 | 3 | 11 | false | <90% | 2657 | |||
NM_003268 | TLR5 | 587 | 605 | c | u | g | C | C | C | C | U | A | G | A | A | u | A | A | G | A | A | C | 56 | 4 | 9 | false | <90% | 3431 | |||
NM_014611 | MDN1 | 11922 | 11940 | u | c | c | C | C | C | C | U | A | G | A | A | a | A | A | G | A | A | C | 56 | 4 | 9 | false | <90% | 17400 | |||
NM_053051 | CNTROB | 1913 | 1931 | G | c | U | g | C | C | C | U | A | G | A | A | G | A | A | G | A | A | C | 51 | 2 | 15 | bc | false | <90% | 3657 | ||
NM_001037144 | CNTROB | 1976 | 1994 | G | c | U | g | C | C | C | U | A | G | A | A | G | A | A | G | A | A | C | 51 | 2 | 15 | bc | false | <90% | 3781 | ||
NM_174916 | UBR1 | 4823 | 4841 | G | G | U | a | C | C | C | U | A | G | A | A | a | A | A | G | A | A | a | 47 | 3 | 8 | false | <90% | 7758 | |||
NM_133378 | TTN | 29412 | 29430 | u | a | U | a | C | C | C | U | A | G | A | A | G | A | A | G | A | A | g | 44 | 4 | 14 | bc | false | <90% | 101519 | ||
NM_003012 | SFRP1 | 977 | 995 | u | G | U | C | C | C | C | a | A | G | A | A | G | A | A | G | A | A | g | 30 | 3 | 10 | bc | false | <90% | 4465 | ||
XR_018225 | LOC647794 | 967 | 985 | a | G | U | C | C | u | C | U | A | G | A | A | G | A | A | G | A | A | g | 29 | 3 | 12 | bc | false | <90% | 1656 | ||
XR_015715 | LOC729936 | 967 | 985 | a | G | U | C | C | u | C | U | A | G | A | A | G | A | A | G | A | A | g | 29 | 3 | 12 | bc | false | <90% | 1656 | ||
NM_002053 | GBP1 | 1314 | 1332 | a | G | U | C | C | u | C | U | A | G | A | A | G | A | A | G | A | A | g | 29 | 3 | 12 | bc | false | <90% | 2881 | ||
NM_018284 | GBP3 | 1445 | 1463 | a | G | U | C | C | u | C | U | A | G | A | A | G | A | A | G | A | A | g | 29 | 3 | 12 | bc | false | <90% | 3051 | ||
NR_003133 | LOC400759 | 12684 | 12702 | a | G | U | C | C | u | C | U | A | G | A | A | G | A | A | G | A | A | g | 29 | 3 | 12 | bc | false | <90% | 16075 | ||
NM_003215 | TEC | 605 | 623 | a | u | U | C | C | a | C | U | A | G | A | A | G | A | A | G | A | A | g | 18 | 4 | 12 | bc | false | <90% | 3620 | ||
NM_194323 | OTOF | 2113 | 2131 | G | G | c | C | C | C | C | g | A | G | A | A | G | A | A | G | A | A | a | 13 | 3 | 10 | bc | false | <90% | 4772 | ||
NM_004802 | OTOF | 2113 | 2131 | G | G | c | C | C | C | C | g | A | G | A | A | G | A | A | G | A | A | a | 13 | 3 | 10 | bc | false | <90% | 4970 | ||
NM_194322 | OTOF | 2267 | 2285 | G | G | c | C | C | C | C | g | A | G | A | A | G | A | A | G | A | A | a | 13 | 3 | 10 | bc | false | <90% | 5124 | ||
NM_194248 | OTOF | 4315 | 4333 | G | G | c | C | C | C | C | g | A | G | A | A | G | A | A | G | A | A | a | 13 | 3 | 10 | bc | false | <90% | 7172 | ||
NM_052942 | GBP5 | 1764 | 1782 | G | G | U | C | C | u | C | U | A | G | A | A | G | A | A | G | c | A | g | 8 | 3 | 10 | c | false | <90% | 2431 | ||
XM_938007 | MAST3 | 1006 | 1024 | a | G | U | C | a | C | C | U | c | G | A | A | G | A | A | G | A | A | C | -13 | 3 | 10 | bc | false | <90% | 5893 | ||
XM_038150 | MAST3 | 1006 | 1024 | a | G | U | C | a | C | C | U | c | G | A | A | G | A | A | G | A | A | C | -13 | 3 | 10 | bc | false | <90% | 5896 | ||
XM_938581 | PLEKHM2 | 1251 | 1269 | G | G | U | C | a | C | C | a | A | G | A | A | G | A | A | G | A | A | a | -18 | 3 | 10 | bc | false | <90% | 4209 | ||
XM_290944 | PLEKHM2 | 1251 | 1269 | G | G | U | C | a | C | C | a | A | G | A | A | G | A | A | G | A | A | a | -18 | 3 | 10 | bc | false | <90% | 4209 | ||
NM_003913 | PRPF4B | 1467 | 1485 | G | G | U | C | u | C | C | a | A | G | A | A | G | A | A | G | A | A | g | -18 | 3 | 10 | bc | false | <90% | 7482 |
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_032581 | FAM126A | 538 | 556 | G | c | U | C | U | U | C | U | U | C | U | A | G | G | G | G | u | u | u | 57 | 4 | 14 | ac | false | <90% | 3768 | ||
NM_017628 | KIAA1546 | 8512 | 8530 | G | U | U | C | U | U | C | U | U | C | U | A | G | G | G | u | g | C | C | 50 | 2 | 15 | c | false | <90% | 9215 | ||
NM_001911 | CTSG | 811 | 829 | a | c | U | C | U | U | C | U | U | C | U | c | G | G | G | G | A | C | a | 47 | 4 | 9 | false | <90% | 924 | |||
XM_001126824 | OSR2 | 1370 | 1388 | a | c | U | C | U | U | C | U | U | C | U | g | G | G | G | G | A | C | u | 47 | 4 | 9 | false | <90% | 1621 | |||
NM_053001 | OSR2 | 1502 | 1520 | a | c | U | C | U | U | C | U | U | C | U | g | G | G | G | G | A | C | u | 47 | 4 | 9 | false | <90% | 1759 | |||
XM_001130084 | LOC731568 | 619 | 637 | u | g | a | g | U | U | C | U | U | C | U | A | G | G | G | G | A | C | C | 30 | 4 | 15 | bc | false | <90% | 1134 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1780
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