Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
38 hits were found for GGAAGUAAACACUCAGAAA (25 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 | |||||||||||||
XR_017780 | MGC45800 | 85 | 103 | G | G | c | A | G | U | A | A | A | C | A | C | U | C | A | G | A | c | u | 72 | 3 | 14 | c | false | <90% | 1761 | ||
XR_017723 | MGC45800 | 85 | 103 | G | G | c | A | G | U | A | A | A | C | A | C | U | C | A | G | A | c | u | 72 | 3 | 14 | c | false | <90% | 1761 | ||
NM_015640 | SERBP1 | 4474 | 4492 | u | a | A | A | G | U | A | A | A | C | A | C | U | u | A | G | A | A | A | 67 | 3 | 11 | c | false | <90% | 6701 | ||
NM_001018069 | SERBP1 | 4492 | 4510 | u | a | A | A | G | U | A | A | A | C | A | C | U | u | A | G | A | A | A | 67 | 3 | 11 | c | false | <90% | 6719 | ||
NM_001018068 | SERBP1 | 4519 | 4537 | u | a | A | A | G | U | A | A | A | C | A | C | U | u | A | G | A | A | A | 67 | 3 | 11 | c | false | <90% | 6746 | ||
NM_001018067 | SERBP1 | 4537 | 4555 | u | a | A | A | G | U | A | A | A | C | A | C | U | u | A | G | A | A | A | 67 | 3 | 11 | c | false | <90% | 6764 | ||
NR_003135 | CEP170L | 20811 | 20829 | c | a | g | A | G | U | A | A | A | C | A | C | U | C | A | G | A | A | g | 62 | 4 | 15 | bc | false | <90% | 90477 | ||
NM_003661 | APOL1 | 2720 | 2738 | G | u | A | A | G | U | A | A | A | C | A | g | U | C | A | G | A | A | A | 54 | 2 | 9 | false | <90% | 2856 | |||
NM_145343 | APOL1 | 2874 | 2892 | G | u | A | A | G | U | A | A | A | C | A | g | U | C | A | G | A | A | A | 54 | 2 | 9 | false | <90% | 3010 | |||
NM_152424 | FAM123B | 5836 | 5854 | G | G | A | A | G | U | A | A | A | C | A | C | U | C | A | c | c | A | A | 50 | 2 | 15 | c | false | <90% | 8443 | ||
NM_030882 | APOL2 | 2415 | 2433 | G | u | A | A | G | U | A | A | A | C | A | g | U | C | A | G | A | A | g | 49 | 3 | 9 | false | <90% | 2545 | |||
NM_145637 | APOL2 | 2556 | 2574 | G | u | A | A | G | U | A | A | A | C | A | g | U | C | A | G | A | A | g | 49 | 3 | 9 | false | <90% | 2686 | |||
NM_004117 | FKBP5 | 1287 | 1305 | G | G | A | A | G | U | A | A | A | C | c | C | c | C | A | G | A | A | u | 23 | 3 | 10 | false | <90% | 3781 | |||
NM_014637 | MTFR1 | 1885 | 1903 | a | G | A | A | G | U | A | A | A | a | A | C | U | C | A | G | A | A | u | 10 | 3 | 8 | bc | false | <90% | 2691 | ||
NM_206963 | RARRES1 | 1073 | 1091 | a | c | A | A | G | U | A | A | A | a | A | C | U | C | A | G | A | A | A | 3 | 3 | 9 | bc | false | <90% | 1545 | ||
XM_944363 | SIRPB2 | 434 | 452 | u | u | g | A | G | U | g | A | A | C | A | C | U | C | A | G | A | A | A | 0 | 4 | 12 | bc | false | <90% | 1429 | ||
XM_939897 | SIRPB2 | 434 | 452 | u | u | g | A | G | U | g | A | A | C | A | C | U | C | A | G | A | A | A | 0 | 4 | 12 | bc | false | <90% | 2642 | ||
XM_209363 | SIRPB2 | 434 | 452 | u | u | g | A | G | U | g | A | A | C | A | C | U | C | A | G | A | A | A | 0 | 4 | 12 | bc | false | <90% | 2642 | ||
NM_014803 | ZNF518 | 4641 | 4659 | G | G | A | A | G | U | A | A | A | g | A | C | U | C | u | G | A | A | A | -7 | 2 | 9 | c | false | <90% | 8296 | ||
NM_199123 | SETD3 | 185 | 203 | u | c | g | A | G | U | A | A | A | a | A | C | U | C | A | G | A | A | A | -15 | 4 | 9 | bc | false | <90% | 1441 | ||
NM_138430 | ADPRHL1 | 796 | 814 | a | u | c | A | G | U | A | A | A | g | A | C | U | C | A | G | A | A | A | -15 | 4 | 9 | bc | false | <90% | 1705 | ||
NM_199162 | ADPRHL1 | 639 | 657 | a | u | c | A | G | U | A | A | A | g | A | C | U | C | A | G | A | A | A | -15 | 4 | 9 | bc | false | <90% | 1917 | ||
NM_032233 | SETD3 | 185 | 203 | u | c | g | A | G | U | A | A | A | a | A | C | U | C | A | G | A | A | A | -15 | 4 | 9 | bc | false | <90% | 2905 | ||
NM_033128 | SCIN | 175 | 193 | G | G | A | A | G | U | g | A | A | C | c | C | U | C | A | G | A | A | c | -32 | 3 | 7 | c | false | <90% | 2571 | ||
NM_024546 | C13orf7 | 538 | 556 | G | G | A | A | G | a | A | A | A | a | A | C | U | C | A | G | A | A | c | -51 | 3 | 8 | bc | false | <90% | 3552 |
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_174962 | SSX9 | 1000 | 1018 | g | U | U | C | U | G | A | G | U | G | U | U | U | A | a | U | U | u | C | 70 | 3 | 13 | c | false | <90% | 1230 | ||
NM_005635 | SSX1 | 1029 | 1047 | g | U | U | C | U | G | A | G | U | G | U | U | U | A | a | U | U | u | C | 70 | 3 | 13 | c | false | <90% | 1271 | ||
NM_175723 | SSX5 | 992 | 1010 | g | U | U | C | U | G | A | G | U | G | U | U | U | A | a | U | U | u | C | 70 | 3 | 13 | c | false | <90% | 1276 | ||
NM_021014 | SSX3 | 1032 | 1050 | g | U | U | C | U | G | A | G | U | G | U | U | U | A | a | U | U | u | C | 70 | 3 | 13 | c | false | <90% | 1290 | ||
NM_175698 | SSX2 | 1046 | 1064 | g | U | U | C | U | G | A | G | U | G | U | U | U | A | a | U | U | u | C | 70 | 3 | 13 | c | false | <90% | 1322 | ||
NM_021015 | SSX5 | 1115 | 1133 | g | U | U | C | U | G | A | G | U | G | U | U | U | A | a | U | U | u | C | 70 | 3 | 13 | c | false | <90% | 1399 | ||
NM_003147 | SSX2 | 1192 | 1210 | g | U | U | C | U | G | A | G | U | G | U | U | U | A | a | U | U | u | C | 70 | 3 | 13 | c | false | <90% | 1466 | ||
NM_016121 | KCTD3 | 1404 | 1422 | g | c | U | C | U | G | A | G | U | G | U | U | U | A | C | c | U | C | a | 55 | 4 | 13 | c | false | <90% | 3946 | ||
XR_016169 | LOC642460 | 734 | 752 | a | U | U | a | U | G | A | G | U | G | U | U | U | A | C | U | U | a | g | 53 | 4 | 13 | c | false | <90% | 2250 | ||
NM_015267 | CUTL2 | 415 | 433 | U | U | U | C | U | G | A | G | U | G | U | U | U | A | C | a | a | g | C | 47 | 3 | 15 | c | false | <90% | 6841 | ||
NM_005859 | PURA | 1355 | 1373 | g | a | a | C | U | G | A | G | U | G | U | U | U | A | u | U | U | C | C | 42 | 4 | 11 | c | false | <90% | 2614 | ||
XM_939476 | KIAA0984 | 7813 | 7831 | U | U | U | C | U | u | A | G | U | G | U | U | U | A | C | a | U | C | C | 10 | 2 | 9 | c | false | <90% | 8019 | ||
XM_037557 | KIAA0984 | 7813 | 7831 | U | U | U | C | U | u | A | G | U | G | U | U | U | A | C | a | U | C | C | 10 | 2 | 9 | c | false | <90% | 8019 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1604
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