Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
44 hits were found for CCAGAGAUCCUGCUGUCUC (20 guide strand hits and 24 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_015113 | ZZEF1 | 6680 | 6698 | g | C | A | G | A | G | A | U | C | C | U | G | C | g | G | U | C | a | C | 75 | 3 | 12 | c | false | <90% | 11412 | ||
NM_015063 | SLC8A2 | 514 | 532 | C | C | u | G | A | G | A | U | C | C | U | G | C | U | G | U | C | a | g | 72 | 3 | 14 | c | false | <90% | 4282 | ||
NM_001014380 | KATNAL1 | 379 | 397 | u | u | A | G | A | G | A | U | C | C | U | G | C | U | G | U | u | U | g | 58 | 4 | 14 | ac | false | <90% | 7506 | ||
NM_032116 | KATNAL1 | 409 | 427 | u | u | A | G | A | G | A | U | C | C | U | G | C | U | G | U | u | U | g | 58 | 4 | 14 | ac | false | <90% | 7536 | ||
NM_052845 | MMAB | 3819 | 3837 | u | g | A | u | A | G | A | U | C | C | U | G | C | U | G | U | C | U | C | 49 | 3 | 15 | bc | false | <90% | 4154 | ||
NM_031939 | MRO | 934 | 952 | C | C | A | G | A | G | A | U | C | C | U | G | C | a | G | U | u | c | u | 49 | 4 | 13 | c | false | <90% | 2108 | ||
NM_001017423 | ALDH18A1 | 627 | 645 | C | a | u | G | A | G | A | U | C | C | U | u | C | U | G | U | C | U | C | 35 | 3 | 8 | false | <90% | 3464 | |||
NM_002860 | ALDH18A1 | 627 | 645 | C | a | u | G | A | G | A | U | C | C | U | u | C | U | G | U | C | U | C | 35 | 3 | 8 | false | <90% | 3470 | |||
NM_021045 | ZNF248 | 3205 | 3223 | u | C | A | G | A | G | A | a | C | C | U | G | C | U | G | U | C | a | a | 28 | 4 | 9 | c | false | <90% | 4883 | ||
NM_001710 | CFB | 325 | 343 | C | C | A | G | g | G | A | U | C | C | U | G | C | U | c | U | C | U | g | 18 | 3 | 9 | c | false | <90% | 2574 | ||
NM_001077206 | SEC31A | 1102 | 1120 | C | C | c | G | A | a | A | U | C | C | U | G | C | U | G | U | C | U | u | 12 | 3 | 12 | bc | false | <90% | 3902 | ||
NM_016211 | SEC31A | 1099 | 1117 | C | C | c | G | A | a | A | U | C | C | U | G | C | U | G | U | C | U | u | 12 | 3 | 12 | bc | false | <90% | 4124 | ||
NM_001077208 | SEC31A | 1102 | 1120 | C | C | c | G | A | a | A | U | C | C | U | G | C | U | G | U | C | U | u | 12 | 3 | 12 | bc | false | <90% | 4199 | ||
NM_014933 | SEC31A | 1099 | 1117 | C | C | c | G | A | a | A | U | C | C | U | G | C | U | G | U | C | U | u | 12 | 3 | 12 | bc | false | <90% | 4241 | ||
NM_001077207 | SEC31A | 1102 | 1120 | C | C | c | G | A | a | A | U | C | C | U | G | C | U | G | U | C | U | u | 12 | 3 | 12 | bc | false | <90% | 4244 | ||
XM_001130353 | LOC731653 | 199 | 217 | g | C | A | G | A | G | A | U | g | C | U | G | C | U | G | g | C | U | C | 11 | 3 | 7 | c | false | <90% | 489 | ||
XM_001130254 | LOC729437 | 199 | 217 | g | C | A | G | A | G | A | U | g | C | U | G | C | U | G | g | C | U | C | 11 | 3 | 7 | c | false | <90% | 489 | ||
NM_003458 | BSN | 12158 | 12176 | C | C | A | G | A | G | A | U | g | C | U | G | C | U | c | U | C | U | g | 10 | 3 | 8 | c | false | <90% | 15966 | ||
NM_014866 | KIAA0310 | 8139 | 8157 | C | C | A | G | A | G | A | g | C | C | g | G | C | U | G | U | C | U | g | -28 | 3 | 7 | c | false | <90% | 9059 | ||
NM_000431 | MVK | 1747 | 1765 | C | C | A | G | A | G | c | a | C | C | U | G | C | U | G | U | C | U | g | -33 | 3 | 10 | bc | false | <90% | 1952 |
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 | |||||||||||||
XM_001133994 | LOC732460 | 1385 | 1403 | G | A | G | A | C | A | G | C | A | G | G | A | c | C | U | C | U | c | u | 81 | 3 | 12 | false | <90% | 4006 | |||
XM_001129628 | LOC729193 | 1385 | 1403 | G | A | G | A | C | A | G | C | A | G | G | A | c | C | U | C | U | c | u | 81 | 3 | 12 | false | <90% | 4008 | |||
NM_014992 | DAAM1 | 2084 | 2102 | a | A | G | A | C | A | G | C | A | G | G | A | U | u | U | C | U | u | u | 70 | 4 | 12 | c | false | <90% | 4256 | ||
NM_003373 | VCL | 623 | 641 | G | A | G | A | C | A | G | C | A | G | G | A | g | C | U | C | a | c | u | 58 | 4 | 12 | false | <90% | 5443 | |||
NM_014000 | VCL | 623 | 641 | G | A | G | A | C | A | G | C | A | G | G | A | g | C | U | C | a | c | u | 58 | 4 | 12 | false | <90% | 5647 | |||
XM_001125924 | KIAA0251 | 607 | 625 | u | u | G | A | C | A | G | C | A | G | G | c | U | C | U | C | U | G | G | 52 | 3 | 9 | false | <90% | 2399 | |||
NM_015027 | PDXDC1 | 2067 | 2085 | u | u | G | A | C | A | G | C | A | G | G | c | U | C | U | C | U | G | G | 52 | 3 | 9 | false | <90% | 4512 | |||
NM_032865 | TNS4 | 925 | 943 | G | g | G | g | C | A | G | C | A | G | G | A | U | C | U | C | U | G | u | 46 | 3 | 14 | bc | false | <90% | 4004 | ||
NM_006071 | PKDREJ | 6967 | 6985 | G | A | G | A | C | A | G | C | A | G | G | A | U | C | a | C | a | G | u | 46 | 3 | 14 | c | false | <90% | 7660 | ||
NM_033387 | FAM78A | 1738 | 1756 | a | A | G | A | a | A | G | C | A | G | G | A | U | C | U | C | U | u | u | 38 | 4 | 12 | c | false | <90% | 3957 | ||
NM_006121 | KRT1 | 1527 | 1545 | a | A | G | A | a | A | G | C | A | G | G | A | U | g | U | C | U | G | G | 27 | 3 | 8 | c | false | <90% | 2451 | ||
NM_017727 | FLJ20254 | 674 | 692 | a | A | G | g | C | A | G | C | A | G | G | g | U | C | U | C | U | G | G | 27 | 3 | 7 | false | <90% | 3064 | |||
XM_001131686 | LOC729895 | 350 | 368 | G | A | G | A | g | A | G | C | A | G | G | A | U | C | c | C | U | G | G | 23 | 2 | 9 | c | false | <90% | 484 | ||
XM_001127936 | LOC730973 | 350 | 368 | G | A | G | A | g | A | G | C | A | G | G | A | U | C | c | C | U | G | G | 23 | 2 | 9 | c | false | <90% | 484 | ||
NM_207047 | ENSA | 2161 | 2179 | G | A | G | A | g | A | G | C | A | G | G | A | U | C | c | C | U | G | G | 23 | 2 | 9 | c | false | <90% | 2747 | ||
NM_207044 | ENSA | 2297 | 2315 | G | A | G | A | g | A | G | C | A | G | G | A | U | C | c | C | U | G | G | 23 | 2 | 9 | c | false | <90% | 2883 | ||
NM_207043 | ENSA | 2345 | 2363 | G | A | G | A | g | A | G | C | A | G | G | A | U | C | c | C | U | G | G | 23 | 2 | 9 | c | false | <90% | 2931 | ||
NM_001009877 | BRD9 | 1292 | 1310 | G | A | G | A | C | A | G | C | A | G | c | A | g | C | U | C | U | G | u | 23 | 3 | 10 | false | <90% | 2395 | |||
NM_023924 | BRD9 | 1761 | 1779 | G | A | G | A | C | A | G | C | A | G | c | A | g | C | U | C | U | G | u | 23 | 3 | 10 | false | <90% | 2843 | |||
NM_181042 | PBRM1 | 1489 | 1507 | G | A | G | A | C | A | G | C | A | u | G | A | U | C | U | C | U | u | c | 9 | 3 | 9 | c | false | <90% | 7448 | ||
NM_018165 | PBRM1 | 1393 | 1411 | G | A | G | A | C | A | G | C | A | u | G | A | U | C | U | C | U | u | c | 9 | 3 | 9 | c | false | <90% | 7508 | ||
NM_018313 | PBRM1 | 1586 | 1604 | G | A | G | A | C | A | G | C | A | u | G | A | U | C | U | C | U | u | c | 9 | 3 | 9 | c | false | <90% | 7545 | ||
NM_002158 | FOXN2 | 1510 | 1528 | G | A | G | g | C | A | G | C | u | G | G | A | U | C | U | C | U | G | c | -1 | 3 | 9 | bc | false | <90% | 5472 | ||
NM_001543 | NDST1 | 4512 | 4530 | u | A | G | A | C | A | G | u | g | G | G | A | U | C | U | C | U | G | G | -24 | 3 | 10 | bc | false | <90% | 7913 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3270
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