Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
63 hits were found for UGCUCUGUGACAUUGGAGA (44 guide strand hits and 19 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_016616 | TXNDC3 | 1226 | 1244 | a | G | C | U | C | U | G | U | G | A | C | A | U | U | G | a | A | G | A | 71 | 2 | 14 | c | false | <90% | 2350 | ||
NM_002581 | PAPPA | 2440 | 2458 | g | a | C | U | C | U | G | U | G | A | C | A | c | U | G | G | A | G | u | 71 | 4 | 10 | false | <90% | 11025 | |||
NM_007235 | XPOT | 1912 | 1930 | a | c | a | U | C | U | G | U | G | A | C | A | U | U | G | G | A | G | u | 62 | 4 | 15 | bc | false | <90% | 3881 | ||
XM_001127869 | ITGAX | 871 | 889 | a | G | C | U | C | U | G | U | G | A | C | c | U | U | G | G | A | c | c | 56 | 4 | 10 | false | <90% | 2617 | |||
NM_000887 | ITGAX | 2084 | 2102 | a | G | C | U | C | U | G | U | G | A | C | c | U | U | G | G | A | c | c | 56 | 4 | 10 | false | <90% | 4666 | |||
NM_015690 | STK36 | 638 | 656 | a | G | C | U | C | U | G | U | G | A | C | u | U | U | G | G | A | u | u | 56 | 4 | 10 | false | <90% | 4887 | |||
NM_003275 | TMOD1 | 414 | 432 | a | a | C | U | C | U | G | U | G | A | C | A | U | U | G | c | A | G | c | 55 | 4 | 13 | c | false | <90% | 2664 | ||
XM_001134445 | LOC339047 | 741 | 759 | a | G | C | U | g | U | G | U | G | A | C | A | U | U | G | G | A | c | A | 43 | 3 | 12 | c | false | <90% | 3655 | ||
XR_016512 | LOC642778 | 754 | 772 | a | G | C | U | g | U | G | U | G | A | C | A | U | U | G | G | A | c | A | 43 | 3 | 12 | c | false | <90% | 3666 | ||
XR_016550 | LOC642799 | 754 | 772 | a | G | C | U | g | U | G | U | G | A | C | A | U | U | G | G | A | c | A | 43 | 3 | 12 | c | false | <90% | 3666 | ||
XM_933869 | LOC23117 | 1043 | 1061 | a | G | C | U | g | U | G | U | G | A | C | A | U | U | G | G | A | c | A | 43 | 3 | 12 | c | false | <90% | 4880 | ||
XR_017424 | RPL23AP9 | 349 | 367 | a | G | C | U | C | U | G | U | G | A | C | A | U | U | G | a | u | G | c | 43 | 4 | 14 | c | false | <90% | 494 | ||
XR_019430 | RPL23AP9 | 349 | 367 | a | G | C | U | C | U | G | U | G | A | C | A | U | U | G | a | u | G | c | 43 | 4 | 14 | c | false | <90% | 494 | ||
NM_153280 | UBE1 | 683 | 701 | U | c | u | U | C | U | G | U | G | A | C | u | U | U | G | G | A | G | A | 35 | 3 | 8 | false | <90% | 3483 | |||
NM_003334 | UBE1 | 722 | 740 | U | c | u | U | C | U | G | U | G | A | C | u | U | U | G | G | A | G | A | 35 | 3 | 8 | false | <90% | 3504 | |||
NM_001077685 | CTGLF4 | 550 | 568 | a | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | 33 | 4 | 8 | false | <90% | 2420 | |||
NM_001077686 | CTGLF5 | 550 | 568 | a | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | 33 | 4 | 8 | false | <90% | 2420 | |||
NM_133446 | CTGLF1 | 550 | 568 | a | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | 33 | 4 | 8 | false | <90% | 2420 | |||
NM_001077665 | CTGLF3 | 550 | 568 | a | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | 33 | 4 | 8 | false | <90% | 2429 | |||
XM_370567 | KIAA1975 | 1214 | 1232 | a | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | 33 | 4 | 8 | false | <90% | 3182 | |||
XM_937229 | KIAA1975 | 1214 | 1232 | a | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | 33 | 4 | 8 | false | <90% | 3182 | |||
XM_001127181 | LOC728005 | 1400 | 1418 | a | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | 33 | 4 | 8 | false | <90% | 3293 | |||
XM_001132582 | LOC729092 | 1401 | 1419 | a | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | 33 | 4 | 8 | false | <90% | 3295 | |||
XR_016668 | LOC653234 | 1666 | 1684 | a | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | 33 | 4 | 8 | false | <90% | 3558 | |||
XR_015281 | LOC728127 | 1930 | 1948 | a | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | 33 | 4 | 8 | false | <90% | 3817 | |||
XR_015233 | LOC642517 | 1930 | 1948 | a | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | 33 | 4 | 8 | false | <90% | 3817 | |||
XM_001132574 | LOC729092 | 2592 | 2610 | a | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | 33 | 4 | 8 | false | <90% | 4402 | |||
XM_001132585 | LOC729092 | 2523 | 2541 | a | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | 33 | 4 | 8 | false | <90% | 4417 | |||
XM_001127197 | LOC728005 | 2563 | 2581 | a | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | 33 | 4 | 8 | false | <90% | 4456 | |||
XM_001132588 | LOC729092 | 2592 | 2610 | a | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | 33 | 4 | 8 | false | <90% | 4486 | |||
XR_016708 | LOC653259 | 2640 | 2658 | a | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | 33 | 4 | 8 | false | <90% | 4536 | |||
XM_001127140 | LOC728005 | 5282 | 5300 | a | u | a | U | C | U | G | U | G | A | C | c | U | U | G | G | A | G | A | 33 | 4 | 8 | false | <90% | 7115 | |||
NM_016610 | TLR8 | 2532 | 2550 | g | c | a | c | C | U | G | U | G | A | C | A | U | U | G | G | A | G | A | 30 | 4 | 15 | bc | false | <90% | 3468 | ||
NM_138636 | TLR8 | 2395 | 2413 | g | c | a | c | C | U | G | U | G | A | C | A | U | U | G | G | A | G | A | 30 | 4 | 15 | bc | false | <90% | 4211 | ||
NM_174941 | CD163L1 | 195 | 213 | U | G | C | U | C | U | G | g | G | A | C | A | g | U | G | G | A | G | g | 22 | 3 | 7 | false | <90% | 4598 | |||
NM_000624 | SERPINA5 | 1853 | 1871 | U | G | C | U | g | U | G | U | G | A | C | A | U | U | G | G | g | a | c | 17 | 4 | 11 | c | false | <90% | 2245 | ||
NM_001008704 | C6orf1 | 380 | 398 | U | G | C | U | C | U | c | U | G | A | C | A | U | g | G | G | A | G | A | 14 | 2 | 6 | c | false | <90% | 932 | ||
NM_001008703 | C6orf1 | 440 | 458 | U | G | C | U | C | U | c | U | G | A | C | A | U | g | G | G | A | G | A | 14 | 2 | 6 | c | false | <90% | 992 | ||
NM_178508 | C6orf1 | 692 | 710 | U | G | C | U | C | U | c | U | G | A | C | A | U | g | G | G | A | G | A | 14 | 2 | 6 | c | false | <90% | 1244 | ||
NM_012285 | KCNH4 | 1514 | 1532 | U | G | C | U | C | U | G | g | G | A | C | A | U | U | G | G | c | u | g | 6 | 4 | 8 | c | false | <90% | 3920 | ||
NM_002649 | PIK3CG | 3848 | 3866 | U | u | g | U | C | U | G | U | G | g | C | A | U | U | G | G | A | G | A | -13 | 3 | 9 | bc | false | <90% | 5379 | ||
XM_001131586 | LOC729871 | 4151 | 4169 | U | G | C | U | C | g | G | U | c | A | C | A | U | U | G | G | A | G | c | -28 | 3 | 9 | bc | false | <90% | 10324 | ||
XM_001128413 | SPEG | 4777 | 4795 | U | G | C | U | C | g | G | U | c | A | C | A | U | U | G | G | A | G | c | -28 | 3 | 9 | bc | false | <90% | 10950 | ||
NM_001918 | DBT | 236 | 254 | a | G | C | U | C | U | c | a | G | A | C | A | U | U | G | G | A | G | A | -30 | 3 | 11 | bc | false | <90% | 10831 |
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_020231 | KTELC1 | 1023 | 1041 | U | C | U | C | C | A | A | U | G | U | C | c | a | A | G | A | G | C | u | 50 | 3 | 11 | false | <90% | 1973 | |||
NM_152305 | KTELC1 | 1023 | 1041 | U | C | U | C | C | A | A | U | G | U | C | c | a | A | G | A | G | C | u | 50 | 3 | 11 | false | <90% | 3538 | |||
XM_064152 | SRL | 2222 | 2240 | U | C | a | u | C | A | A | U | G | U | C | A | C | A | G | A | G | C | c | 38 | 3 | 14 | bc | false | <90% | 5587 | ||
XM_942054 | SRL | 2222 | 2240 | U | C | a | u | C | A | A | U | G | U | C | A | C | A | G | A | G | C | c | 38 | 3 | 14 | bc | false | <90% | 5587 | ||
NM_003637 | ITGA10 | 1075 | 1093 | U | C | U | u | C | A | A | U | G | U | C | A | C | A | G | A | u | g | A | 37 | 3 | 12 | c | false | <90% | 5189 | ||
NM_172016 | TRIM39 | 1915 | 1933 | U | C | U | a | C | A | A | U | G | U | C | A | C | A | G | A | c | C | g | 34 | 3 | 12 | c | false | <90% | 3545 | ||
NM_021253 | TRIM39 | 2005 | 2023 | U | C | U | a | C | A | A | U | G | U | C | A | C | A | G | A | c | C | g | 34 | 3 | 12 | c | false | <90% | 3635 | ||
NM_015431 | TRIM58 | 1317 | 1335 | U | C | U | a | C | A | A | U | G | U | C | A | C | A | G | A | u | g | g | 32 | 4 | 12 | c | false | <90% | 5158 | ||
XM_925853 | LOC653053 | 861 | 879 | U | C | U | C | C | A | A | U | G | U | C | A | C | A | c | u | c | C | u | 20 | 4 | 14 | c | false | <90% | 1317 | ||
NM_005215 | DCC | 1475 | 1493 | U | C | U | C | C | A | A | U | G | U | g | A | C | A | G | A | u | g | A | 12 | 3 | 10 | c | false | <90% | 5690 | ||
NR_001558 | C20orf56 | 5222 | 5240 | g | C | U | C | C | A | A | U | u | U | C | A | C | A | G | c | G | C | A | 11 | 3 | 7 | c | false | <90% | 18090 | ||
XM_001132046 | LOC732164 | 528 | 546 | U | C | U | C | C | A | u | U | G | U | C | A | C | A | c | A | G | C | A | 9 | 2 | 7 | c | false | <90% | 999 | ||
XM_001132359 | LOC730091 | 528 | 546 | U | C | U | C | C | A | u | U | G | U | C | A | C | A | c | A | G | C | A | 9 | 2 | 7 | c | false | <90% | 999 | ||
NM_152536 | FGD5 | 2995 | 3013 | U | C | U | C | C | A | A | a | G | U | C | A | C | A | G | A | c | C | g | 9 | 3 | 8 | c | false | <90% | 5384 | ||
NM_198969 | AES | 141 | 159 | g | a | g | C | C | A | A | g | G | U | C | A | C | A | G | A | G | C | A | 4 | 4 | 11 | bc | false | <90% | 1754 | ||
NM_015556 | SIPA1L1 | 2127 | 2145 | c | a | c | C | C | A | A | g | G | U | C | A | C | A | G | A | G | C | A | 4 | 4 | 11 | bc | false | <90% | 6028 | ||
NM_024569 | MPZL1 | 1800 | 1818 | U | C | U | C | C | A | A | U | c | U | C | c | C | A | G | A | G | C | u | 1 | 3 | 8 | false | <90% | 3795 | |||
NM_003953 | MPZL1 | 1903 | 1921 | U | C | U | C | C | A | A | U | c | U | C | c | C | A | G | A | G | C | u | 1 | 3 | 8 | false | <90% | 3898 | |||
NM_006977 | ZBTB25 | 1166 | 1184 | U | C | U | C | C | A | A | a | G | a | C | A | C | A | G | A | G | C | c | -49 | 3 | 8 | bc | false | <90% | 1609 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3623
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