Automatic recommendation
Not OK - siRNA is not specific
51 hits were found for GCUUUGGCAGCUCCUCAUU (22 guide strand hits and 29 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_001008901 | FAM112A | 108 | 126 | c | u | U | U | U | G | G | C | A | G | C | U | C | C | U | C | A | U | c | 81 | 3 | 16 | abc | false | <90% | 773 | ||
NM_176791 | FAM112A | 108 | 126 | c | u | U | U | U | G | G | C | A | G | C | U | C | C | U | C | A | U | c | 81 | 3 | 16 | abc | false | <90% | 842 | ||
NM_003420 | ZNF35 | 481 | 499 | c | C | c | U | U | G | G | C | A | G | C | U | a | C | U | C | A | U | U | 68 | 3 | 9 | false | <90% | 2664 | |||
NM_015568 | PPP1R16B | 5194 | 5212 | c | C | U | a | U | G | G | C | A | G | C | U | C | C | U | C | A | U | U | 61 | 2 | 15 | bc | false | <90% | 6251 | ||
NM_002946 | RPA2 | 305 | 323 | G | C | U | a | U | G | G | C | A | G | C | U | C | C | U | C | A | U | a | 58 | 2 | 14 | bc | false | <90% | 1741 | ||
NM_004604 | STX4 | 1260 | 1278 | G | g | g | U | U | G | G | C | A | G | C | U | g | C | U | C | A | U | U | 58 | 3 | 9 | false | <90% | 1403 | |||
XM_001128219 | LOC731040 | 17 | 35 | G | C | U | U | U | G | G | C | A | G | C | U | C | C | a | C | c | c | U | 49 | 3 | 14 | c | false | <90% | 384 | ||
NM_003947 | KALRN | 522 | 540 | a | C | U | U | U | G | G | C | A | G | C | U | C | C | a | a | A | U | U | 47 | 3 | 13 | c | false | <90% | 6481 | ||
NM_001024660 | KALRN | 522 | 540 | a | C | U | U | U | G | G | C | A | G | C | U | C | C | a | a | A | U | U | 47 | 3 | 13 | c | false | <90% | 10777 | ||
XM_001133644 | LOC732436 | 211 | 229 | G | C | U | g | U | G | G | C | A | G | C | U | C | C | U | u | A | U | U | 37 | 2 | 11 | c | false | <90% | 405 | ||
XM_001133214 | LOC732390 | 33 | 51 | G | C | U | g | U | G | G | C | A | G | C | U | C | C | U | u | A | U | U | 37 | 2 | 11 | c | false | <90% | 1604 | ||
NM_005577 | LPA | 364 | 382 | G | C | U | g | U | G | G | C | A | G | C | U | C | C | U | u | A | U | U | 37 | 2 | 11 | c | false | <90% | 6489 | ||
NM_005577 | LPA | 706 | 724 | G | C | U | g | U | G | G | C | A | G | C | U | C | C | U | u | A | U | U | 37 | 2 | 11 | c | false | <90% | 6489 | ||
NM_005577 | LPA | 1048 | 1066 | G | C | U | g | U | G | G | C | A | G | C | U | C | C | U | u | A | U | U | 37 | 2 | 11 | c | false | <90% | 6489 | ||
NM_005577 | LPA | 1390 | 1408 | G | C | U | g | U | G | G | C | A | G | C | U | C | C | U | u | A | U | U | 37 | 2 | 11 | c | false | <90% | 6489 | ||
NM_005577 | LPA | 1732 | 1750 | G | C | U | g | U | G | G | C | A | G | C | U | C | C | U | u | A | U | U | 37 | 2 | 11 | c | false | <90% | 6489 | ||
NM_005577 | LPA | 2074 | 2092 | G | C | U | g | U | G | G | C | A | G | C | U | C | C | U | u | A | U | U | 37 | 2 | 11 | c | false | <90% | 6489 | ||
NM_005577 | LPA | 2416 | 2434 | G | C | U | g | U | G | G | C | A | G | C | U | C | C | U | u | A | U | U | 37 | 2 | 11 | c | false | <90% | 6489 | ||
NM_173608 | C14orf80 | 165 | 183 | G | C | U | c | U | G | G | C | A | G | C | U | C | C | U | C | u | U | c | 34 | 3 | 12 | c | false | <90% | 1419 | ||
NM_182918 | ERG | 1029 | 1047 | G | C | U | U | U | G | G | C | A | G | u | U | C | C | U | C | c | U | g | 10 | 3 | 10 | c | false | <90% | 3055 | ||
NM_004449 | ERG | 1071 | 1089 | G | C | U | U | U | G | G | C | A | G | u | U | C | C | U | C | c | U | g | 10 | 3 | 10 | c | false | <90% | 3097 | ||
NM_002373 | MAP1A | 6967 | 6985 | c | C | U | U | U | G | G | C | u | u | C | U | C | C | U | C | A | U | U | -44 | 3 | 9 | bc | false | <90% | 10275 |
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_138338 | POLR3H | 580 | 598 | A | g | U | G | A | G | G | A | G | C | U | G | C | C | A | A | A | G | a | 83 | 2 | 16 | abc | false | <90% | 4159 | ||
NM_001018052 | POLR3H | 799 | 817 | A | g | U | G | A | G | G | A | G | C | U | G | C | C | A | A | A | G | a | 83 | 2 | 16 | abc | false | <90% | 4378 | ||
NM_001018050 | POLR3H | 886 | 904 | A | g | U | G | A | G | G | A | G | C | U | G | C | C | A | A | A | G | a | 83 | 2 | 16 | abc | false | <90% | 4465 | ||
NM_016489 | NT5C3 | 170 | 188 | A | A | g | G | A | G | G | A | G | C | U | G | C | C | A | A | A | c | u | 72 | 3 | 14 | c | false | <90% | 1552 | ||
NM_001002010 | NT5C3 | 306 | 324 | A | A | g | G | A | G | G | A | G | C | U | G | C | C | A | A | A | c | u | 72 | 3 | 14 | c | false | <90% | 1688 | ||
NM_001002009 | NT5C3 | 361 | 379 | A | A | g | G | A | G | G | A | G | C | U | G | C | C | A | A | A | c | u | 72 | 3 | 14 | c | false | <90% | 1743 | ||
NM_006377 | UNC13B | 175 | 193 | c | A | U | G | A | G | G | A | G | C | U | G | C | C | A | g | A | c | C | 69 | 3 | 14 | c | false | <90% | 6398 | ||
NM_001042467 | MLPH | 1520 | 1538 | g | A | U | G | A | G | G | A | G | C | U | G | u | C | A | g | A | G | C | 61 | 3 | 11 | false | <90% | 3687 | |||
NM_024101 | MLPH | 1604 | 1622 | g | A | U | G | A | G | G | A | G | C | U | G | u | C | A | g | A | G | C | 61 | 3 | 11 | false | <90% | 3771 | |||
NM_032435 | KIAA1804 | 1629 | 1647 | c | A | g | G | A | G | G | A | G | C | U | G | C | u | A | A | A | G | C | 58 | 3 | 10 | c | false | <90% | 4667 | ||
XR_017100 | LOC149501 | 936 | 954 | A | A | U | G | A | G | G | A | G | C | U | G | C | a | A | g | A | G | C | 54 | 2 | 13 | c | false | <90% | 1794 | ||
XR_018597 | LOC649344 | 939 | 957 | A | A | U | G | A | G | G | A | G | C | U | G | C | a | A | g | A | G | C | 54 | 2 | 13 | c | false | <90% | 1797 | ||
NM_002218 | ITIH4 | 474 | 492 | u | A | U | G | A | G | G | A | G | C | U | G | C | u | c | A | A | G | C | 53 | 3 | 12 | c | false | <90% | 3260 | ||
NM_052855 | ANKRD40 | 441 | 459 | A | A | U | c | A | G | G | A | G | C | U | G | a | C | A | A | A | G | a | 47 | 3 | 8 | false | <90% | 2060 | |||
NM_015894 | STMN3 | 330 | 348 | c | u | g | G | A | G | G | A | G | C | U | G | C | a | A | A | A | G | C | 47 | 4 | 10 | c | false | <90% | 2255 | ||
NR_003261 | CDRT15P | 541 | 559 | A | A | U | G | A | G | G | A | G | C | U | G | C | C | u | g | A | a | a | 41 | 4 | 14 | c | false | <90% | 1101 | ||
NM_001017974 | P4HA2 | 483 | 501 | A | g | a | u | A | G | G | A | G | C | U | G | C | C | A | A | A | G | C | 32 | 3 | 15 | bc | false | <90% | 2110 | ||
NM_001017973 | P4HA2 | 955 | 973 | A | g | a | u | A | G | G | A | G | C | U | G | C | C | A | A | A | G | C | 32 | 3 | 15 | bc | false | <90% | 2582 | ||
NM_004199 | P4HA2 | 955 | 973 | A | g | a | u | A | G | G | A | G | C | U | G | C | C | A | A | A | G | C | 32 | 3 | 15 | bc | false | <90% | 2588 | ||
NM_002022 | FMO4 | 1066 | 1084 | A | A | U | G | A | u | G | A | G | C | U | G | C | C | A | A | A | c | u | 29 | 3 | 11 | c | false | <90% | 2148 | ||
NM_006915 | RP2 | 232 | 250 | g | A | g | G | A | G | G | A | G | C | g | G | C | C | A | A | A | G | C | 17 | 3 | 8 | c | false | <90% | 3813 | ||
NM_152586 | USP54 | 5952 | 5970 | A | A | U | G | c | G | G | A | G | C | U | G | C | C | A | A | c | a | u | 17 | 4 | 11 | c | false | <90% | 6202 | ||
NM_020345 | NKIRAS1 | 608 | 626 | g | g | c | G | u | G | G | A | G | C | U | G | C | C | A | A | A | G | C | 15 | 4 | 14 | bc | false | <90% | 2013 | ||
NM_005514 | HLA-B | 861 | 879 | c | A | U | G | A | G | G | g | G | C | U | G | C | C | g | A | A | G | C | 11 | 3 | 6 | c | false | <90% | 1533 | ||
XM_001131713 | LOC730410 | 1188 | 1206 | c | A | U | G | A | G | G | g | G | C | U | G | C | C | g | A | A | G | C | 11 | 3 | 6 | c | false | <90% | 1853 | ||
NM_001004349 | FLJ45422 | 712 | 730 | c | A | U | G | A | G | G | g | G | C | U | G | C | C | A | g | A | G | C | 9 | 3 | 7 | c | false | <90% | 4587 | ||
XM_001132499 | LOC646985 | 108 | 126 | u | u | c | G | A | G | a | A | G | C | U | G | C | C | A | A | A | G | C | 0 | 4 | 12 | bc | false | <90% | 195 | ||
XM_001127349 | LOC648361 | 108 | 126 | u | u | c | G | A | G | a | A | G | C | U | G | C | C | A | A | A | G | C | 0 | 4 | 12 | bc | false | <90% | 195 | ||
NM_012087 | GTF3C5 | 956 | 974 | g | A | U | G | A | G | G | A | G | g | U | G | C | C | c | A | A | G | C | -9 | 3 | 8 | c | false | <90% | 2380 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2760
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