Automatic recommendation
Not OK - siRNA is not specific
60 hits were found for CCUUGCCCAUCAGGAACAU (11 guide strand hits and 49 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_024772 | ZMYM1 | 1218 | 1236 | C | C | U | U | G | C | C | C | A | U | C | A | u | G | A | A | C | A | c | 84 | 2 | 12 | false | <90% | 4172 | |||
XM_001128273 | LOC728719 | 2405 | 2423 | g | g | U | U | G | C | C | C | A | U | C | A | G | G | A | A | g | A | g | 58 | 4 | 14 | ac | false | <90% | 2571 | ||
XM_001128242 | LOC728704 | 2564 | 2582 | g | g | U | U | G | C | C | C | A | U | C | A | G | G | A | A | g | A | g | 58 | 4 | 14 | ac | false | <90% | 2730 | ||
NM_153366 | SVEP1 | 1297 | 1315 | g | C | U | U | G | C | C | C | A | U | C | g | G | G | g | A | C | A | U | 39 | 3 | 10 | false | <90% | 11415 | |||
NM_006288 | THY1 | 918 | 936 | C | C | U | U | G | C | C | C | A | U | C | g | G | G | A | c | C | A | g | 35 | 3 | 11 | false | <90% | 1791 | |||
NM_182587 | C2orf21 | 778 | 796 | u | g | a | a | G | C | C | C | A | U | C | A | G | G | A | A | C | A | U | 30 | 4 | 15 | bc | false | <90% | 2771 | ||
NM_014548 | TMOD2 | 1288 | 1306 | u | C | U | U | c | C | C | C | A | U | C | A | G | G | A | c | C | A | U | 20 | 3 | 10 | c | false | <90% | 2945 | ||
NM_001039 | SCNN1G | 1272 | 1290 | a | C | g | U | G | C | C | a | A | U | C | A | G | G | A | A | C | A | U | 16 | 3 | 11 | bc | false | <90% | 3516 | ||
NR_003281 | GMCL1L | 178 | 196 | C | C | U | U | G | C | C | C | A | g | C | A | G | G | A | A | C | A | g | 12 | 2 | 9 | bc | false | <90% | 2923 | ||
NM_032446 | MEGF10 | 2565 | 2583 | a | a | g | U | G | C | C | C | u | U | C | A | G | G | A | A | C | A | U | 6 | 4 | 10 | bc | false | <90% | 7522 | ||
NM_030765 | B3GNT4 | 967 | 985 | C | C | c | U | G | C | C | C | A | a | C | A | G | G | A | A | C | A | c | -7 | 3 | 8 | bc | false | <90% | 1554 |
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 | |||||||||||||
XR_015980 | LOC731825 | 799 | 817 | c | U | G | U | U | C | C | U | G | A | U | G | G | c | C | A | A | G | u | 73 | 3 | 12 | c | false | <90% | 1406 | ||
XR_016662 | LOC390924 | 799 | 817 | c | U | G | U | U | C | C | U | G | A | U | G | G | c | C | A | A | G | u | 73 | 3 | 12 | c | false | <90% | 1406 | ||
NM_138703 | MAGEE2 | 1415 | 1433 | A | U | c | U | U | C | C | U | G | A | U | G | G | G | C | A | A | c | c | 72 | 3 | 14 | c | false | <90% | 2249 | ||
NM_004399 | DDX11 | 2813 | 2831 | c | U | c | U | U | C | C | U | G | A | U | G | G | G | C | A | A | c | c | 70 | 4 | 14 | c | false | <90% | 3797 | ||
NM_152438 | DDX11 | 2958 | 2976 | c | U | c | U | U | C | C | U | G | A | U | G | G | G | C | A | A | c | c | 70 | 4 | 14 | c | false | <90% | 3942 | ||
NM_030653 | DDX11 | 2963 | 2981 | c | U | c | U | U | C | C | U | G | A | U | G | G | G | C | A | A | c | c | 70 | 4 | 14 | c | false | <90% | 3947 | ||
XR_017754 | LOC642846 | 2768 | 2786 | c | U | c | U | U | C | C | U | G | A | U | G | G | G | C | A | A | c | c | 70 | 4 | 14 | c | false | <90% | 4413 | ||
XM_495908 | DDX12 | 2769 | 2787 | c | U | c | U | U | C | C | U | G | A | U | G | G | G | C | A | A | c | c | 70 | 4 | 14 | c | false | <90% | 4417 | ||
XM_001126721 | CTNND1 | 2393 | 2411 | u | U | u | U | U | C | C | U | G | A | U | G | G | G | g | A | A | G | G | 53 | 3 | 11 | c | false | <90% | 5190 | ||
XM_001126793 | CTNND1 | 2555 | 2573 | u | U | u | U | U | C | C | U | G | A | U | G | G | G | g | A | A | G | G | 53 | 3 | 11 | c | false | <90% | 5352 | ||
XM_001126767 | CTNND1 | 2561 | 2579 | u | U | u | U | U | C | C | U | G | A | U | G | G | G | g | A | A | G | G | 53 | 3 | 11 | c | false | <90% | 5358 | ||
XM_001126823 | CTNND1 | 2610 | 2628 | u | U | u | U | U | C | C | U | G | A | U | G | G | G | g | A | A | G | G | 53 | 3 | 11 | c | false | <90% | 5407 | ||
XM_001126781 | CTNND1 | 2624 | 2642 | u | U | u | U | U | C | C | U | G | A | U | G | G | G | g | A | A | G | G | 53 | 3 | 11 | c | false | <90% | 5421 | ||
XM_001126756 | CTNND1 | 2642 | 2660 | u | U | u | U | U | C | C | U | G | A | U | G | G | G | g | A | A | G | G | 53 | 3 | 11 | c | false | <90% | 5439 | ||
NM_001331 | CTNND1 | 3803 | 3821 | u | U | u | U | U | C | C | U | G | A | U | G | G | G | g | A | A | G | G | 53 | 3 | 11 | c | false | <90% | 6232 | ||
NM_005912 | MC4R | 1062 | 1080 | A | U | G | U | U | C | C | U | G | A | U | G | G | c | C | A | g | G | c | 51 | 3 | 13 | c | false | <90% | 1438 | ||
NM_021220 | OVOL2 | 1313 | 1331 | A | U | G | a | U | C | C | U | G | A | U | G | G | c | C | A | A | G | a | 38 | 3 | 9 | c | false | <90% | 1555 | ||
NM_017983 | WIPI1 | 688 | 706 | c | U | G | U | c | C | C | U | G | A | U | G | G | G | C | A | A | a | a | 38 | 4 | 12 | c | false | <90% | 1892 | ||
NM_021123 | GAGE7 | 322 | 340 | A | U | G | g | U | C | C | U | G | A | U | G | G | G | C | A | g | G | a | 34 | 3 | 12 | c | false | <90% | 498 | ||
NM_001475 | GAGE5 | 343 | 361 | A | U | G | g | U | C | C | U | G | A | U | G | G | G | C | A | g | G | a | 34 | 3 | 12 | c | false | <90% | 524 | ||
NM_001477 | GAGE7B | 323 | 341 | A | U | G | g | U | C | C | U | G | A | U | G | G | G | C | A | g | G | a | 34 | 3 | 12 | c | false | <90% | 526 | ||
NM_001476 | GAGE6 | 350 | 368 | A | U | G | g | U | C | C | U | G | A | U | G | G | G | C | A | g | G | a | 34 | 3 | 12 | c | false | <90% | 527 | ||
NM_001474 | GAGE4 | 351 | 369 | A | U | G | g | U | C | C | U | G | A | U | G | G | G | C | A | g | G | a | 34 | 3 | 12 | c | false | <90% | 528 | ||
NM_012196 | GAGE8 | 338 | 356 | A | U | G | g | U | C | C | U | G | A | U | G | G | G | C | A | g | G | a | 34 | 3 | 12 | c | false | <90% | 528 | ||
NM_001472 | GAGE2 | 349 | 367 | A | U | G | g | U | C | C | U | G | A | U | G | G | G | C | A | g | G | a | 34 | 3 | 12 | c | false | <90% | 538 | ||
XM_930008 | LOC645037 | 382 | 400 | A | U | G | g | U | C | C | U | G | A | U | G | G | G | C | A | g | G | a | 34 | 3 | 12 | c | false | <90% | 542 | ||
XM_001130827 | LOC729408 | 382 | 400 | A | U | G | g | U | C | C | U | G | A | U | G | G | G | C | A | g | G | a | 34 | 3 | 12 | c | false | <90% | 561 | ||
XM_001130991 | LOC729447 | 382 | 400 | A | U | G | g | U | C | C | U | G | A | U | G | G | G | C | A | g | G | a | 34 | 3 | 12 | c | false | <90% | 561 | ||
XM_001130767 | LOC729396 | 385 | 403 | A | U | G | g | U | C | C | U | G | A | U | G | G | G | C | A | g | G | a | 34 | 3 | 12 | c | false | <90% | 564 | ||
XM_001130787 | GAGE12D | 385 | 403 | A | U | G | g | U | C | C | U | G | A | U | G | G | G | C | A | g | G | a | 34 | 3 | 12 | c | false | <90% | 564 | ||
XM_001130891 | LOC729422 | 385 | 403 | A | U | G | g | U | C | C | U | G | A | U | G | G | G | C | A | g | G | a | 34 | 3 | 12 | c | false | <90% | 564 | ||
XM_001130905 | LOC729428 | 385 | 403 | A | U | G | g | U | C | C | U | G | A | U | G | G | G | C | A | g | G | a | 34 | 3 | 12 | c | false | <90% | 564 | ||
XM_001130926 | LOC729431 | 385 | 403 | A | U | G | g | U | C | C | U | G | A | U | G | G | G | C | A | g | G | a | 34 | 3 | 12 | c | false | <90% | 564 | ||
XM_001130959 | GAGE12G | 385 | 403 | A | U | G | g | U | C | C | U | G | A | U | G | G | G | C | A | g | G | a | 34 | 3 | 12 | c | false | <90% | 564 | ||
XM_001130972 | LOC729442 | 385 | 403 | A | U | G | g | U | C | C | U | G | A | U | G | G | G | C | A | g | G | a | 34 | 3 | 12 | c | false | <90% | 564 | ||
NM_001040663 | GAGE1 | 385 | 403 | A | U | G | g | U | C | C | U | G | A | U | G | G | G | C | A | g | G | a | 34 | 3 | 12 | c | false | <90% | 810 | ||
NM_001468 | GAGE1 | 385 | 403 | A | U | G | g | U | C | C | U | G | A | U | G | G | G | C | A | g | G | a | 34 | 3 | 12 | c | false | <90% | 953 | ||
NM_033011 | PLAT | 796 | 814 | A | U | G | a | U | C | C | U | G | A | U | a | G | G | C | A | A | G | G | 29 | 2 | 7 | false | <90% | 3035 | |||
NM_000930 | PLAT | 934 | 952 | A | U | G | a | U | C | C | U | G | A | U | a | G | G | C | A | A | G | G | 29 | 2 | 7 | false | <90% | 3173 | |||
NM_177939 | PH-4 | 1624 | 1642 | A | c | c | U | g | C | C | U | G | A | U | G | G | G | C | A | A | G | G | 17 | 3 | 14 | bc | false | <90% | 2111 | ||
NM_177938 | PH-4 | 1807 | 1825 | A | c | c | U | g | C | C | U | G | A | U | G | G | G | C | A | A | G | G | 17 | 3 | 14 | bc | false | <90% | 2294 | ||
NM_207332 | ERICH1 | 1526 | 1544 | u | U | G | U | U | C | C | U | G | g | U | G | G | G | C | A | A | G | a | 10 | 3 | 8 | bc | false | <90% | 1836 | ||
XR_015562 | LOC729493 | 397 | 415 | A | U | G | U | U | C | g | U | G | A | U | G | G | G | C | A | u | G | a | 5 | 3 | 9 | c | false | <90% | 1017 | ||
XR_015759 | LOC732193 | 397 | 415 | A | U | G | U | U | C | g | U | G | A | U | G | G | G | C | A | u | G | a | 5 | 3 | 9 | c | false | <90% | 1017 | ||
XR_016109 | LOC642259 | 403 | 421 | A | U | G | U | U | C | a | U | G | A | U | G | G | G | C | A | u | a | a | 2 | 4 | 9 | c | false | <90% | 1045 | ||
XR_018113 | LOC642203 | 403 | 421 | A | U | G | U | U | C | a | U | G | A | U | G | G | G | C | A | u | a | a | 2 | 4 | 9 | c | false | <90% | 1045 | ||
XR_019141 | LOC390860 | 154 | 172 | A | U | G | g | U | g | C | U | G | A | U | G | G | G | C | A | A | G | a | -5 | 3 | 12 | bc | false | <90% | 951 | ||
XR_016593 | LOC390860 | 154 | 172 | A | U | G | g | U | g | C | U | G | A | U | G | G | G | C | A | A | G | a | -5 | 3 | 12 | bc | false | <90% | 951 | ||
NM_017797 | BTBD2 | 362 | 380 | c | a | c | U | U | C | C | U | G | g | U | G | G | G | C | A | A | G | G | -15 | 4 | 9 | bc | false | <90% | 2656 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2622
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