Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
76 hits were found for CCCCCCUCCCGGGAGAGCC (41 guide strand hits and 35 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_152707 | SLC25A16 | 254 | 272 | C | g | C | C | C | C | U | C | C | C | G | G | c | A | G | A | G | C | C | 78 | 2 | 10 | false | <90% | 2560 | |||
NM_002973 | ATXN2 | 349 | 367 | C | C | u | C | C | C | U | C | C | C | G | G | c | A | G | A | G | C | u | 65 | 3 | 9 | false | <90% | 4702 | |||
NM_002501 | NFIX | 5113 | 5131 | g | g | C | C | C | C | U | C | C | C | G | G | G | A | G | A | u | C | C | 63 | 3 | 14 | ac | false | <90% | 5576 | ||
NM_015059 | TLN2 | 7727 | 7745 | C | C | u | C | C | C | U | C | C | C | G | G | G | u | G | A | G | C | C | 60 | 2 | 10 | c | false | <90% | 8500 | ||
NM_005708 | GPC6 | 184 | 202 | u | C | u | C | C | C | U | C | C | C | G | G | G | g | G | A | G | C | C | 58 | 3 | 10 | c | false | <90% | 2760 | ||
NM_203425 | C17orf82 | 483 | 501 | g | C | a | C | C | C | U | C | C | C | G | G | G | A | G | c | G | C | C | 52 | 3 | 12 | c | false | <90% | 1546 | ||
NM_001037165 | FOXK1 | 4368 | 4386 | g | C | g | C | C | C | U | C | C | C | G | G | G | A | G | c | G | C | C | 52 | 3 | 12 | c | false | <90% | 11191 | ||
NM_004211 | SLC6A5 | 591 | 609 | g | C | C | C | C | C | U | C | C | C | G | G | G | A | G | c | u | C | C | 48 | 3 | 14 | c | false | <90% | 2863 | ||
XM_932202 | LOC644472 | 425 | 443 | g | C | C | C | C | C | U | C | C | C | G | c | G | g | G | A | G | C | C | 44 | 3 | 10 | false | <90% | 963 | |||
NM_001998 | FBLN2 | 1951 | 1969 | u | u | C | u | C | C | U | C | C | C | G | G | G | A | G | A | G | C | u | 44 | 4 | 14 | bc | false | <90% | 4193 | ||
NM_001004019 | FBLN2 | 1951 | 1969 | u | u | C | u | C | C | U | C | C | C | G | G | G | A | G | A | G | C | u | 44 | 4 | 14 | bc | false | <90% | 4334 | ||
NM_058230 | ZNF354B | 150 | 168 | C | C | g | u | C | C | U | C | C | C | G | G | G | A | G | A | G | C | C | 43 | 2 | 15 | bc | false | <90% | 2140 | ||
NM_005649 | ZNF354A | 169 | 187 | C | C | g | u | C | C | U | C | C | C | G | G | G | A | G | A | G | C | C | 43 | 2 | 15 | bc | false | <90% | 2555 | ||
XM_942328 | LOC652710 | 1552 | 1570 | u | g | C | C | a | C | U | C | C | C | G | G | G | A | G | A | G | C | C | 35 | 3 | 14 | bc | false | <90% | 2523 | ||
NM_000719 | CACNA1C | 5711 | 5729 | u | g | C | C | a | C | U | C | C | C | G | G | G | A | G | A | G | C | C | 35 | 3 | 14 | bc | false | <90% | 13432 | ||
XM_944303 | SETD5 | 196 | 214 | g | C | C | g | C | C | U | C | C | C | G | G | G | A | G | u | G | C | C | 35 | 3 | 11 | c | false | <90% | 6306 | ||
XM_931455 | SETD5 | 196 | 214 | g | C | C | g | C | C | U | C | C | C | G | G | G | A | G | u | G | C | C | 35 | 3 | 11 | c | false | <90% | 6306 | ||
XM_944298 | SETD5 | 196 | 214 | g | C | C | g | C | C | U | C | C | C | G | G | G | A | G | u | G | C | C | 35 | 3 | 11 | c | false | <90% | 6575 | ||
XM_931447 | SETD5 | 196 | 214 | g | C | C | g | C | C | U | C | C | C | G | G | G | A | G | u | G | C | C | 35 | 3 | 11 | c | false | <90% | 6575 | ||
NM_001080517 | SETD5 | 196 | 214 | g | C | C | g | C | C | U | C | C | C | G | G | G | A | G | u | G | C | C | 35 | 3 | 11 | c | false | <90% | 6827 | ||
XM_939712 | SETD5 | 196 | 214 | g | C | C | g | C | C | U | C | C | C | G | G | G | A | G | u | G | C | C | 35 | 3 | 11 | c | false | <90% | 6827 | ||
XM_944295 | SETD5 | 196 | 214 | g | C | C | g | C | C | U | C | C | C | G | G | G | A | G | u | G | C | C | 35 | 3 | 11 | c | false | <90% | 7060 | ||
XM_931444 | SETD5 | 196 | 214 | g | C | C | g | C | C | U | C | C | C | G | G | G | A | G | u | G | C | C | 35 | 3 | 11 | c | false | <90% | 7060 | ||
XM_944260 | SETD5 | 215 | 233 | g | C | C | g | C | C | U | C | C | C | G | G | G | A | G | u | G | C | C | 35 | 3 | 11 | c | false | <90% | 7071 | ||
XM_931376 | SETD5 | 215 | 233 | g | C | C | g | C | C | U | C | C | C | G | G | G | A | G | u | G | C | C | 35 | 3 | 11 | c | false | <90% | 7110 | ||
NM_198496 | VWA2 | 158 | 176 | g | C | C | C | C | C | U | C | C | C | a | G | G | A | G | A | G | a | C | 34 | 3 | 9 | c | false | <90% | 2946 | ||
NM_001002029 | C4B | 4639 | 4657 | C | C | C | a | C | C | U | C | C | C | G | G | G | A | G | u | G | C | g | 32 | 3 | 11 | c | false | <90% | 5426 | ||
NM_007293 | C4A | 4639 | 4657 | C | C | C | a | C | C | U | C | C | C | G | G | G | A | G | u | G | C | g | 32 | 3 | 11 | c | false | <90% | 5426 | ||
NM_015023 | WDTC1 | 211 | 229 | C | C | C | C | C | u | U | C | C | C | G | G | G | A | G | A | G | g | g | 29 | 3 | 11 | c | false | <90% | 4305 | ||
XM_001131903 | LOC729963 | 440 | 458 | u | C | C | C | C | C | U | C | C | C | c | G | G | A | G | A | G | g | a | 29 | 4 | 9 | c | false | <90% | 477 | ||
NM_198227 | RGS12 | 2610 | 2628 | g | C | C | C | C | g | U | C | C | C | G | G | G | u | G | A | G | C | C | 15 | 3 | 7 | c | false | <90% | 2916 | ||
NM_198229 | RGS12 | 5187 | 5205 | g | C | C | C | C | g | U | C | C | C | G | G | G | u | G | A | G | C | C | 15 | 3 | 7 | c | false | <90% | 5486 | ||
NM_004979 | KCND1 | 459 | 477 | C | C | C | C | C | C | U | C | C | C | u | G | G | A | G | A | c | a | C | 12 | 3 | 10 | c | false | <90% | 4720 | ||
NM_024018 | BTN2A3 | 970 | 988 | g | a | C | C | C | C | U | C | C | a | G | G | G | A | G | A | G | C | a | -1 | 4 | 8 | bc | false | <90% | 1761 | ||
NM_001703 | BAI2 | 10 | 28 | C | C | C | g | C | C | g | C | C | C | G | G | G | A | G | A | G | C | g | -8 | 3 | 11 | bc | false | <90% | 5434 | ||
NM_024301 | FKRP | 2499 | 2517 | C | u | u | C | C | C | U | C | C | u | G | G | G | A | G | A | G | C | C | -13 | 3 | 9 | bc | false | <90% | 3349 | ||
NM_001039885 | FKRP | 2718 | 2736 | C | u | u | C | C | C | U | C | C | u | G | G | G | A | G | A | G | C | C | -13 | 3 | 9 | bc | false | <90% | 3568 | ||
NM_145175 | FAM84A | 426 | 444 | a | C | C | C | C | C | U | g | C | C | c | G | G | A | G | A | G | C | C | -25 | 3 | 8 | c | false | <90% | 2586 | ||
XM_943480 | LOC648831 | 193 | 211 | u | C | C | C | C | a | U | C | C | g | G | G | G | A | G | A | G | C | C | -48 | 3 | 9 | bc | false | <90% | 486 | ||
XM_931952 | LOC643972 | 193 | 211 | u | C | C | C | C | a | U | C | C | g | G | G | G | A | G | A | G | C | C | -48 | 3 | 9 | bc | false | <90% | 486 | ||
NM_001013627 | LOC340527 | 584 | 602 | u | C | C | C | C | C | a | C | C | u | G | G | G | A | G | A | G | C | C | -51 | 3 | 9 | bc | false | <90% | 3978 |
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_001127838 | ALDH7A1 | 83 | 101 | G | G | u | U | C | U | C | C | C | G | G | G | c | G | G | G | G | G | G | 70 | 2 | 9 | false | <90% | 1728 | |||
XM_211040 | LOC283440 | 515 | 533 | G | G | C | U | C | U | C | C | C | G | G | G | A | G | u | G | G | c | a | 67 | 3 | 14 | c | false | <90% | 572 | ||
XM_943149 | LOC647957 | 515 | 533 | G | G | C | U | C | U | C | C | C | G | G | G | A | G | u | G | G | c | a | 67 | 3 | 14 | c | false | <90% | 572 | ||
NM_001079881 | PRKD2 | 379 | 397 | G | G | C | U | C | U | C | C | C | G | G | G | c | c | G | G | G | G | u | 65 | 3 | 12 | false | <90% | 3202 | |||
NM_001079880 | PRKD2 | 515 | 533 | G | G | C | U | C | U | C | C | C | G | G | G | c | c | G | G | G | G | u | 65 | 3 | 12 | false | <90% | 3338 | |||
NM_016457 | PRKD2 | 794 | 812 | G | G | C | U | C | U | C | C | C | G | G | G | c | c | G | G | G | G | u | 65 | 3 | 12 | false | <90% | 3617 | |||
NM_014955 | KIAA0859 | 544 | 562 | a | c | u | U | C | U | C | C | C | G | G | G | A | G | G | G | G | u | G | 64 | 4 | 14 | c | false | <90% | 3096 | ||
NM_015935 | KIAA0859 | 869 | 887 | a | c | u | U | C | U | C | C | C | G | G | G | A | G | G | G | G | u | G | 64 | 4 | 14 | c | false | <90% | 3421 | ||
NM_030758 | OSBP2 | 483 | 501 | c | G | C | U | C | U | C | C | C | G | G | G | c | G | G | u | G | G | G | 61 | 3 | 11 | false | <90% | 4349 | |||
NM_001116 | ADCY9 | 5508 | 5526 | u | G | C | g | C | U | C | C | C | G | G | G | A | G | G | G | G | u | G | 58 | 3 | 13 | c | false | <90% | 7732 | ||
NM_001080436 | WTIP | 82 | 100 | G | G | C | U | C | U | C | C | C | G | G | u | c | G | G | G | G | G | c | 50 | 3 | 11 | false | <90% | 2204 | |||
XM_939855 | WTIP | 1012 | 1030 | G | G | C | U | C | U | C | C | C | G | G | u | c | G | G | G | G | G | c | 50 | 3 | 11 | false | <90% | 3134 | |||
XM_001129340 | LOC284952 | 1831 | 1849 | G | G | C | U | C | U | C | C | C | G | G | G | A | u | G | G | c | u | u | 49 | 4 | 13 | c | false | <90% | 3218 | ||
XM_001126137 | LOC284952 | 1831 | 1849 | G | G | C | U | C | U | C | C | C | G | G | G | A | u | G | G | c | u | u | 49 | 4 | 13 | c | false | <90% | 3218 | ||
NM_002358 | MAD2L1 | 87 | 105 | a | G | C | U | C | U | C | C | C | G | G | G | A | G | c | a | G | G | G | 47 | 3 | 13 | c | false | <90% | 1390 | ||
NM_018652 | GOLGA | 1526 | 1544 | G | G | C | U | C | U | C | C | C | G | G | G | A | G | a | a | G | G | a | 44 | 3 | 14 | c | false | <90% | 3178 | ||
NM_025251 | KIAA1688 | 3968 | 3986 | c | G | C | U | C | U | C | C | C | G | G | c | A | G | a | G | G | G | G | 39 | 3 | 10 | false | <90% | 5147 | |||
XM_944418 | LOC650922 | 28 | 46 | c | G | C | g | C | U | C | C | C | G | G | G | A | G | G | G | c | G | G | 37 | 3 | 12 | c | false | <90% | 734 | ||
XM_498965 | LOC441009 | 28 | 46 | c | G | C | g | C | U | C | C | C | G | G | G | A | G | G | G | c | G | G | 37 | 3 | 12 | c | false | <90% | 734 | ||
NM_020064 | BARHL1 | 1261 | 1279 | c | c | C | U | u | U | C | C | C | G | G | G | A | G | G | G | G | G | c | 30 | 4 | 13 | bc | false | <90% | 1907 | ||
NM_015995 | KLF13 | 3594 | 3612 | u | G | C | U | C | U | C | C | a | G | G | G | A | G | G | G | G | u | c | 30 | 4 | 8 | c | false | <90% | 6817 | ||
XM_944879 | LOC651694 | 62 | 80 | G | c | C | U | C | c | C | C | C | G | G | G | A | G | G | G | G | G | a | 20 | 3 | 12 | bc | false | <90% | 525 | ||
XM_931443 | LOC643260 | 62 | 80 | G | c | C | U | C | c | C | C | C | G | G | G | A | G | G | G | G | G | a | 20 | 3 | 12 | bc | false | <90% | 525 | ||
XM_001130169 | BAI1 | 3288 | 3306 | G | G | C | U | C | U | C | C | C | u | G | G | A | G | G | G | G | G | G | 17 | 1 | 9 | bc | false | <90% | 4791 | ||
NM_001702 | BAI1 | 3435 | 3453 | G | G | C | U | C | U | C | C | C | u | G | G | A | G | G | G | G | G | G | 17 | 1 | 9 | bc | false | <90% | 5535 | ||
XM_372755 | LOC390988 | 29 | 47 | G | c | C | U | C | U | g | C | C | G | G | G | A | G | G | G | G | G | a | 17 | 3 | 11 | bc | false | <90% | 2244 | ||
XM_936778 | LOC647718 | 491 | 509 | G | c | C | U | C | U | g | C | C | G | G | G | A | G | G | G | G | G | a | 17 | 3 | 11 | bc | false | <90% | 2706 | ||
NR_001575 | RNF138P1 | 8 | 26 | G | G | C | U | g | U | C | C | C | G | G | G | A | G | G | G | c | u | u | 17 | 4 | 11 | c | false | <90% | 5701 | ||
NM_004621 | TRPC6 | 383 | 401 | G | G | C | U | C | c | C | C | C | G | G | G | A | G | c | G | G | G | G | 12 | 2 | 8 | c | false | <90% | 4537 | ||
NM_018379 | FAM63A | 3090 | 3108 | u | G | C | U | C | U | C | C | u | G | G | G | A | G | G | u | G | G | G | 11 | 3 | 7 | c | false | <90% | 4043 | ||
NM_001319 | CSNK1G2 | 1789 | 1807 | G | G | C | c | C | U | C | C | u | G | G | G | A | G | G | G | G | G | a | -1 | 3 | 9 | bc | false | <90% | 2446 | ||
NM_006958 | ZNF16 | 489 | 507 | c | c | C | U | C | U | C | C | C | a | G | G | A | G | G | G | G | G | a | -1 | 4 | 8 | bc | false | <90% | 2546 | ||
NM_001029976 | ZNF16 | 575 | 593 | c | c | C | U | C | U | C | C | C | a | G | G | A | G | G | G | G | G | a | -1 | 4 | 8 | bc | false | <90% | 2632 | ||
NM_002583 | PAWR | 403 | 421 | G | G | C | c | C | c | C | C | C | G | G | G | A | G | G | G | G | G | c | -5 | 3 | 12 | bc | false | <90% | 1967 | ||
NM_001703 | BAI2 | 3561 | 3579 | G | G | C | U | C | U | C | C | C | u | G | G | A | G | G | G | c | G | G | -6 | 2 | 9 | c | false | <90% | 5434 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1688
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