Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
97 hits were found for GCAGAAAGAAAAAUCCAAC (56 guide strand hits and 41 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_024915 | GRHL2 | 1273 | 1291 | G | C | A | G | A | A | A | G | A | A | A | A | A | U | C | C | g | A | g | 71 | 2 | 16 | ac | false | <90% | 4792 | ||
NM_002393 | MDM4 | 1296 | 1314 | a | a | A | G | A | A | A | G | A | A | A | A | c | U | C | C | A | A | a | 71 | 4 | 10 | false | <90% | 2554 | |||
NM_031292 | PUS7L | 745 | 763 | a | a | A | G | A | A | A | G | A | A | A | A | u | U | C | C | A | A | a | 71 | 4 | 10 | false | <90% | 3959 | |||
NR_001458 | BIC | 11203 | 11221 | a | C | A | G | A | A | A | G | A | A | A | A | A | U | u | C | A | g | C | 70 | 3 | 13 | c | false | <90% | 12969 | ||
NM_000328 | RPGR | 2256 | 2274 | a | a | A | G | A | A | A | G | A | A | A | A | A | g | C | C | A | A | C | 67 | 3 | 11 | c | false | <90% | 3082 | ||
NM_001040102 | TMEM10 | 2620 | 2638 | G | C | A | G | A | A | A | G | A | A | A | A | A | U | C | a | A | g | a | 66 | 3 | 15 | c | false | <90% | 3521 | ||
NM_033207 | TMEM10 | 2689 | 2707 | G | C | A | G | A | A | A | G | A | A | A | A | A | U | C | a | A | g | a | 66 | 3 | 15 | c | false | <90% | 3590 | ||
NM_001040103 | TMEM10 | 2728 | 2746 | G | C | A | G | A | A | A | G | A | A | A | A | A | U | C | a | A | g | a | 66 | 3 | 15 | c | false | <90% | 3629 | ||
NM_006379 | SEMA3C | 3716 | 3734 | u | C | A | G | A | A | A | G | A | A | A | A | A | U | C | a | A | A | g | 66 | 3 | 14 | c | false | <90% | 5189 | ||
NM_019083 | CCDC76 | 689 | 707 | a | C | A | G | A | A | A | G | A | A | A | A | A | U | u | C | A | g | u | 65 | 4 | 13 | c | false | <90% | 3129 | ||
NM_001498 | GCLC | 2310 | 2328 | a | C | A | G | A | A | A | G | A | A | A | A | A | U | g | C | A | u | u | 65 | 4 | 13 | c | false | <90% | 3717 | ||
NM_014837 | SMG7 | 3511 | 3529 | a | C | A | a | A | A | A | G | A | A | A | A | A | U | C | C | A | u | C | 58 | 3 | 13 | c | false | <90% | 5648 | ||
NM_201569 | SMG7 | 3539 | 3557 | a | C | A | a | A | A | A | G | A | A | A | A | A | U | C | C | A | u | C | 58 | 3 | 13 | c | false | <90% | 5676 | ||
NM_201568 | SMG7 | 3571 | 3589 | a | C | A | a | A | A | A | G | A | A | A | A | A | U | C | C | A | u | C | 58 | 3 | 13 | c | false | <90% | 5708 | ||
NM_173156 | SMG7 | 3709 | 3727 | a | C | A | a | A | A | A | G | A | A | A | A | A | U | C | C | A | u | C | 58 | 3 | 13 | c | false | <90% | 5846 | ||
XM_379194 | LOC401068 | 1137 | 1155 | G | g | A | G | A | A | A | G | A | A | A | A | A | U | C | u | A | A | a | 57 | 3 | 13 | c | false | <90% | 2060 | ||
NM_181783 | TMTC3 | 2702 | 2720 | a | a | g | G | A | A | A | G | A | A | A | A | u | U | C | C | A | A | C | 56 | 4 | 9 | false | <90% | 4997 | |||
NM_020449 | THOC2 | 4003 | 4021 | a | g | A | G | A | A | A | G | A | A | A | A | A | U | u | C | A | A | g | 56 | 4 | 12 | c | false | <90% | 5618 | ||
NM_001081550 | THOC2 | 4010 | 4028 | a | g | A | G | A | A | A | G | A | A | A | A | A | U | u | C | A | A | g | 56 | 4 | 12 | c | false | <90% | 5625 | ||
NR_001564 | XIST | 16619 | 16637 | a | a | A | G | A | A | A | G | A | A | A | A | A | U | g | C | A | A | g | 56 | 4 | 12 | c | false | <90% | 19271 | ||
NM_000670 | ADH4 | 40 | 58 | u | C | A | G | A | A | A | G | A | A | A | c | u | U | C | C | A | A | C | 53 | 3 | 10 | false | <90% | 1980 | |||
NM_024546 | C13orf7 | 2178 | 2196 | a | C | A | a | A | A | A | G | A | A | A | A | A | U | C | C | A | g | a | 53 | 4 | 13 | c | false | <90% | 3552 | ||
NM_001037225 | LOC283129 | 551 | 569 | a | g | g | G | A | A | A | G | A | A | A | A | A | c | C | C | A | A | C | 47 | 4 | 10 | c | false | <90% | 843 | ||
NM_001546 | ID4 | 1011 | 1029 | G | a | g | G | A | A | A | G | A | A | A | A | A | U | a | C | A | A | C | 44 | 3 | 11 | c | false | <90% | 2389 | ||
NM_014712 | SETD1A | 121 | 139 | c | C | A | G | u | A | A | G | A | A | A | A | A | U | C | C | A | A | a | 41 | 3 | 13 | bc | false | <90% | 6447 | ||
XR_017227 | LOC645944 | 1337 | 1355 | G | C | A | G | A | A | A | G | A | A | A | g | A | U | C | C | g | u | C | 40 | 3 | 11 | false | <90% | 3352 | |||
XR_015802 | LOC731409 | 1341 | 1359 | G | C | A | G | A | A | A | G | A | A | A | g | A | U | C | C | g | u | C | 40 | 3 | 11 | false | <90% | 3356 | |||
NM_007158 | CSDE1 | 2732 | 2750 | G | C | A | G | A | A | A | G | A | A | A | g | A | U | C | C | g | u | C | 40 | 3 | 11 | false | <90% | 4041 | |||
NM_001007553 | CSDE1 | 2825 | 2843 | G | C | A | G | A | A | A | G | A | A | A | g | A | U | C | C | g | u | C | 40 | 3 | 11 | false | <90% | 4115 | |||
NM_002851 | PTPRZ1 | 541 | 559 | G | g | g | G | A | A | A | G | A | A | A | u | A | U | C | C | A | A | C | 35 | 3 | 8 | false | <90% | 8169 | |||
NM_025076 | UXS1 | 1771 | 1789 | G | C | A | u | A | A | A | G | A | A | A | A | A | U | C | C | u | A | g | 34 | 3 | 12 | c | false | <90% | 2132 | ||
NM_024583 | SCRN3 | 2331 | 2349 | a | a | c | a | A | A | A | G | A | A | A | A | A | U | C | C | A | A | C | 30 | 4 | 15 | bc | false | <90% | 2497 | ||
NM_004543 | NEB | 17276 | 17294 | G | g | A | G | A | A | A | G | g | A | A | A | A | U | C | C | A | A | C | 28 | 2 | 10 | bc | false | <90% | 20632 | ||
NM_182835 | SCFD1 | 1698 | 1716 | c | C | A | G | A | A | A | u | A | A | A | A | A | U | C | C | A | u | u | 28 | 4 | 9 | c | false | <90% | 2101 | ||
NM_016106 | SCFD1 | 1769 | 1787 | c | C | A | G | A | A | A | u | A | A | A | A | A | U | C | C | A | u | u | 28 | 4 | 9 | c | false | <90% | 2172 | ||
NM_001905 | CTPS | 1207 | 1225 | a | C | A | G | A | A | g | G | A | A | A | A | A | U | C | C | A | A | g | 26 | 3 | 11 | bc | false | <90% | 2758 | ||
NM_014676 | PUM1 | 4469 | 4487 | u | g | A | G | A | A | A | a | A | A | A | A | A | U | C | C | A | A | C | 24 | 3 | 11 | bc | false | <90% | 5410 | ||
NM_001020658 | PUM1 | 4475 | 4493 | u | g | A | G | A | A | A | a | A | A | A | A | A | U | C | C | A | A | C | 24 | 3 | 11 | bc | false | <90% | 5416 | ||
NM_007356 | LAMB4 | 5233 | 5251 | u | u | A | G | A | A | A | G | g | A | A | A | A | U | C | C | A | A | g | 21 | 4 | 9 | bc | false | <90% | 5858 | ||
NM_138400 | NOM1 | 5725 | 5743 | G | C | A | G | A | A | A | c | A | A | A | A | A | c | C | C | A | A | C | 18 | 2 | 7 | c | false | <90% | 6082 | ||
NM_015576 | ERC2 | 5199 | 5217 | a | C | A | G | A | A | A | a | A | A | A | A | A | a | C | C | A | A | C | 16 | 3 | 6 | c | false | <90% | 6138 | ||
NM_014679 | CEP57 | 837 | 855 | G | C | A | G | A | A | A | a | A | A | A | A | A | U | g | C | A | A | g | 8 | 3 | 7 | c | false | <90% | 3158 | ||
NM_000188 | HK1 | 2952 | 2970 | G | a | g | G | A | A | A | G | c | A | A | A | A | U | C | C | A | A | C | 8 | 3 | 10 | bc | false | <90% | 3580 | ||
NM_033496 | HK1 | 3008 | 3026 | G | a | g | G | A | A | A | G | c | A | A | A | A | U | C | C | A | A | C | 8 | 3 | 10 | bc | false | <90% | 3636 | ||
NM_033497 | HK1 | 3187 | 3205 | G | a | g | G | A | A | A | G | c | A | A | A | A | U | C | C | A | A | C | 8 | 3 | 10 | bc | false | <90% | 3815 | ||
NM_033498 | HK1 | 3241 | 3259 | G | a | g | G | A | A | A | G | c | A | A | A | A | U | C | C | A | A | C | 8 | 3 | 10 | bc | false | <90% | 3869 | ||
NM_033500 | HK1 | 3334 | 3352 | G | a | g | G | A | A | A | G | c | A | A | A | A | U | C | C | A | A | C | 8 | 3 | 10 | bc | false | <90% | 3962 | ||
NM_021141 | XRCC5 | 313 | 331 | a | u | u | G | A | A | A | G | c | A | A | A | A | U | C | C | A | A | C | 6 | 4 | 10 | bc | false | <90% | 3310 | ||
NM_017419 | ACCN5 | 53 | 71 | G | C | A | G | A | c | A | G | A | A | A | A | A | U | C | a | A | A | a | 5 | 3 | 9 | c | false | <90% | 1692 | ||
NM_001007088 | ZNF182 | 508 | 526 | G | C | A | G | A | A | g | G | A | A | A | A | A | U | C | C | c | A | u | 5 | 3 | 9 | c | false | <90% | 3504 | ||
NM_006962 | ZNF182 | 602 | 620 | G | C | A | G | A | A | g | G | A | A | A | A | A | U | C | C | c | A | u | 5 | 3 | 9 | c | false | <90% | 3598 | ||
NM_148955 | SNX1 | 1284 | 1302 | u | g | A | G | A | A | A | G | A | g | A | A | A | U | C | C | A | A | g | -1 | 4 | 8 | bc | false | <90% | 8026 | ||
NM_152826 | SNX1 | 1335 | 1353 | u | g | A | G | A | A | A | G | A | g | A | A | A | U | C | C | A | A | g | -1 | 4 | 8 | bc | false | <90% | 8077 | ||
NM_003099 | SNX1 | 1479 | 1497 | u | g | A | G | A | A | A | G | A | g | A | A | A | U | C | C | A | A | g | -1 | 4 | 8 | bc | false | <90% | 8221 | ||
NM_001040157 | KIAA1712 | 686 | 704 | G | C | A | G | A | A | u | G | g | A | A | A | A | U | C | C | A | A | a | -31 | 3 | 9 | bc | false | <90% | 4503 | ||
NM_001942 | DSG1 | 2979 | 2997 | a | C | A | G | A | A | A | G | A | g | u | A | A | U | C | C | A | A | C | -46 | 3 | 8 | c | false | <90% | 5447 |
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_016132 | MYEF2 | 2362 | 2380 | a | a | U | G | G | A | U | U | U | U | U | C | U | c | U | C | U | G | C | 67 | 3 | 11 | c | false | <90% | 4544 | ||
NM_007190 | SEC23IP | 3462 | 3480 | c | U | U | G | G | A | U | U | U | U | U | C | U | U | U | u | U | a | u | 64 | 4 | 14 | c | false | <90% | 4243 | ||
NM_003489 | NRIP1 | 2762 | 2780 | u | c | a | G | G | A | U | U | U | U | U | C | U | U | U | C | U | c | C | 64 | 4 | 14 | c | false | <90% | 7292 | ||
NM_005295 | GPR22 | 826 | 844 | a | a | U | G | G | A | U | U | U | U | U | C | U | a | U | C | U | G | a | 62 | 4 | 11 | c | false | <90% | 2976 | ||
NM_182705 | FAM101B | 2762 | 2780 | a | a | U | G | G | A | U | U | U | U | U | C | U | g | U | C | U | G | a | 62 | 4 | 11 | c | false | <90% | 3895 | ||
NM_199482 | PREI3 | 346 | 364 | a | a | U | G | G | A | U | U | U | U | U | C | U | U | U | g | U | G | C | 60 | 3 | 13 | c | false | <90% | 2698 | ||
NM_015387 | PREI3 | 357 | 375 | a | a | U | G | G | A | U | U | U | U | U | C | U | U | U | g | U | G | C | 60 | 3 | 13 | c | false | <90% | 2709 | ||
XM_931631 | ZC3H12C | 3334 | 3352 | u | U | U | G | G | A | U | U | U | U | U | u | U | U | U | C | U | G | u | 59 | 3 | 10 | false | <90% | 8772 | |||
XM_938482 | ZC3H12C | 4104 | 4122 | u | U | U | G | G | A | U | U | U | U | U | u | U | U | U | C | U | G | u | 59 | 3 | 10 | false | <90% | 9542 | |||
XM_370654 | ZC3H12C | 4104 | 4122 | u | U | U | G | G | A | U | U | U | U | U | u | U | U | U | C | U | G | u | 59 | 3 | 10 | false | <90% | 9542 | |||
NM_017599 | VEZT | 237 | 255 | G | U | U | G | G | A | U | U | U | U | U | u | U | U | U | C | U | c | a | 58 | 3 | 11 | false | <90% | 3949 | |||
NM_153045 | C9orf91 | 3280 | 3298 | c | c | U | G | G | A | U | U | U | U | U | C | U | U | c | C | U | G | a | 56 | 4 | 12 | c | false | <90% | 3699 | ||
XM_940802 | SR140 | 5304 | 5322 | a | U | U | G | G | A | U | U | U | U | U | u | U | U | U | C | U | u | g | 56 | 4 | 10 | false | <90% | 7464 | |||
NM_001080415 | SR140 | 5304 | 5322 | a | U | U | G | G | A | U | U | U | U | U | u | U | U | U | C | U | u | g | 56 | 4 | 10 | false | <90% | 7464 | |||
NM_004897 | MINPP1 | 2300 | 2318 | G | U | U | u | G | A | U | U | U | U | U | C | U | U | U | C | U | u | u | 55 | 3 | 13 | c | false | <90% | 2412 | ||
NM_003725 | HSD17B6 | 1486 | 1504 | a | U | U | u | G | A | U | U | U | U | U | C | U | U | U | C | U | c | u | 53 | 4 | 13 | c | false | <90% | 1512 | ||
NM_032414 | PROK1 | 420 | 438 | c | c | U | G | G | A | U | U | U | U | U | a | U | U | U | C | U | G | C | 52 | 3 | 9 | false | <90% | 1372 | |||
NM_001080114 | LDB3 | 3424 | 3442 | u | U | U | G | G | A | U | U | U | U | U | C | U | c | U | u | U | G | C | 52 | 3 | 12 | c | false | <90% | 4978 | ||
NM_007078 | LDB3 | 3754 | 3772 | u | U | U | G | G | A | U | U | U | U | U | C | U | c | U | u | U | G | C | 52 | 3 | 12 | c | false | <90% | 5308 | ||
NM_004477 | FRG1 | 971 | 989 | c | U | g | G | G | A | U | U | U | U | U | g | U | U | U | C | U | G | C | 44 | 3 | 8 | false | <90% | 1053 | |||
XM_001126144 | LOC730510 | 1861 | 1879 | c | U | g | G | G | A | U | U | U | U | U | g | U | U | U | C | U | G | C | 44 | 3 | 8 | false | <90% | 2947 | |||
NM_080876 | DUSP19 | 4224 | 4242 | c | U | U | G | G | A | U | U | U | U | U | u | U | U | U | C | a | G | C | 40 | 3 | 10 | false | <90% | 5183 | |||
XM_001128600 | LOC731150 | 633 | 651 | c | U | U | G | G | A | U | U | U | U | U | a | U | U | U | a | U | G | C | 38 | 3 | 10 | false | <90% | 768 | |||
XM_001128744 | LOC728896 | 909 | 927 | c | U | U | G | G | A | U | U | U | U | U | a | U | U | U | a | U | G | C | 38 | 3 | 10 | false | <90% | 1044 | |||
NM_016488 | PPHLN1 | 2753 | 2771 | c | U | U | G | G | A | U | U | U | U | U | a | U | U | U | u | U | G | C | 38 | 3 | 10 | false | <90% | 3483 | |||
NM_006526 | ZNF217 | 5470 | 5488 | G | U | U | G | G | A | U | U | U | U | U | g | U | U | U | a | U | G | u | 35 | 3 | 11 | false | <90% | 5653 | |||
NM_002547 | OPHN1 | 3773 | 3791 | u | U | U | G | G | A | U | U | a | U | U | C | U | U | U | C | U | c | C | 35 | 3 | 8 | c | false | <90% | 7350 | ||
NM_003326 | TNFSF4 | 2188 | 2206 | G | U | U | G | G | A | U | U | U | U | U | u | U | U | U | C | c | u | g | 35 | 4 | 11 | false | <90% | 3510 | |||
NM_006675 | TSPAN9 | 1833 | 1851 | G | U | U | G | G | u | U | U | U | U | U | C | U | U | U | C | U | c | C | 34 | 2 | 11 | c | false | <90% | 4338 | ||
NM_152437 | ZNF664 | 4381 | 4399 | G | U | U | u | G | A | U | U | U | U | U | C | U | U | U | C | c | a | u | 32 | 4 | 12 | c | false | <90% | 5125 | ||
NM_003412 | ZIC1 | 100 | 118 | u | U | U | G | G | c | U | U | U | U | U | C | U | U | U | C | U | u | u | 27 | 4 | 11 | c | false | <90% | 5231 | ||
NM_016260 | IKZF2 | 7692 | 7710 | G | U | U | G | G | A | U | U | U | U | a | C | a | U | U | C | U | G | a | 23 | 3 | 10 | false | <90% | 9443 | |||
NM_001079526 | IKZF2 | 7761 | 7779 | G | U | U | G | G | A | U | U | U | U | a | C | a | U | U | C | U | G | a | 23 | 3 | 10 | false | <90% | 9512 | |||
XM_001133529 | LOC731712 | 28 | 46 | a | a | U | G | G | A | c | U | U | U | U | C | U | U | U | C | U | G | g | 15 | 4 | 11 | bc | false | <90% | 420 | ||
XM_001133304 | LOC729302 | 28 | 46 | a | a | U | G | G | A | c | U | U | U | U | C | U | U | U | C | U | G | g | 15 | 4 | 11 | bc | false | <90% | 420 | ||
NM_152515 | CKAP2L | 2584 | 2602 | a | U | g | G | G | A | c | U | U | U | U | C | U | U | U | C | U | G | C | 12 | 3 | 12 | bc | false | <90% | 3220 | ||
NR_003366 | ANKRD20B | 51374 | 51392 | u | U | U | G | G | u | U | U | U | U | U | C | U | U | c | C | U | G | C | 9 | 3 | 8 | c | false | <90% | 96524 | ||
NM_024779 | PIP5K2C | 2356 | 2374 | G | U | U | G | G | A | U | U | U | g | U | u | U | U | U | C | U | G | u | -21 | 3 | 9 | false | <90% | 2937 | |||
NM_001033576 | UNC45B | 3160 | 3178 | G | U | U | G | G | A | U | c | a | U | U | C | U | U | U | C | U | G | u | -27 | 3 | 9 | bc | false | <90% | 5688 | ||
NM_173167 | UNC45B | 3166 | 3184 | G | U | U | G | G | A | U | c | a | U | U | C | U | U | U | C | U | G | u | -27 | 3 | 9 | bc | false | <90% | 5694 | ||
NM_080821 | C20orf108 | 2213 | 2231 | G | U | U | G | c | A | U | U | U | a | U | C | U | U | U | C | U | G | g | -39 | 3 | 8 | bc | false | <90% | 3066 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3135
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