DNA & RNA Element - microRNA Mirbase Acc miRNA Name Gene ID Gene Symbol miRNA Alignment Alignment Gene Alignment miRNA Start miRNA End Gene Start Gene End Genome Coordinates Conservation Align Score Seed Cat Energy mirSVR Score MIMAT0004645 rno-miR-148b-5p 29231 Ciao1 ggACUCACAUAUUGUCUUGAAg ||| ||| |: ||||||| aaUGAAUGUUUG--AGAACUUu 2 21 275 294 [rn4:3:114740717-114740736:-] 0.5477 157 7 -11.94 -1.0194 MIMAT0004646 rno-miR-338* 29231 Ciao1 gugagucgUGGUCCUAUA-ACAa |:||| |||| ||| aaaauauaAUCAGUAUAUAUGUa 2 15 250 272 [rn4:3:114740739-114740761:-] 0.5477 122 0 -8.29 -1.2347 MIMAT0000604 rno-miR-350 29231 Ciao1 cacuuucacauacccgaAACACUu |||||| uuugagaacuuuugaaaUUGUGAg 2 8 283 306 [rn4:3:114740705-114740728:-] 0.5477 120 6 -9.74 -0.1132 MIMAT0004708 rno-miR-9* 29231 Ciao1 ugAAAGC--CAAUAGAUCGAAAUa |||:| ||:| ||||||| acUUUUGAAAUUGU-GAGCUUUAu 2 21 290 312 [rn4:3:114740699-114740721:-] 0.5477 149 7 -15.76 -0.8729 MIMAT0004718 rno-miR-29a* 29231 Ciao1 gacuugugGUUUUCU-UUAGUCa :|||| | |||||| uauauuuaUAAAAUAUAAUCAGu 2 15 241 263 [rn4:3:114740748-114740770:-] 0.5477 122 6 -9.21 -1.2599 MIMAT0005445 rno-miR-29b-1* 29231 Ciao1 uuUAGAUUUGGUGGUAUACUUu ||| : |: ::|||||| uaAUCAGUAUAUAUGUAUGAAu 2 21 256 277 [rn4:3:114740734-114740755:-] 0.5477 132 6 -8.06 -0.1603 MIMAT0004724 rno-miR-99a* 29231 Ciao1 guCUGGGUAUCUUU---GCUCGAAc || |: | |||| :|||||| gaGAACUUUUGAAAUUGUGAGCUUu 2 21 286 310 [rn4:3:114740701-114740725:-] 0.5477 139 6 -13.22 -0.1242 MIMAT0004725 rno-miR-99b* 29231 Ciao1 gcCUGGGUGUCU---GUGCUCGAAc || |: : || :::|||||| gaGAACUUUUGAAAUUGUGAGCUUu 2 21 286 310 [rn4:3:114740701-114740725:-] 0.5477 127 6 -10.64 -0.1254 MIMAT0004731 rno-miR-125b* 29231 Ciao1 uccaggguucUCGGACUGAACa |||:||||||| -----gcugcAGCUUGACUUGg 2 13 1 17 [rn4:3:114740994-114741010:-] 0.5798 156 7 -16.94 -0.2160 MIMAT0000847 rno-miR-142-5p 29231 Ciao1 ucaucacGAAAGAUGAAAUAc :| | :|||||| uuugaaaUUGUGAGCUUUAUa 2 15 293 313 [rn4:3:114740698-114740718:-] 0.5477 126 6 -6.66 -0.1259 MIMAT0000893 rno-miR-290 29231 Ciao1 uuuuucacggggguauCAAACUc |||||| auauguaugaaugaauGUUUGAg 2 8 266 288 [rn4:3:114740723-114740745:-] 0.5477 120 6 -10.66 -0.1732 MIMAT0000894 rno-miR-291a-5p 29231 Ciao1 ucucucccggAGGUGAAACUAc |:: ||||||| ccauucacugUUUCCUUUGAUg 2 13 106 127 [rn4:3:114740884-114740905:-] 0.5477 144 7 -14.25 -0.3776 MIMAT0003175 rno-miR-543* 29231 Ciao1 ucuucACGUG-GCGCUUACAAa ||:|: :||||||| auauaUGUAUGAAUGAAUGUUu 2 17 264 285 [rn4:3:114740726-114740747:-] 0.5477 143 7 -12.68 -1.1454 MIMAT0003202 rno-miR-382* 29231 Ciao1 uuCACA-ACAGGCACUUACUaa || | | | : ||||||| caGUAUAUAUGUAUGAAUGAau 3 20 260 281 [rn4:3:114740730-114740751:-] 0.5477 130 0 -8.49 -0.1107 MIMAT0003207 rno-miR-369-3p 29231 Ciao1 uuUCUA-GUUGGUACAUA-AUAa | || :||:|| |||| ||| uaAAAUAUAAUCA-GUAUAUAUg 2 20 249 270 [rn4:3:114740741-114740762:-] 0.5477 120 0 -7.16 -1.1001 MIMAT0003382 rno-miR-664 29231 Ciao1 auccgaccccucAUUUACUUAu |:||||||| aguauauauguaUGAAUGAAUg 2 11 261 282 [rn4:3:114740729-114740750:-] 0.5477 146 7 -8.68 -0.8949 MIMAT0005333 rno-miR-742 29231 Ciao1 aaauGGGUUGUACCAC-CGAAAg ::::| || ||| ||||| aacuUUUGAAAUUGUGAGCUUUa 2 19 289 311 [rn4:3:114740700-114740722:-] 0.5477 122 0 -9.82 -1.2318 MIMAT0005337 rno-miR-760-3p 29231 Ciao1 aggGGUGUCUGGGUCUCGGc |||: |: ||||||| aagCCAUUGG--CAGAGCCa 2 18 133 150 [rn4:3:114740861-114740878:-] 0.5477 146 7 -18.02 -0.5197 MIMAT0012824 rno-miR-513 29231 Ciao1 uacuuucuguggaagAACACUu |||||| ugagaacuuuugaaaUUGUGAg 2 8 285 306 [rn4:3:114740705-114740726:-] 0.5477 120 6 -12.68 -0.1166 MIMAT0012832 rno-miR-568 29231 Ciao1 caCACAUAUGUAAAUAUGUa || |||:||||||| | ggGUAAAUAUAUUUAUAAAa 2 19 234 253 [rn4:3:114740758-114740777:-] 0.5477 138 0 -9.69 -0.1337 MIMAT0012847 rno-miR-293 29231 Ciao1 guUUCACA-GUGUGU-CAAACUCa | || | |:: | ||||||| auAUGUAUGAAUGAAUGUUUGAGa 2 21 266 289 [rn4:3:114740722-114740745:-] 0.5477 142 7 -9.47 -1.2969 MIMAT0012848 rno-miR-294 29231 Ciao1 ucuaucccggagguAAAACUc |||||| gaauguuugagaacUUUUGAa 2 8 278 298 [rn4:3:114740713-114740733:-] 0.5477 120 6 -5.71 -0.2676 MIMAT0012849 rno-miR-295 29231 Ciao1 cuucacacggggUGUAAACUCa |::|||||| auguaugaaugaAUGUUUGAGa 2 11 268 289 [rn4:3:114740722-114740743:-] 0.5477 130 6 -8.90 -0.3379 MIMAT0004650 rno-miR-340-5p 29231 Ciao1 uuagucagaguaaCGAAAUAUu |||||||| uuugaaauugugaGCUUUAUAg 2 10 293 314 [rn4:3:114740697-114740718:-] 0.5477 145 7 -9.33 -0.7038 MIMAT0004650 rno-miR-340-5p 29231 Ciao1 uuagucagaguaacgAAAUAUu |||||| uuggggguaaauauaUUUAUAa 2 8 230 251 [rn4:3:114740760-114740781:-] 0.5477 120 6 -4.98 -0.3625 MIMAT0000589 rno-miR-342-3p 29231 Ciao1 ugcccacgcuaaagacACACUCu |||||| ugagaacuuuugaaauUGUGAGc 2 8 285 307 [rn4:3:114740704-114740726:-] 0.5477 120 6 -10.44 -0.2185 MIMAT0000611 rno-miR-135b 29231 Ciao1 aguGUAUCCUUACU-UUUCGGUAu | | | :||| |||||||| uucCUUUGAUGUGAGAAAGCCAUu 2 21 117 140 [rn4:3:114740871-114740894:-] 0.5477 155 7 -13.92 -0.3825 MIMAT0000841 rno-miR-135a 29231 Ciao1 aguguauccuuaUUUUUCGGUAu |:|||||||| uccuuugaugugAGAAAGCCAUu 2 12 118 140 [rn4:3:114740871-114740893:-] 0.5477 151 7 -12.45 -0.3825 MIMAT0000853 rno-miR-150 29231 Ciao1 gugACCAUGUUCCCAACCCUCu || |||| |||||:| aggUGUUACA--UUUUGGGGGu 2 20 218 237 [rn4:3:114740774-114740793:-] 0.5477 132 0 -15.79 -0.1151 MIMAT0000857 rno-miR-181c 29231 Ciao1 ugaguggcuguccaACUUACAa ||||||| uauauauguaugaaUGAAUGUu 2 9 263 284 [rn4:3:114740727-114740748:-] 0.5477 140 7 -9.18 -1.1879 MIMAT0000858 rno-miR-181a 29231 Ciao1 ugaguggcugucgcaACUUACAa ||||||| guauauauguaugaaUGAAUGUu 2 9 262 284 [rn4:3:114740727-114740749:-] 0.5477 140 7 -9.92 -1.1862 MIMAT0000859 rno-miR-181b 29231 Ciao1 uggGUGGCUGUCGUUACUUACAa :|: ::| ||||||||| guaUAUAUGUAUGAAUGAAUGUu 2 21 262 284 [rn4:3:114740727-114740749:-] 0.5477 152 7 -11.66 -1.1862 MIMAT0000873 rno-miR-200c 29231 Ciao1 gguaguaaugggccGUCAUAau |||||| uuauaaaauauaauCAGUAUau 3 9 246 267 [rn4:3:114740744-114740765:-] 0.5477 120 0 -6.87 -0.1789 MIMAT0000875 rno-miR-200b 29231 Ciao1 caguagUAAUGGUCCGUCAUAau | || :| |||||| uuauaaAAUA-UAAUCAGUAUau 3 18 246 267 [rn4:3:114740744-114740765:-] 0.5477 123 0 -6.04 -0.1789 MIMAT0000896 rno-miR-292-5p 29231 Ciao1 guuuucucggggguCAAACUCa ||||||| auguaugaaugaauGUUUGAGa 2 9 268 289 [rn4:3:114740722-114740743:-] 0.5477 140 7 -7.86 -1.2984 MIMAT0000903 rno-miR-320 29231 Ciao1 agcgggagaguugggUCGAAAa |||||| acuuuugaaauugugAGCUUUa 2 8 290 311 [rn4:3:114740700-114740721:-] 0.5477 120 6 -10.06 -0.2416 MIMAT0001538 rno-miR-429 29231 Ciao1 ugccgUAAUGGUCUGUCAUAau | || :| |||||| uauaaAAUA-UAAUCAGUAUau 3 18 247 267 [rn4:3:114740744-114740764:-] 0.5477 123 0 -7.12 -0.1789 MIMAT0003122 rno-miR-370 29231 Ciao1 uugguccaaGGUG--GGGUCGUCcg |||| |||||| uuggcagagCCACGGAACAGCAGaa 3 15 139 163 [rn4:3:114740848-114740872:-] 0.5477 121 0 -20.11 -0.1909 MIMAT0003123 rno-miR-377 29231 Ciao1 gguuuuCAACGGAAAC-ACACUa ||| |||||| ||||| uucacuGUUUCCUUUGAUGUGAg 2 17 109 131 [rn4:3:114740880-114740902:-] 0.5477 136 0 -17.65 -0.6451 MIMAT0003193 rno-miR-494 29231 Ciao1 uccaaagggcACAUACAAAgu || |||||| uauguaugaaUGAAUGUUUga 3 12 267 287 [rn4:3:114740724-114740744:-] 0.5477 127 0 -5.57 -0.1467 MIMAT0005299 rno-miR-181d 29231 Ciao1 uggGUGGCUGUUGUUACUUACAa :|: ::| ||||||||| guaUAUAUGUAUGAAUGAAUGUu 2 21 262 284 [rn4:3:114740727-114740749:-] 0.5477 152 7 -10.94 -1.1862

DNA & RNA Element - TRANSFAC Accession AS Description Species Entrez Pubmed Binding Info G099130 Ciao1 Rattus norvegicus 29231

DNA & RNA Element - miRNAMap Gene Name Mature miRNA Target Start Target End miRNA 3-5 Alignment Target 5-3 Ciao1; Wdr39 rno-miR-128a 102 118 UUUUCUCUGGCCAAGUGACACU :|||| |||||||| ----AGGACCA-UUCACUGUU- Ciao1; Wdr39 rno-miR-128b 102 118 CUUUCUCUGGCCAAGUGACACU :|||| |||||||| ----AGGACCA-UUCACUGUU- Ciao1; Wdr39 rno-miR-129 140 165 -UCGU-UCGG-GUCUGG-CGUUUUUC :||| |||| |:|| |||:|| UGGCAGAGCCACGGAACAGCAGAAU- Ciao1; Wdr39 rno-miR-133a 3 24 -UGUCGACCAACUU--CCCCUGGUU :||||| ||| |||||:| UGCAGCU---UGACUUGGGGAUCU- Ciao1; Wdr39 rno-miR-133b 1 24 AUCGACC---AACUU--CCCCUGGUU |||| |||| |||||:| --GCUGCAGCUUGACUUGGGGAUCU- Ciao1; Wdr39 rno-miR-135a 120 141 -AGUGUAUCCUUAUUUUUCGGUAU |: ||: || :|||||||| CUUUGAUGUGA---GAAAGCCAUU Ciao1; Wdr39 rno-miR-135b 121 141 -GUGUAUCCUUACUUUUCGGUAU : ||: || :|||||||| UUUGAUGUGA---GAAAGCCAUU Ciao1; Wdr39 rno-miR-140 134 153 GAUGGUAUCCCAUUUUGGUGA :|||| || |:|:|||| -AGCCAUU-GGCAGAGCCACG Ciao1; Wdr39 rno-miR-150 213 238 GUGACCAUGUUCCCA-------ACCCUCU || :||:| || ||||:| ---AGG-GCAGGUGUUACAUUUUGGGGGU Ciao1; Wdr39 rno-miR-24 112 140 -GAC-AAGGACGACUUGACU----CGGU- ||| ||||| :||| ||| |||| ACUGUUUCCU-UUGAUGUGAGAAAGCCAU Ciao1; Wdr39 rno-miR-27a 47 71 CGCCUUGA-----AUCGGUGACACUU- :||| |||:||||| ||| ---AGACUUUUCCUAGUCACUGAGAAG Ciao1; Wdr39 rno-miR-27b 286 308 CGUCUUGAAU-CGGUGACACUU- ||||||| | |:|||||: -GAGAACUUUUGAAAUUGUGAGC Ciao1; Wdr39 rno-miR-31 4 33 -GUCGAUAC-GG--UCGUAGAAC----GGA ||||| || |: :| |||||| || GCAGCU-UGACUUGGGGAUCUUGAUUCCCA Ciao1; Wdr39 rno-miR-324-5p 1 23 UGUGGUUACGGGAU---CCCCUACGC :| || ||:: |||||| GCUGCA--GCUUGACUUGGGGAUC-- Ciao1; Wdr39 rno-miR-339 197 222 ACUCGA---GGACC---UCCUGUCCCU ||: |:|| |||:|||| -AAGUUUUGCUUGAUUUAGGGCAGGU- Ciao1; Wdr39 rno-miR-34c 91 120 CGUUAGUCGA---UUGAU--GUGACGGA- || |:|||| :|| |||||::| UCAUUUAGCUCAGGACCAUUCACUGUUUC Ciao1; Wdr39 rno-miR-370 133 163 -UUGGU--CCAA---GGUGGG--GUCGUCCG |:||| || |||| |||||| AAGCCAUUGGCAGAGCCACGGAACAGCAGA- Ciao1; Wdr39 rno-miR-377 105 132 -GGUUUU---CAACGGAAAC-ACACUA ||| ||| |||||| ||||| ACCAUUCACUGUUUCCUUUGAUGUGAG Ciao1; Wdr39 rno-miR-493 58 82 GACCGUGUGUCAUCUGGAA---GU- | ||| || |||||| || -AGUCACUGAGAAGACCUGAAGCAU Ciao1; Wdr39 rno-miR-128a 99 118 uuuUCUCUGGCCAAGUGACAcu || |||| |||||||| ctcAG-GACC-ATTCACTGTtt Ciao1; Wdr39 rno-miR-128b 99 118 cuuUCUCUGGCCAAGUGACAcu || |||| |||||||| ctcAG-GACC-ATTCACTGTtt Ciao1; Wdr39 rno-miR-129 141 165 uCGU-UCGG-GUC-UGGCGUUUUuc ||| |||| |:| || |||:|| gGCAGAGCCACGGAACAGCAGAAta Ciao1; Wdr39 rno-miR-133a 1 24 uGUCGACCAACU--UCCCCUGGuu | || | |||| |||||:| gCTGCAGCTTGACTTGGGGATCtt Ciao1; Wdr39 rno-miR-133b 2 24 auCGACCAACU--UCCCCUGGuu || | |||| |||||:| ctGCAGCTTGACTTGGGGATCtt Ciao1; Wdr39 rno-miR-140 133 152 gauGGUAUCCCAUUUUGGUGa |||| || |:|:|||| aagCCAT-TGGCAGAGCCACg Ciao1; Wdr39 rno-miR-150 218 237 gugACCAUGUUCCCAACCCUCu || |||| |||||:| aggTGTTACA--TTTTGGGGGt Ciao1; Wdr39 rno-miR-24 113 150 GAC-AAGG--ACGAC-----UU--------GACUCGGU ||| |||| || || || | |||||| CTGTTTCCTTTGATGTGAGAAAGCCATTGGCAGAGCCA Ciao1; Wdr39 rno-miR-27a 49 69 cgccuuGAAUCGGUGACACUU | |||:||||| ||| acttttCCTAGTCACTGAGAA Ciao1; Wdr39 rno-miR-27b 285 306 cgUCUUG-AAUCGGUGACACUu ||||| || | |:||||| tgAGAACTTTTGAAATTGTGAg Ciao1; Wdr39 rno-miR-291-5p 98 127 ucucUCCCGG-AGGU-------GAAACUAC ||| || |:|| |||||||| gctcAGGACCATTCACTGTTTCCTTTGATG Ciao1; Wdr39 rno-miR-31 5 28 GUCGAUACGG---UCGUAGAACgga ||||| || | :| |||||| CAGCT-TGACTTGGGGATCTTGatt Ciao1; Wdr39 rno-miR-324-5p 4 24 uGUGGUUACGGGAUCCCCUAcgc || | || |:| |||||| gCAGC-TTGACTT-GGGGATctt Ciao1; Wdr39 rno-miR-339 201 222 acuCGAG-GACCUCCUGUCCcu |||: | |||:|||| tttGCTTGATTTAGGGCAGGtg Ciao1; Wdr39 rno-miR-370 134 163 UUGGU---C--CAAGGUG--GGGUCGUCcg |:||| | | |||| |||||| AGCCATTGGCAGAGCCACGGAACAGCAGaa Ciao1; Wdr39 rno-miR-377 106 131 GGU---UUUCAACGGAAAC-ACACUa ||| | ||| |||||| ||||| CCATTCACTGTTTCCTTTGATGTGAg Ciao1; Wdr39 rno-miR-493 73 93 GAC--CGUGUGUCAUCUGGAAGU ||| |||: | | |||:|||| CTGAAGCATCC--TTGACTTTCA Ciao1; Wdr39 rno-miR-135a 133 140 AGUGUAUCCUUA----------------------UUUUUCGGUAU :| |||| |:|||||||| --GCUCAGGACCAUUCACUGUUUCCUUUGAUGUGAGAAAGCCAUU Ciao1; Wdr39 rno-miR-135b 133 140 GUGUAUCCU---------------------UAC-UUUUCGGUAU :| |||| :|| :|||||||| -GCUCAGGACCAUUCACUGUUUCCUUUGAUGUGAGAAAGCCAUU Ciao1; Wdr39 rno-miR-291-5p 120 127 UCUC-------------UCCCGG-AGGU-------GAAACUAC ||| || |:|| |||||||| UGACUUUCAUUUAGCUCAGGACCAUUCACUGUUUCCUUUGAUGU

DNA & RNA Element - RAID2 Gene Name RAID ID Interactor 1 Category 1 ID 1 Interactor 2 Category 2 ID 2 Methods Score Ciao1 RAID00226125 rno-miR-3589 miRNA MIMAT0017888 Ciao1 mRNA 29231 Prediction 0.1828 Ciao1 RAID00421064 rno-miR-7578 miRNA MIMAT0029579 Ciao1 mRNA 29231 Prediction 0.1828 Ciao1 RAID00711040 rno-miR-150-5p miRNA MIMAT0000853 Ciao1 mRNA 29231 Prediction 0.1828 Ciao1 RAID00927581 rno-miR-181a-5p miRNA MIMAT0000858 Ciao1 mRNA 29231 Prediction 0.1828 Ciao1 RAID01122967 rno-miR-181c-5p miRNA MIMAT0000857 Ciao1 mRNA 29231 Prediction 0.1828 Ciao1 RAID01263475 rno-miR-181b-5p miRNA MIMAT0000859 Ciao1 mRNA 29231 Prediction 0.1828 Ciao1 RAID01361965 rno-miR-494-3p miRNA MIMAT0003193 Ciao1 mRNA 29231 Prediction 0.1828 Ciao1 RAID01446317 rno-miR-760-3p miRNA MIMAT0005337 Ciao1 mRNA 29231 Prediction 0.1828 Ciao1 RAID01537216 rno-miR-3580-3p miRNA MIMAT0017869 Ciao1 mRNA 29231 Prediction 0.1828 Ciao1 RAID01677534 rno-miR-135b-5p miRNA MIMAT0000611 Ciao1 mRNA 29231 Prediction 0.1828 Ciao1 RAID02061428 rno-miR-429 miRNA MIMAT0001538 Ciao1 mRNA 29231 Prediction 0.1828 Ciao1 RAID02091038 rno-miR-200c-3p miRNA MIMAT0000873 Ciao1 mRNA 29231 Prediction 0.1828 Ciao1 RAID02174787 rno-miR-320-3p miRNA MIMAT0000903 Ciao1 mRNA 29231 Prediction 0.1828 Ciao1 RAID02174909 rno-miR-370-3p miRNA MIMAT0003122 Ciao1 mRNA 29231 Prediction 0.1828 Ciao1 RAID02203849 rno-miR-200b-3p miRNA MIMAT0000875 Ciao1 mRNA 29231 Prediction 0.1828 Ciao1 RAID02443030 rno-miR-340-5p miRNA MIMAT0004650 Ciao1 mRNA 29231 Prediction 0.1828 Ciao1 RAID03304041 rno-miR-181d-5p miRNA MIMAT0005299 Ciao1 mRNA 29231 Prediction 0.1828 Ciao1 RAID03599348 rno-miR-292-5p miRNA MIMAT0000896 Ciao1 mRNA 29231 Prediction 0.1828 Ciao1 RAID03610251 rno-miR-377-3p miRNA MIMAT0003123 Ciao1 mRNA 29231 Prediction 0.1828 Ciao1 RAID03865540 rno-miR-135a-5p miRNA MIMAT0000841 Ciao1 mRNA 29231 Prediction 0.1828 Ciao1 RAID03933724 rno-miR-342-3p miRNA MIMAT0000589 Ciao1 mRNA 29231 Prediction 0.1828