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 MIMAT0004489 hsa-miR-16-1* 373856 USP41 agucgucgugucaaUUAUGACc ||||||| ucaacuauuccuaaAAUACUGc 2 9 100 121 [hg19:22:20704938-20704959:-] 0.5443 140 7 -6.47 -1.0177 MIMAT0000685 hsa-miR-34b* 373856 USP41 guUAGUCGAUUACUG-----UGACGGAu | || | :|||:| :|||||| uaAACACCAGAUGGCCCUUUGCUGCCUu 2 22 3 30 [hg19:22:20705029-20705056:-] 0.5443 132 6 -16.37 -0.1616 MIMAT0003386 hsa-miR-376a* 373856 USP41 augAGUAUCUUC---CUCUUAGAUg |:| |||| | ||||||| aaaUUAAUGAAGUUUGUGAAUCUAa 2 20 165 189 [hg19:22:20704870-20704894:-] 0.5469 150 7 -11.44 -1.0660 MIMAT0003165 hsa-miR-545 373856 USP41 cgUGUG--UUAUUUACAAACGACu |||| :||:: ||||||| aaACACCAGAUGGCCCUUUGCUGc 2 21 4 27 [hg19:22:20705032-20705055:-] 0.5443 151 7 -15.07 -0.2908 MIMAT0003303 hsa-miR-633 373856 USP41 aaauaacaccaucuaUGAUAAuc |||||| gugaucauacuuucaACUAUUcc 3 9 88 110 [hg19:22:20704949-20704971:-] 0.5443 120 0 -3.56 -0.1261 MIMAT0003321 hsa-miR-651 373856 USP41 guuuucAGUUCGAAUAGGAUUu |||| || |||||| auacuuUCAA-CUAUUCCUAAa 2 17 94 114 [hg19:22:20704945-20704965:-] 0.5443 126 6 -10.96 -0.1805 MIMAT0005797 hsa-miR-1301 373856 USP41 cuuCAGUGAGGGUCCGUCG-ACGUu || ||: || |:||| |||| auuGUGCCUUACAUGUAGCUUGCAg 2 22 38 62 [hg19:22:20704997-20705021:-] 0.5443 129 0 -16.25 -1.0336 MIMAT0010251 hsa-miR-449c 373856 USP41 ugUCGGCGAUCGUUAUGUGACGGAu | | | |:|| | ::|||||| acACCAGAUGGCCCUUUGCUGCCUu 2 24 6 30 [hg19:22:20705029-20705053:-] 0.5443 143 6 -19.78 -0.1601 MIMAT0006790 hsa-miR-675* 373856 USP41 acucgccacucccGUAUGUc |||||| cugccgaggauuuCAUACAa 2 8 147 166 [hg19:22:20704893-20704912:-] 0.5456 120 6 -10.95 -0.1161 MIMAT0004908 hsa-miR-220b 373856 USP41 uucacagucugugcCACCACc |||||| uacgcuuauguuuuGUGGUGa 2 8 71 91 [hg19:22:20704968-20704988:-] 0.5443 120 6 -12.77 -0.1223 MIMAT0004983 hsa-miR-940 373856 USP41 ccccucgcccccggGACGGAa |||||| cagauggcccuuugCUGCCUu 2 8 10 30 [hg19:22:20705029-20705049:-] 0.5443 120 6 -17.33 -0.1616 MIMAT0004450 hsa-miR-297 373856 USP41 guacguguacguguGUAUGUa |||||| acugccgaggauuuCAUACAa 2 8 146 166 [hg19:22:20704893-20704913:-] 0.5456 120 6 -11.75 -0.1184 MIMAT0005829 hsa-miR-1184 373856 USP41 ccuuCGGUA-GUUCAGCG-ACGUCc ||| | || || || ||||| uuguGCCUUACAUGUAGCUUGCAGg 2 20 39 63 [hg19:22:20704996-20705020:-] 0.5443 126 0 -19.25 -1.0116 MIMAT0005889 hsa-miR-548l 373856 USP41 cuguuuugggcguuUAUGAAAa ||||||| guuuuguggugaucAUACUUUc 2 9 80 101 [hg19:22:20704958-20704979:-] 0.5443 140 7 -6.18 -0.6084 MIMAT0005907 hsa-miR-1256 373856 USP41 ucGAUCACUCUUCAGUU-ACGGa || || |::||||| |||| auCU-GUUUGGGGUCAACUGCCg 2 21 131 152 [hg19:22:20704907-20704928:-] 0.5443 126 0 -18.73 -0.5174 MIMAT0005909 hsa-miR-1258 373856 USP41 aaGGUGCUGGAUUAGGAUUga |: : | ||| |||||| uaCUUUCAACUAUUCCUAAaa 3 20 95 115 [hg19:22:20704944-20704964:-] 0.5443 135 0 -12.47 -0.1299 MIMAT0005919 hsa-miR-548o 373856 USP41 cguUUUCAUUGACGUCAAA-ACc ||| ||| || ||||| || uacAAAUUAA-UGAAGUUUGUGa 2 20 162 183 [hg19:22:20704876-20704897:-] 0.5469 129 0 -9.20 -1.1132 MIMAT0005788 hsa-miR-513b 373856 USP41 uaUUUACUGUGGAGGAACACUu |||| | :|||||| acAAAUUAAUGAAGUUUGUGAa 2 21 163 184 [hg19:22:20704875-20704896:-] 0.5469 128 6 -11.74 -0.1120 MIMAT0006767 hsa-miR-1827 373856 USP41 uaaguuAGAUGACGGAGu |:|:||||||: uggcccUUUGCUGCCUUa 2 13 14 31 [hg19:22:20705028-20705045:-] 0.5443 136 0 -17.97 -0.2030 MIMAT0011775 hsa-miR-2276 373856 USP41 ggaGCGGAG---ACUGUGAACGUCu :||||: || :||||||| uugUGCCUUACAUGUAGCUUGCAGg 2 20 39 63 [hg19:22:20704996-20705020:-] 0.5443 150 7 -22.08 -0.7754 MIMAT0015022 hsa-miR-3149 373856 USP41 uauguGUGUGUAUAGGUAUGUUu |: : || |:||||||| acugcCGAGGAU-UUCAUACAAa 2 19 146 167 [hg19:22:20704892-20704913:-] 0.5456 148 7 -12.80 -1.1741 MIMAT0016897 hsa-miR-4269 373856 USP41 cggucccGACAG--ACACGGAcg :|||| ||||||| gccuuauUUGUCAUUGUGCCUua 3 15 26 48 [hg19:22:20705011-20705033:-] 0.5443 133 0 -18.96 -0.1196 MIMAT0000227 hsa-miR-197 373856 USP41 cgacccaccucuucCACCACUu ||||||| uacgcuuauguuuuGUGGUGAu 2 9 71 92 [hg19:22:20704967-20704988:-] 0.5443 140 7 -11.23 -1.0058 MIMAT0000278 hsa-miR-221 373856 USP41 cuuugggucgucUGUUACAUCGa || ||||||| ucauugugccuuAC-AUGUAGCu 2 12 36 57 [hg19:22:20705002-20705023:-] 0.5443 141 7 -13.40 -0.6446 MIMAT0000279 hsa-miR-222 373856 USP41 ugGGUCAU-CGG--UCUACAUCGa :|| |: ||| | ||||||| ugUCAUUGUGCCUUACAUGUAGCu 2 20 34 57 [hg19:22:20705002-20705025:-] 0.5443 149 7 -16.74 -0.6697 MIMAT0000416 hsa-miR-1 373856 USP41 uauGUAUGAAGAAAUG-UAAGGu ||||||| | || ||||| gauCAUACUU-UCAACUAUUCCu 2 20 90 111 [hg19:22:20704948-20704969:-] 0.5443 129 0 -14.86 -1.1607 MIMAT0000422 hsa-miR-124 373856 USP41 ccGUAAGUGG-CGCACGGAAu :|||:::| :||||||| cuUAUUUGUCAUUGUGCCUUa 2 19 28 48 [hg19:22:20705011-20705031:-] 0.5443 153 7 -18.49 -1.2226 MIMAT0000422 hsa-miR-124 373856 USP41 ccguaaguggcgcACGGAAu |||||| gauggcccuuugcUGCCUUa 2 8 12 31 [hg19:22:20705028-20705047:-] 0.5443 120 6 -17.30 -0.2285 MIMAT0000462 hsa-miR-206 373856 USP41 gguGUGUGAAGGAAUG-UAAGGu ||:||||:| || ||||| gauCAUACUUUC-AACUAUUCCu 2 20 90 111 [hg19:22:20704948-20704969:-] 0.5443 129 0 -18.09 -1.1626 MIMAT0004763 hsa-miR-488 373856 USP41 cugguucuuuaucgGAAAGUu |||||| uuguggugaucauaCUUUCAa 2 8 83 103 [hg19:22:20704956-20704976:-] 0.5443 120 6 -10.09 -0.1395 MIMAT0002817 hsa-miR-495 373856 USP41 uucUUCACGUGGUACAAACAaa || | |: | |||||| uacAAAUUAAUGAAGUUUGUga 3 20 162 183 [hg19:22:20704876-20704897:-] 0.5469 131 0 -5.87 -0.1077 MIMAT0002870 hsa-miR-499-5p 373856 USP41 uuUGUAGUGACG--UUCAGAAUu | | :||||| ||||||| cuAAAAUACUGCUUCAGUCUUAu 2 20 110 132 [hg19:22:20704927-20704949:-] 0.5443 154 7 -16.27 -0.4953 MIMAT0002878 hsa-miR-506 373856 USP41 agAUGAGUCUUCCCACGGAAu ||:|:: | ||||||| cuUAUUUGUCAUUGUGCCUUa 2 20 28 48 [hg19:22:20705011-20705031:-] 0.5443 151 7 -14.06 -1.2254 MIMAT0002878 hsa-miR-506 373856 USP41 agaugagucuucccACGGAAu |||||| agauggcccuuugcUGCCUUa 2 8 11 31 [hg19:22:20705028-20705048:-] 0.5443 120 6 -9.87 -0.2306 MIMAT0003328 hsa-miR-653 373856 USP41 guCAUCUCUA--A-CAAAGUUGug ||:| ||| | ||||||| uuGUGGUGAUCAUACUUUCAACua 3 20 83 106 [hg19:22:20704953-20704976:-] 0.5443 133 0 -10.78 -0.1417

DNA & RNA Element - TRANSFAC Accession AS Description Species Entrez Pubmed Binding Info G036584 USP41 Homo sapiens 373856

DNA & RNA Element - TargetScan Gene Name UTR Region Start UTR Region End AIR Total Normalized 3P-seq-tags & Pseudocounts Strand hg19_chromosome Genome Start Genome End USP41 1 2 100 5.01 - chr22 20717914 20717916 USP41 3 356 99.8 5.01 - chr22 20704867 20705221

DNA & RNA Element - miRcode Gene Name Type microRNA Seed Position Seed Type Total Cons% Tr Region USP41 High_conserved miR-7/7ab chr22:20721908 7-mer-A1 4 CDS, ncRNA USP41 High_conserved miR-148ab-3p/152 chr22:20721916 7-mer-m8 7 CDS, ncRNA USP41 High_conserved miR-15abc/16/16abc/195/322/424/497/1907 chr22:20729859 7-mer-m8 7 CDS USP41 High_conserved miR-181abcd/4262 chr22:20731468 7-mer-m8 2 CDS USP41 High_conserved miR-183 chr22:20723797 7-mer-m8 4 CDS, ncRNA USP41 High_conserved let-7/98/4458/4500 chr22:20724454 7-mer-A1 4 CDS, ncRNA USP41 High_conserved miR-199ab-5p chr22:20721932 8-mer 2 CDS, ncRNA USP41 High_conserved miR-205/205ab chr22:20723825 8-mer 4 CDS, ncRNA USP41 High_conserved miR-214/761/3619-5p chr22:20731504 7-mer-m8 4 CDS USP41 High_conserved miR-219-5p/508/508-3p/4782-3p chr22:20720985 7-mer-m8 7 CDS, ncRNA USP41 High_conserved miR-221/222/222ab/1928 chr22:20705002 7-mer-m8 4 3pUTR, ncRNA USP41 High_conserved miR-24/24ab/24-3p chr22:20731611 7-mer-A1 4 CDS USP41 High_conserved miR-30abcdef/30abe-5p/384-5p chr22:20731526 7-mer-A1 4 CDS USP41 High_conserved miR-103a/107/107ab chr22:20724467 7-mer-m8 2 CDS, ncRNA USP41 High_conserved miR-124/124ab/506 chr22:20705011 8-mer 4 3pUTR, ncRNA USP41 High_conserved miR-124/124ab/506 chr22:20705028 7-mer-A1 4 3pUTR, ncRNA USP41 High_conserved miR-124/124ab/506 chr22:20731500 7-mer-A1 4 CDS USP41 High_conserved miR-338/338-3p chr22:20705103 7-mer-m8 4 3pUTR, ncRNA USP41 High_conserved miR-338/338-3p chr22:20729857 7-mer-A1 7 CDS USP41 High_conserved miR-128/128ab chr22:20744808 7-mer-m8 18 CDS USP41 High_conserved miR-499-5p chr22:20704927 7-mer-m8 4 3pUTR, ncRNA USP41 Medium_conserved miR-544/544ab/544-3p chr22:20723783 7-mer-A1 2 CDS, ncRNA USP41 Medium_conserved miR-544/544ab/544-3p chr22:20729793 7-mer-m8 7 CDS USP41 Medium_conserved miR-544/544ab/544-3p chr22:20729832 7-mer-A1 4 CDS USP41 Medium_conserved miR-876-5p/3167 chr22:20717926 7-mer-m8 4 CDS, ncRNA USP41 Medium_conserved miR-136 chr22:20705177 7-mer-A1 4 3pUTR, ncRNA USP41 Medium_conserved miR-136 chr22:20723793 7-mer-A1 4 CDS, ncRNA USP41 Medium_conserved miR-149 chr22:20720898 7-mer-A1 2 CDS, ncRNA USP41 Medium_conserved miR-185/882/3473/4306/4644 chr22:20726865 7-mer-A1 2 ncRNA USP41 Medium_conserved miR-197 chr22:20704967 7-mer-m8 4 3pUTR, ncRNA USP41 Medium_conserved miR-197 chr22:20705058 8-mer 4 3pUTR, ncRNA USP41 Medium_conserved miR-202-3p chr22:20724454 7-mer-A1 4 CDS, ncRNA USP41 Medium_conserved miR-326/330/330-5p chr22:20720914 7-mer-m8 4 CDS, ncRNA USP41 Medium_conserved miR-326/330/330-5p chr22:20726948 7-mer-m8 2 ncRNA USP41 Medium_conserved miR-329/329ab/362-3p chr22:20705098 7-mer-m8 0 3pUTR, ncRNA USP41 Medium_conserved miR-342-3p chr22:20721867 7-mer-A1 4 CDS, ncRNA USP41 Medium_conserved miR-346 chr22:20718553 7-mer-m8 4 CDS, ncRNA USP41 Medium_conserved miR-488 chr22:20704956 7-mer-A1 4 3pUTR, ncRNA

DNA & RNA Element - RAID2 Gene Name RAID ID Interactor 1 Category 1 ID 1 Interactor 2 Category 2 ID 2 Methods Score USP41 RAID00426224 hsa-miR-206 miRNA MIMAT0000462 USP41 mRNA 373856 Prediction 0.1828 USP41 RAID00444779 hsa-miR-222-3p miRNA MIMAT0000279 USP41 mRNA 373856 Prediction 0.1828 USP41 RAID01208948 hsa-miR-488-3p miRNA MIMAT0004763 USP41 mRNA 373856 Prediction 0.1828 USP41 RAID01313947 hsa-miR-1-3p miRNA MIMAT0000416 USP41 mRNA 373856 Prediction 0.1828 USP41 RAID01799399 hsa-miR-495-3p miRNA MIMAT0002817 USP41 mRNA 373856 Prediction 0.1828 USP41 RAID01944359 hsa-miR-506-3p miRNA MIMAT0002878 USP41 mRNA 373856 Prediction 0.1828 USP41 RAID01973280 hsa-miR-197-3p miRNA MIMAT0000227 USP41 mRNA 373856 Prediction 0.1828 USP41 RAID02420118 hsa-miR-124-3p miRNA MIMAT0000422 USP41 mRNA 373856 Prediction 0.1828 USP41 RAID02764513 hsa-miR-653-5p miRNA MIMAT0003328 USP41 mRNA 373856 Prediction 0.1828 USP41 RAID02986294 hsa-miR-499a-5p miRNA MIMAT0002870 USP41 mRNA 373856 Prediction 0.1828 USP41 RAID03430199 hsa-miR-221-3p miRNA MIMAT0000278 USP41 mRNA 373856 Prediction 0.1828