DNA & RNA Element - AREsite Gene Name Motif CDS Area ARE Area Evidence Upf1; Rent1 ATTTA 287-3661 4093-4097

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 MIMAT0000137 mmu-miR-126-5p 19704 Upf1 gcGCAUGGUUUUCAUUAUUac | ||:: ::||||||| auCUUAUUCUGGGUAAUAAaa 3 20 46 66 [mm9:8:72856316-72856336:-] 0.6838 135 0 -7.43 -0.2329 MIMAT0004530 mmu-miR-127* 19704 Upf1 uagucucgggAGACUCGAAGUc |:||||||||| uguuuuugagUUUGAGCUUCAg 2 13 730 751 [mm9:8:72855631-72855652:-] 0.5710 156 7 -21.44 -0.1752 MIMAT0004573 mmu-miR-293* 19704 Upf1 guuuuACAGUGUGUCAAACUCa |||: : |||||||| ggauuUGUUUUUGAGUUUGAGc 2 18 725 746 [mm9:8:72855636-72855657:-] 0.5710 153 7 -12.56 -0.4696 MIMAT0004574 mmu-miR-294* 19704 Upf1 ucuaucCCGGAGGUAAAACUCa || :|: ||||||| gccggaGGAUUUGUUUUUGAGu 2 17 719 740 [mm9:8:72855642-72855663:-] 0.5710 148 7 -15.00 -0.5518 MIMAT0004579 mmu-miR-302a* 19704 Upf1 cguUCAUGUUGGUGCAAAUUCa ||| ||:: |||||| uuuAGUCAAAUUUGUUUUAAGc 2 20 907 928 [mm9:8:72855454-72855475:-] 0.5296 123 6 -9.54 -0.1024 MIMAT0004617 mmu-miR-148a* 19704 Upf1 ucagccucacagaGUCUUGAAa ::|||||| ugcgccaacgcaaUGGAACUUa 2 10 882 903 [mm9:8:72855479-72855500:-] 0.5296 125 6 -9.94 -0.1064 MIMAT0004636 mmu-miR-93* 19704 Upf1 gcccuUCACGAUCGAGUCGUca ||| ||| |||||| ggcuuAGU-CUA--UCAGCAuc 3 18 30 48 [mm9:8:72856334-72856352:-] 0.6838 128 0 -11.14 -0.1037 MIMAT0004666 mmu-miR-33* 19704 Upf1 cacuAC-GUGACACCUUUGUAac || ||| |||||| uuuuUGUCACCAAUAAAACAUga 3 19 929 951 [mm9:8:72855431-72855453:-] 0.5194 121 0 -7.26 -0.1223 MIMAT0004670 mmu-miR-7a* 19704 Upf1 auaccgucugacacUAAACAAc ||||||| uaauuuuuagucaaAUUUGUUu 2 9 902 923 [mm9:8:72855459-72855480:-] 0.5296 140 7 -4.25 -1.0293 MIMAT0004670 mmu-miR-7a* 19704 Upf1 auaccgucuGACACUAAACAAc :| | :|||||| gguuuuuuuUUUUUGUUUGUUu 2 14 492 513 [mm9:8:72855869-72855890:-] 0.5297 129 6 -3.96 -0.1961 MIMAT0004758 mmu-miR-463 19704 Upf1 gauggaAUAUACC--A-CAGAUAGu |||:||| | ||||||| cuaagcUAUGUGGCUUAGUCUAUCa 2 17 19 43 [mm9:8:72856339-72856363:-] 0.6838 154 7 -20.00 -1.1256 MIMAT0004187 mmu-miR-744 19704 Upf1 acgacaaUCGGGAUCGGGGCGu ||||: |||||||| gcugagaAGCCUGAGCCCCGCa 2 16 672 693 [mm9:8:72855689-72855710:-] 0.5710 163 7 -34.13 -0.2651 MIMAT0003472 mmu-miR-693-5p 19704 Upf1 cuUUUGAAAGCCUACACCGAc :|:|| |||||||| aaGAGCUAAGCUAUGUGGCUu 2 20 14 34 [mm9:8:72856348-72856368:-] 0.6838 147 7 -15.86 -0.6415 MIMAT0003496 mmu-miR-706 19704 Upf1 aaaaaacucuguccCAAAGAGa ||||||| uguucuuuuucuuuGUUUCUCg 2 9 311 332 [mm9:8:72856050-72856071:-] 0.4778 140 7 -7.53 -0.4161 MIMAT0003782 mmu-miR-676 19704 Upf1 ucgaGUUGUUGGA--GUCCUGCc | ||: ::| ||||||| ggggCUACGUUUUAGCAGGACGa 2 18 340 362 [mm9:8:72856020-72856042:-] 0.5540 144 7 -18.30 -0.4486 MIMAT0005835 mmu-miR-1-2-as 19704 Upf1 acCUUACAUUUC--UUC-AUACAu |:| | |:|| ||| ||||| gcGGAGGAAGAGCUAAGCUAUGUg 2 20 7 30 [mm9:8:72856352-72856375:-] 0.6838 122 0 -13.64 -0.8210 MIMAT0009411 mmu-miR-1306 19704 Upf1 guaGUGGUGGUCUCGGUUGCa || |||| | ||||||| aggCA-CACCUGCGCCAACGc 2 19 873 892 [mm9:8:72855490-72855509:-] 0.5296 160 7 -22.82 -0.1544 MIMAT0009414 mmu-miR-1937b 19704 Upf1 acccccgaGCAGGCCCUa | ||||||| gcgagaagCUUCCGGGAa 2 11 647 664 [mm9:8:72855718-72855735:-] 0.5710 142 7 -16.01 -0.5514 MIMAT0009422 mmu-miR-1951 19704 Upf1 aucggUGUGGUC-AGAGGUGAUg |:||| | |:||||||: aauggAUACCUGUUUUCCACUGc 2 18 77 99 [mm9:8:72856283-72856305:-] 0.7054 144 0 -22.43 -0.1196 MIMAT0009429 mmu-miR-1937c 19704 Upf1 acccccgaGAAGGCCCUa ||||||||| gcgagaagCUUCCGGGAa 2 11 647 664 [mm9:8:72855718-72855735:-] 0.5710 150 7 -18.82 -0.5514 MIMAT0009431 mmu-miR-1958 19704 Upf1 ugAAUGACGAAGGUGAAAGGAu || :|| ||:: ||||||| ucUUUUUGGUUUUCCUUUCCUc 2 21 533 554 [mm9:8:72855828-72855849:-] 0.5605 164 7 -17.72 -0.3497 MIMAT0000140 mmu-miR-128 19704 Upf1 uuucucuggccaaGUGACACu ||||||| aaaacugaagcacCACUGUGu 2 9 101 121 [mm9:8:72856261-72856281:-] 0.7054 140 7 -13.75 -0.3080 MIMAT0000144 mmu-miR-132 19704 Upf1 gcugguaccgacauCUGACAAu ||||||| gucucuagagaccuGACUGUUa 2 9 613 634 [mm9:8:72855748-72855769:-] 0.5605 140 7 -14.96 -0.7129 MIMAT0000148 mmu-miR-136 19704 Upf1 gguagUAGUUUUGUUUACCUca || ||||:||||||| aaaaaAUAAAAAUAAAUGGAua 3 18 63 84 [mm9:8:72856298-72856319:-] 0.6946 153 0 -11.66 -0.1424 MIMAT0000215 mmu-miR-186 19704 Upf1 ucggguuuuccUCUUAAGAAAc | :||||||| uacccccuucaAAGAUUCUUUc 2 12 560 581 [mm9:8:72855801-72855822:-] 0.5605 143 7 -10.16 -0.3477 MIMAT0000215 mmu-miR-186 19704 Upf1 ucggguuuuccucuuAAGAAAc |||||| ggguuuuucugguuuUUCUUUu 2 8 455 476 [mm9:8:72855906-72855927:-] 0.5795 120 6 -7.53 -0.1608 MIMAT0000215 mmu-miR-186 19704 Upf1 ucggguuuuccucuuAAGAAAc |||||| guuuuucuuuuuuuuUUCUUUu 2 8 466 487 [mm9:8:72855895-72855916:-] 0.5392 120 6 -3.59 -0.2330 MIMAT0000237 mmu-miR-204 19704 Upf1 ucCGUAUCCUACUGUUUC-CCUu | | |||| : |||| ||| gaGGAGAGGAGAGGAAAGAGGAg 2 21 130 152 [mm9:8:72856230-72856252:-] 0.5073 120 0 -20.22 -0.1023 MIMAT0000366 mmu-miR-290-5p 19704 Upf1 uuucACGGGGGUAUCAAACUCa ||:::::: |||||||| gauuUGUUUUUG-AGUUUGAGc 2 19 726 746 [mm9:8:72855636-72855656:-] 0.5710 152 7 -13.54 -0.4831 MIMAT0000369 mmu-miR-292-5p 19704 Upf1 guuuucucGGGGGUCAAACUCa :::: |||||||| ggauuuguUUUUGAGUUUGAGc 2 15 725 746 [mm9:8:72855636-72855657:-] 0.5710 146 7 -12.97 -0.4797 MIMAT0000381 mmu-miR-34c 19704 Upf1 cgUUAGUCGAU-UGAUGUGACGGa :|| | ||: :| ||||||: ugGAU-ACCUGUUUUCCACUGCUa 2 22 79 101 [mm9:8:72856281-72856303:-] 0.7054 130 0 -10.98 -0.1248 MIMAT0000382 mmu-miR-34b-5p 19704 Upf1 ugUUAGUCGAU-UAAUGUGACGGa :|| | ||: || ||||||: ugGAU-ACCUGUUUUCCACUGCUa 2 22 79 101 [mm9:8:72856281-72856303:-] 0.7054 134 0 -10.46 -0.1248 MIMAT0000530 mmu-miR-21 19704 Upf1 aguuguagucagacuAUUCGAu |||||| uagucaaauuuguuuUAAGCUu 2 8 909 930 [mm9:8:72855452-72855473:-] 0.5296 120 6 -10.82 -0.1085 MIMAT0000542 mmu-miR-34a 19704 Upf1 uguUGGUCGAUUCUGUGACGGu ||| |:| ||||||: gauACCUGUU-UUCCACUGCUa 2 20 81 101 [mm9:8:72856281-72856301:-] 0.7054 129 0 -18.05 -0.1248 MIMAT0000590 mmu-miR-342-3p 19704 Upf1 ugcccacgcuaaaGACACACUCu ||||||||| aacugaagcaccaCUGUGUGAGc 2 11 103 125 [mm9:8:72856257-72856279:-] 0.7054 150 7 -17.15 -0.2936 MIMAT0000659 mmu-miR-212 19704 Upf1 accggcacugaccuCUGACAAu ||||||| gucucuagagaccuGACUGUUa 2 9 613 634 [mm9:8:72855748-72855769:-] 0.5605 140 7 -14.28 -0.7017 MIMAT0000668 mmu-miR-211 19704 Upf1 ucCGUUUCCUACUGUUUC-CCUu | |:|||| : |||| ||| gaGGAGAGGAGAGGAAAGAGGAg 2 21 130 152 [mm9:8:72856230-72856252:-] 0.5073 124 0 -21.48 -0.1023 MIMAT0000741 mmu-miR-377 19704 Upf1 uguUUUCAACGGAAACACACUa :||| || ||||||| acuGAAG-CACCACUGUGUGAg 2 20 104 124 [mm9:8:72856258-72856278:-] 0.7054 145 7 -13.93 -0.1704 MIMAT0000747 mmu-miR-382 19704 Upf1 gcuuAGGUGGUGCUUG-UUGAAg |::| || |:|| ||||| acguUUUAGCA-GGACGAACUUc 2 19 346 367 [mm9:8:72856015-72856036:-] 0.5540 120 0 -17.99 -0.1498 MIMAT0001542 mmu-miR-449a 19704 Upf1 uggucgauuguuAUGUGACGGu | ||||||: ggauaccuguuuUCCACUGCUa 2 11 80 101 [mm9:8:72856281-72856302:-] 0.7054 126 0 -16.92 -0.1273 MIMAT0003172 mmu-miR-542-3p 19704 Upf1 aaAGUCAAUAGUU---AGACAGUGu |: ||| | |: |:|||||| aaUUUGUUUUAAGCUUUUUGUCACc 2 21 915 939 [mm9:8:72855443-72855467:-] 0.5296 135 6 -10.87 -0.1384 MIMAT0003456 mmu-miR-495 19704 Upf1 uucuucacgugguACAAACAAa |||||||| gguuuuuuuuuuuUGUUUGUUu 2 10 492 513 [mm9:8:72855869-72855890:-] 0.5297 145 7 -7.83 -1.2317 MIMAT0003460 mmu-miR-449c 19704 Upf1 ggUCGAUCGUUACGUGACGGa | || |: | ||||||: auACCU-GUUUUCCACUGCUa 2 20 82 101 [mm9:8:72856281-72856300:-] 0.7054 129 0 -12.50 -0.1273 MIMAT0004895 mmu-miR-590-5p 19704 Upf1 gacGUGAAAAUACUUAUUCGAg || |||:| |||||| aguCAAAUUUGU-UUUAAGCUu 2 20 910 930 [mm9:8:72855452-72855472:-] 0.5296 121 6 -9.91 -0.1085 MIMAT0005447 mmu-miR-449b 19704 Upf1 cggucgauuguuGUGACGGa ||||||: auaccuguuuucCACUGCUa 2 9 82 101 [mm9:8:72856281-72856300:-] 0.7054 124 0 -14.40 -0.1248 MIMAT0004941 mmu-miR-544 19704 Upf1 cucgaacGA-UUUUUACG-UCUUa || |:|:|||| |||| guuaaacCUGAGAGAUGCGAGAAg 2 16 631 654 [mm9:8:72855728-72855751:-] 0.5657 122 0 -11.52 -0.4100 MIMAT0005850 mmu-miR-1192 19704 Upf1 uuAAACCAGACAAACAAACAAa ||| |:|||||||||||| uuUUUUUUUUGUUUGUUUGUUu 2 21 496 517 [mm9:8:72855865-72855886:-] 0.5297 180 7 -16.89 -1.1819

DNA & RNA Element - TRANSFAC Accession AS Description Species Entrez Pubmed Binding Info G065631 Upf1 Mus musculus 19704 19536157

DNA & RNA Element - RepTar Gene Name miRNA Begin End Profile Upf1 mmu-miR-511 beg:651 end:670 pic:3' ACTCACGTCT-CGTTTTCCGTA 5'& || | .||||||| &5' -----GCTTCCGGGAAAGGCA- 3' Upf1 mcmv-miR-m59-1 beg:85 end:103 pic:3' GACTGCCAGCTCCGTGACGATT 5'& ||. ||||||||| &5' ------GTTTTC-CACTGCTAA 3' Upf1 mmu-miR-127star beg:734 end:752 pic:3' TAGTCTCGGGAGACTCGAAGTC 5'& |||. .|||||||||| &5' ----GAGT---TTGAGCTTCAG 3' Upf1 mmu-miR-7astar beg:716 end:734 pic:3' ATACCGTCTGACACTAAACAAC 5'& | |.|| |||||||| &5' ---GCCGGAG---GATTTGTT- 3' Upf1 mmu-miR-2141 beg:838 end:848 pic:3' TTGAAAAGACTGTGGAGGA 5'& ||||||| &5' -----------CACCTCC- 3' Upf1 mmu-miR-676 beg:345 end:362 pic:3' TCGAGTTGTTGGAGTCCTGCC 5'& |.|. ||||||| &5' -GTTTTAG-----CAGGACG- 3' Upf1 mmu-miR-106bstar beg:390 end:409 pic:3' CGTC-GTTCATGGGTGTCACGCC 5'& | ||.| .| ||||||| &5' ---GCCAGGAGCAT-CAGTGCG- 3' Upf1 mmu-miR-2140 beg:698 end:716 pic:3' TGGTGGTTCTAGACGTGGA 5'& |.||||. ||||||| &5' ATCACCGC---CTGCACC- 3' Upf1 mmu-miR-130bstar beg:133 end:150 pic:3' TCATCACGTTGTC-CCTTTCTCA 5'& |. || |||||||| &5' --------AGGAGAGGAAAGAG- 3' Upf1 mmu-miR-132 beg:619 end:635 pic:3' GCTGGTACCGACATCTGACAAT 5'& |||| |||||||| &5' -GACCT--------GACTGTTA 3' Upf1 mcmv-miR-M55-1 beg:688 end:707 pic:3' TGCCGATCGTGCGG---CTAGTGGT 5'& ||| ||| ||||||| &5' -------GCA-GCCTGGGATCACC- 3' Upf1 mmu-miR-1306 beg:875 end:892 pic:3' GTAGTGGTGGTCTCGGTTGCA 5'& |||| | ||||||| &5' ------CACCTGCGCCAACG- 3' Upf1 mmu-miR-744 beg:676 end:694 pic:3' ACGACAATCGGGATCGGGGCGT 5'& ||||. ||||||||| &5' -------AGCCTGAGCCCCGCA 3' Upf1 mmu-miR-615-5p beg:822 end:842 pic:3' CTAGGCTCGTGGCCCCTGGGGG 5'& || || || |||||||| &5' ---CCCTGC-CCC-GGACCCCC 3' Upf1 mmu-miR-1952 beg:796 end:809 pic:3' GTCTTCCTCCCACCTCT 5'& ||||||||||. &5' ------GAGGGTGGAGG 3' Upf1 mmu-miR-463 beg:24 end:44 pic:3' GATGGAATATACCA---CAGATAGT 5'& |||.||| |||||||| &5' ------TATGTGGCTTAGTCTATCA 3' Upf1 mmu-miR-342-3p beg:107 end:125 pic:3' TGCCCACGCTAAAGACACACTCT 5'& || ||||||||| &5' ------GCACCA-CTGTGTGAG- 3' Upf1 mmu-miR-293star beg:727 end:746 pic:3' GTTTTACAGTGTGTCAAACTCA 5'& |||. |||||||| &5' -----TGTTTTTGAGTTTGAG- 3' Upf1 mcmv-miR-m01-1 beg:531 end:555 pic:3' GGCAAGCTGCAATAAGAGGAGA 5'& |. ||.|. || |.||||| &5' CTTTTTGGTTTTCCTTTCCTC- 3' Upf1 mcmv-miR-m21-1 beg:553 end:562 pic:3' GCCGAACTTGCACAGGGGATA 5'& |||||| &5' --------------CCCCTA- 3' Upf1 mmu-miR-105 beg:583 end:605 pic:3' TGGTGTTCGTAGAC-TCGTGAACC 5'& .||.|| | ||.|||||| &5' -----GAGTATGGGAAGTACTTGG 3' Upf1 mmu-miR-1191 beg:338 end:361 pic:3' ATCCCGATGTA---TCATTCTGAC 5'& .|||||||.| || |.||| &5' -GGGGCTACGTTTTAGCAGGAC-- 3' Upf1 mmu-miR-1192 beg:486 end:518 pic:3' TTAAACCAG---------ACAAACAAACAAA 5'& ||||||. ||||||||||||| &5' --TTTGGTTTTTTTTTTTTGTTTGTTTGTTT 3' Upf1 mmu-miR-1196 beg:0 end:18 pic:3' TCCGTCTCCGTCCATCTAAA 5'& |||.|| || ||| ||| &5' AGGTAGCGG-AGGAAGA--- 3' Upf1 mmu-miR-1196 beg:128 end:149 pic:3' TCCGTCTCCG-TCCA-TCTAAA 5'& ||| ||||| ||| ||| &5' AGG-AGAGGAGAGGAAAGA--- 3' Upf1 mmu-miR-1274a beg:610 end:629 pic:3' ACCGCGGACTTGTCCCTGGACT 5'& |.|| .|| ||||||| &5' ----GTCTC--TAGAGACCTGA 3' Upf1 mmu-miR-127star beg:414 end:433 pic:3' TAGTCTCGGGAGACTCGAAGTC 5'& ||| ||. |.|.|||| &5' --CAGCGCTAAG-GGGTTTCA- 3' Upf1 mmu-miR-130bstar beg:217 end:239 pic:3' TCATCACGTTG-TC-CCTTTCTCA 5'& ||.| ||..| || |||.|||| &5' -GTGG-GCGGCGAGAGGAGAGAG- 3' Upf1 mmu-miR-139-3p beg:600 end:620 pic:3' GAGGTTGTCCCGGC---GCAGAGGT 5'& || || .|||||.| &5' --------GGATCGGTTTGTCTCTA 3' Upf1 mmu-miR-145star beg:380 end:399 pic:3' GTTCTTGTCATAAAGGTCCTTA 5'& |.|.| ||||||. &5' ----AGCGGGCGG-CCAGGAG- 3' Upf1 mmu-miR-18a beg:28 end:52 pic:3' GATAGACGTGATCTA-----CGTGGAAT 5'& || .||| |||.|||| &5' ------GC-TTAGTCTATCAGCATCTTA 3' Upf1 mmu-miR-18b beg:31 end:52 pic:3' GATTGTCGTGATCTACGTGGAAT 5'& .||. ||| |||.|||| &5' ----TAGT-CTATCAGCATCTTA 3' Upf1 mmu-miR-1903 beg:267 end:290 pic:3' ACAGAGTCCTTCTTCTTCTTCC 5'& || | | |||.|.|||.| &5' -GTGCCCGCCAGAGGGAGAGG- 3' Upf1 mmu-miR-1903 beg:0 end:17 pic:3' ACAGAGTCCTTCTTCTTCTTCC 5'& ||| || .||.|||| &5' ------AGGTAGCGGAGGAAG- 3' Upf1 mmu-miR-1904 beg:150 end:168 pic:3' GGAGGGAGGTCTC-CTCGTCTTG 5'& | |||| |||||||. &5' -------CGAGAGCGAGCAGAG- 3' Upf1 mmu-miR-1928 beg:13 end:34 pic:3' CTCGAC-CGTTACATCGA 5'& ||||| || ||||.||| &5' GAGCTAAGCTATGTGGCT 3' Upf1 mmu-miR-1934 beg:276 end:305 pic:3' TCTCCTGCTTCGTCC----CCTGGTCT 5'& ||||| ||.|| |||||.| &5' AGAGGGAGAGGCCTCGCCAGGACCGG- 3' Upf1 mmu-miR-1937a beg:688 end:703 pic:3' ACCCCCGAGCAGGCCCTAA 5'& || | |.||||| &5' -----GCA-GCCTGGGAT- 3' Upf1 mmu-miR-1940 beg:549 end:571 pic:3' TTGACGAGGTGGAAGAGTCAGGAGGTA 5'& |||| || || |||.|| &5' -----CTCC-CCC-CTACCCCCTTCA- 3' Upf1 mmu-miR-1951 beg:79 end:100 pic:3' ATCGGTGTGGTC-AGAGGTGATG 5'& |.||| | |.||||||.| &5' -----ATACCTGTTTTCCACTGC 3' Upf1 mmu-miR-1952 beg:131 end:151 pic:3' GTCTTC-CTCCCACCTCT 5'& |||.| |||| |||. &5' -AGAGGAGAGGAAAGAGG 3' Upf1 mmu-miR-1955 beg:683 end:703 pic:3' TTTTCGACGTCACGTAGGACCCTGA 5'& || ||| |||||||. &5' -------GCCCCGCAGCCTGGGAT- 3' Upf1 mmu-miR-1958 beg:531 end:554 pic:3' TGAATGACGAAGGTGAAAGGAT 5'& ||| .|| ||. ||||||| &5' -CTTTTTGGTTTTCCTTTCCT- 3' Upf1 mmu-miR-1958 beg:460 end:479 pic:3' TGAATGACGAAGGTGAAAGGAT 5'& ||| ||. ||||..| &5' -----CTGGTTTTTCTTTTTT- 3' Upf1 mmu-miR-1982star beg:287 end:308 pic:3' GGAGGGGTCCTGGGAGGGTT 5'& |||| |||||||| ||| &5' CCTCGCCAGGACCGGCCC-- 3' Upf1 mmu-miR-201 beg:41 end:61 pic:3' TTCTTGTTACGGAAT--GACTCAT 5'& ||. .|||| |||.||| &5' -----CAGCATCTTATTCTGGGTA 3' Upf1 mmu-miR-207 beg:127 end:154 pic:3' CTCC-CTCCTCTCGGTCCTCTTCG 5'& |||| |||||||| | |||.||| &5' GAGGAGAGGAGAGGAAAGAGGAGC 3' Upf1 mmu-miR-211 beg:273 end:287 pic:3' TCCGTTTCCTACTGTTTCCCTT 5'& | ||.|||||. &5' -----------GCCAGAGGGAG 3' Upf1 mmu-miR-2139 beg:381 end:413 pic:3' CGTCAA-TGGTCCTCGT-----CGCGTCGA 5'& ||.| .||||||||| ||||.|. &5' GCGGGCGGCCAGGAGCATCAGTGCGCGGT- 3' Upf1 mmu-miR-2140 beg:864 end:888 pic:3' TGGTGGTTCTA----GACGTGGA 5'& |.||| ||. ||||.|| &5' -CTACCCAGGCACACCTGCGCC- 3' Upf1 mmu-miR-2145 beg:291 end:312 pic:3' TTGGTCCGGGCTGGGACGA 5'& .||||| |||.||| ||| &5' -GCCAGGACCGGCCCCGCT 3' Upf1 mmu-miR-2145 beg:814 end:831 pic:3' TTGGTCCGGGCTGGGACGA 5'& .| ||| .|||||| &5' -GCTGGGC---GCCCTGC- 3' Upf1 mmu-miR-218 beg:869 end:880 pic:3' TGTACCAATCTAGTTCGTGTT 5'& ||.||||| &5' ------------CAGGCACA- 3' Upf1 mmu-miR-24 beg:669 end:689 pic:3' GACAAGGACGACTT----GACTCGGT 5'& |||||. ||||||| &5' --------GCTGAGAAGCCTGAGCC- 3' Upf1 mmu-miR-26a beg:588 end:606 pic:3' TCGGATAGGACCTA--ATGAACTT 5'& |||. ||||||.| &5' ---------TGGGAAGTACTTGGA 3' Upf1 mmu-miR-26b beg:591 end:606 pic:3' TGGATAGGACTTAATGAACTT 5'& ||| ||||||.| &5' ---------GAAGTACTTGGA 3' Upf1 mmu-miR-27astar beg:669 end:690 pic:3' ACGAGTGTTCGTCGATTCGGGA 5'& ||| | |||| ||.||||| &5' -GCTGAGAAGC--CTGAGCCC- 3' Upf1 mmu-miR-2861 beg:820 end:841 pic:3' GGCGGG-CGGCGGTCCGGGG 5'& ||||| ||| ||.| |||| &5' -CGCCCTGCC-CCGGACCCC 3' Upf1 mmu-miR-291b-3p beg:65 end:88 pic:3' TGTTTGT-TTTACCTACGTGAAA 5'& |.||| |||||||| | || &5' ATAAAAATAAATGGATAC-CT-- 3' Upf1 mmu-miR-295 beg:569 end:603 pic:3' TCTGAG------TTTTCAT-CA--TCGTGAAA 5'& |||.|| |..|||| | ||.|||| &5' AGATTCTTTCAAAGGAGTATGGGAAGTACTT- 3' Upf1 mmu-miR-302b beg:93 end:114 pic:3' GATGATTTTGTACCTTCGTGAAT 5'& ||.||||||| ||||||| &5' CTGCTAAAACT--GAAGCAC--- 3' Upf1 mmu-miR-302b beg:590 end:604 pic:3' GATGATTTTGTACCTTCGTGAAT 5'& |||||.||||. &5' ------------GGAAGTACTTG 3' Upf1 mmu-miR-302c beg:582 end:603 pic:3' GGTGACTTTGTA-CCTTCGTGAA 5'& |.|..|| |||||.|||| &5' -----GGAGTATGGGAAGTACTT 3' Upf1 mmu-miR-30estar beg:662 end:679 pic:3' CGACATTTGTAGGCTGACTTTC 5'& |..|| || ||||.| &5' -----AGGCAG-CG-CTGAGA- 3' Upf1 mmu-miR-343 beg:268 end:288 pic:3' AGACCCGTGTACTTCCCTCT 5'& || |.| .||||||| &5' --TGCCCGCCA-GAGGGAGA 3' Upf1 mmu-miR-34a beg:81 end:102 pic:3' TGTTGGTCGATTCTGTGACGGT 5'& ||| |.| ||||||.| &5' ---ACCTGTTTTC-CACTGCTA 3' Upf1 mmu-miR-370 beg:338 end:359 pic:3' TGGTCCAAGGTG--GGGTCGTCCG 5'& ||| |.|| ...|||||| &5' ---AGGGGCTACGTTTTAGCAGG- 3' Upf1 mmu-miR-375 beg:147 end:167 pic:3' AGTGCGCTCGG-CTTGCTTGTTT 5'& |||| ||.|||.||.| &5' ------GAGCGAGAGCGAGCAGA 3' Upf1 mmu-miR-377 beg:104 end:124 pic:3' TGTTTTCAACGGAAACACACTA 5'& .||| || ||||||| &5' ---GAAGCA-CCACTGTGTGA- 3' Upf1 mmu-miR-379 beg:21 end:44 pic:3' GGATGCAAGGTATCAGATGGT 5'& |||.|| | |||||||.|| &5' -CTATGTGGCTTAGTCTATCA 3' Upf1 mmu-miR-431 beg:340 end:361 pic:3' ACGTACTGCCGGA-CGTTCTGT 5'& || ||| .| |||.||| &5' -GCT--ACGTTTTAGCAGGAC- 3' Upf1 mmu-miR-431star beg:282 end:307 pic:3' TCTTCGGGAC-GTTCT-GCTGGAC 5'& |||.||| | ||.|| ||.|| &5' AGAGGCCTCGCCAGGACCGGCC-- 3' Upf1 mmu-miR-470 beg:396 end:418 pic:3' TGAGTGGTCACG-GTCAGGTTCTT 5'& ||.|||||| |.|||| || &5' ---CATCAGTGCGCGGTCCCAG-- 3' Upf1 mmu-miR-540-3p beg:292 end:317 pic:3' GGTCCTAGCTGGA--GACTGGA 5'& |||||| ||.|| ||| || &5' CCAGGACCGGCCCCGCTGTTCT 3' Upf1 mmu-miR-582-3p beg:337 end:359 pic:3' AACCCAAGT-CAACAAGTTGTCC 5'& ||| .| || ||.|.|||| &5' --GGGGCTACGT--TTTAGCAGG 3' Upf1 mmu-miR-652 beg:255 end:272 pic:3' GTGTTGGGATCACCGCGGTAA 5'& |..||| |||||.| &5' --CGGCCCA----GCGCCGT- 3' Upf1 mmu-miR-666-5p beg:252 end:278 pic:3' CCGAGA-GTGTCGA--CACGGGCGA 5'& ||| | | |||| |||||||| &5' GGC-CGGCCCAGCGCCGTGCCCGC- 3' Upf1 mmu-miR-670 beg:160 end:180 pic:3' AAGTGGTGTA-TGTGAGTCCCTA 5'& || | .|. |||||| &5' -----CAGAGAGCGGCCAGGGA- 3' Upf1 mmu-miR-671-5p beg:857 end:883 pic:3' GAGGTCGGGGA--GGTCCCGAAGGA 5'& ||| ||||| ||||| ||| &5' --CCAACCCCTACCCAGGCACACCT 3' Upf1 mmu-miR-673-3p beg:813 end:837 pic:3' CCACGTGTCTTGAGT--CGGGGCCT 5'& ||| |..| |||||||| &5' --TGCT--GGGCGCCCTGCCCCGGA 3' Upf1 mmu-miR-675-5p beg:694 end:716 pic:3' TGACACCCG---GGAAAGGCGTGGT 5'& |||| || |.||||| &5' ----TGGGATCACCGC-CTGCACC- 3' Upf1 mmu-miR-675-5p beg:871 end:889 pic:3' TGACACCCGGGAAAGGCGTGGT 5'& ||| |.||.||| &5' ------GGCACAC-CTGCGCCA 3' Upf1 mmu-miR-676 beg:682 end:703 pic:3' TCGAGTTGTTGGAGTCCTGCC 5'& ||| | .||.||| .|||. &5' AGCCCCGCAGCCT-GGGAT-- 3' Upf1 mmu-miR-684 beg:168 end:184 pic:3' AACTGAACTTCCCTTTTGA 5'& |.| |||||..|| &5' --GGCC---AGGGAGGAC- 3' Upf1 mmu-miR-692 beg:118 end:137 pic:3' CTCACTCCGCGAGTTTCTCTA 5'& ||||| || |.|.|||| &5' --GTGAGCAGC-CGAGGAGA- 3' Upf1 mmu-miR-692 beg:217 end:236 pic:3' CTCACTCCG-CGAGTTTCTCTA 5'& ||| ||| || .|.|||| &5' --GTG-GGCGGCGAGAGGAGA- 3' Upf1 mmu-miR-692 beg:127 end:151 pic:3' CTCA-CTCCGCGAGTTTCTCTA 5'& ||| |||| | ||||||. &5' GAGGAGAGGAGAGGAAAGAGG- 3' Upf1 mmu-miR-693-5p beg:12 end:34 pic:3' CTTTTGAAAGCCTACACCGAC 5'& |.|.|| |||||||| &5' -AGAGCTAAGCTATGTGGCT- 3' Upf1 mmu-miR-696 beg:863 end:881 pic:3' GGGTGTCGTTCGTGTGCG 5'& ||.|| ||.|||||| &5' CCTACC-CAGGCACAC-- 3' Upf1 mmu-miR-698 beg:133 end:152 pic:3' TCCCTTCCTTTGCTCTTAC 5'& ||| |||||| |||.| &5' AGGAGAGGAAA-GAGGA-- 3' Upf1 mmu-miR-703 beg:527 end:546 pic:3' AAGAAAGGAAGACTTCCAAAA 5'& |.|||.|||.| |||||| &5' -TTTTTTCTTTTT--GGTTTT 3' Upf1 mmu-miR-705 beg:826 end:851 pic:3' ACGGGT----GGGGTGGAGGGTGG 5'& |||| |||||||||||.| &5' -GCCCCGGACCCCCACCTCCCGC- 3' Upf1 mmu-miR-705 beg:849 end:872 pic:3' ACG--GGTGGGGTGGAGGGTGG 5'& || |||||| ||| ||.||| &5' -GCAGCCACCCAACC-CCTACC 3' Upf1 mmu-miR-706 beg:446 end:465 pic:3' AAAAAACTCTGTCCCAAAGAGA 5'& || ..||||||.||| &5' -----TGTT-TGGGGTTTTTCT 3' Upf1 mmu-miR-706 beg:462 end:474 pic:3' AAAAAACTCTGTCCCAAAGAGA 5'& |||||.||| &5' -------------GGTTTTTCT 3' Upf1 mmu-miR-713 beg:388 end:408 pic:3' CGACACACGGAAGTCACGT 5'& || | || ||||||| &5' GCCAGGAGCA-TCAGTGC- 3' Upf1 mmu-miR-744 beg:291 end:311 pic:3' ACGACAATCGGGATCGGGGCGT 5'& || .| || .||||||| &5' -GCCA--GGACC-GGCCCCGC- 3' Upf1 mmu-miR-764-5p beg:756 end:777 pic:3' TCCTCCTGTACACTCGTGG 5'& ||| | || |||||||| &5' AGGCGAACTCGTGAGCAC- 3' Upf1 mmu-miR-7b beg:74 end:96 pic:3' TGTTGTTTTAGTGTTCAGAAGGT 5'& || .| .|| ||.||||| &5' --AATGGA--TACCTGTTTTCCA 3' Upf1 mmu-miR-871 beg:41 end:61 pic:3' GTACTGACCGT-GATT-AGACTTAT 5'& ||| || ||||..|| &5' --------GCATCTTATTCTGGGTA 3' Upf1 mmu-miR-879 beg:797 end:814 pic:3' CCGAATCTCGATATTCGGAGA 5'& ||.|. |.||||| &5' -----AGGGTGG-AGGCCTC- 3' Upf1 mmu-miR-92astar beg:825 end:846 pic:3' CATTACGGTGGTTA-GGGGTGGA 5'& |||| ||.. |||||||| &5' ----TGCC-CCGGACCCCCACCT 3' Upf1 mmu-miR-92astar beg:548 end:564 pic:3' CATTACGGTGGTTAGGGGTGGA 5'& || || |||.||| &5' ------CCTCCC--CCCTACC- 3' Upf1 mmu-miR-92astar beg:852 end:872 pic:3' CATTACGGT-GGTTAGGGGTGGA 5'& |||| |||| |||.||| &5' -----GCCACCCAACCCCTACC- 3' Upf1 mmu-miR-1937b beg:651 end:664 pic:3' ACCCCCGAGCAGGCCCTA 5'& ||| ||||||| &5' -----GCT--TCCGGGA- 3' Upf1 mmu-miR-1937c beg:652 end:664 pic:3' ACCCCCGAGAAGGCCCTA 5'& ||||||||| &5' --------CTTCCGGGA- 3' Upf1 mmu-miR-294star beg:721 end:741 pic:3' TCTATCCCGGAGGTAAAACTCA 5'& ||| .|. |||||||| &5' ----AGGA-TTTGTTTTTGAGT 3'

DNA & RNA Element - RAID2 Gene Name RAID ID Interactor 1 Category 1 ID 1 Interactor 2 Category 2 ID 2 Methods Score Upf1 RAID00131581 mmu-miR-21a-5p miRNA MIMAT0000530 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID00297906 mmu-miR-34c-5p miRNA MIMAT0000381 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID00473239 mmu-miR-7118-5p miRNA MIMAT0028133 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID00479353 mmu-miR-34b-5p miRNA MIMAT0000382 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID00510472 mmu-miR-34a-5p miRNA MIMAT0000542 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID00717707 mmu-miR-449a-5p miRNA MIMAT0001542 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID00784733 mmu-miR-292a-5p miRNA MIMAT0000369 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID00822389 mmu-miR-290a-5p miRNA MIMAT0000366 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID00880533 mmu-miR-7001-3p miRNA MIMAT0027905 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID00970641 mmu-miR-7030-5p miRNA MIMAT0027964 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID01026899 mmu-miR-495-3p miRNA MIMAT0003456 Upf1 mRNA 19704 Prediction 0.2202 Upf1 RAID01055862 mmu-miR-6930-5p miRNA MIMAT0027760 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID01152142 mmu-miR-194-1-3p miRNA MIMAT0016999 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID01227098 mmu-miR-211-5p miRNA MIMAT0000668 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID01346846 mmu-miR-377-3p miRNA MIMAT0000741 Upf1 mRNA 19704 Prediction 0.2202 Upf1 RAID01567419 mmu-miR-342-3p miRNA MIMAT0000590 Upf1 mRNA 19704 Prediction 0.2381 Upf1 RAID01589231 mmu-miR-186-5p miRNA MIMAT0000215 Upf1 mRNA 19704 Prediction 0.2202 Upf1 RAID01591835 mmu-miR-216c-5p miRNA MIMAT0029888 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID01718302 mmu-miR-212-3p miRNA MIMAT0000659 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID01746492 mmu-miR-542-3p miRNA MIMAT0003172 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID01771185 mmu-miR-136-5p miRNA MIMAT0000148 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID01944715 mmu-miR-449c-5p miRNA MIMAT0003460 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID02121619 mmu-miR-7010-5p miRNA MIMAT0027924 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID02295223 mmu-miR-204-5p miRNA MIMAT0000237 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID02313626 mmu-miR-3102-5p.2-5p miRNA MIMAT0014934 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID02379496 mmu-miR-744-5p miRNA MIMAT0004187 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID02487250 mmu-miR-7076-5p miRNA MIMAT0028058 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID02524739 mmu-miR-6929-5p miRNA MIMAT0027758 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID02539335 mmu-miR-132-3p miRNA MIMAT0000144 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID02584975 mmu-miR-9769-5p miRNA MIMAT0036461 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID02597949 mmu-miR-1192 miRNA MIMAT0005850 Upf1 mRNA 19704 Prediction 0.2202 Upf1 RAID02646657 mmu-miR-325-3p miRNA MIMAT0004640 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID02672239 mmu-miR-128-3p miRNA MIMAT0000140 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID02795415 mmu-miR-7075-5p miRNA MIMAT0028056 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID02809293 mmu-miR-3094-3p miRNA MIMAT0014910 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID02848704 mmu-miR-7683-3p miRNA MIMAT0029887 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID02899262 mmu-miR-6539 miRNA MIMAT0025584 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID02926200 mmu-miR-7008-3p miRNA MIMAT0027921 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID02958450 mmu-miR-7027-5p miRNA MIMAT0027958 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID03042423 mmu-miR-590-5p miRNA MIMAT0004895 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID03235247 mmu-miR-7651-5p miRNA MIMAT0029804 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID03347153 mmu-miR-544-3p miRNA MIMAT0004941 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID03369014 mmu-miR-672-3p miRNA MIMAT0017241 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID03446758 mmu-miR-7673-5p miRNA MIMAT0029852 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID03563982 mmu-mir-325 miRNA MI0000597 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID03662235 mmu-miR-6909-5p miRNA MIMAT0027718 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID03768053 mmu-miR-8118 miRNA MIMAT0031424 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID03829766 mmu-miR-449b miRNA MIMAT0005447 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID03859167 mmu-miR-382-5p miRNA MIMAT0000747 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID03907434 mmu-miR-7042-5p miRNA MIMAT0027988 Upf1 mRNA 19704 Prediction 0.1828 Upf1 RAID03982240 mmu-miR-126b-5p miRNA MIMAT0029894 Upf1 mRNA 19704 Prediction 0.1828