DNA & RNA Element - AREsite Gene Name Motif CDS Area ARE Area Evidence Ubb ATTTA 99-1016 1081-1085

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 22187 Ubb gcgcaugguuuucaUUAUUAc |||||| aaauuacaaguuucAAUAAUa 2 8 77 97 [mm9:11:62366642-62366662:+] 0.5314 120 6 -4.44 -0.1155 MIMAT0004545 mmu-miR-200b* 22187 Ubb agguuACGACGGGUCAUUC-UAc ||:||| ::||||| || gguuuUGUUGCAUGGUAAGCAU- 2 18 128 149 [mm9:11:62366693-62366714:+] 0.4957 129 0 -14.87 -0.7394 MIMAT0000376 mmu-miR-298 22187 Ubb cccUUCUUGUCGG-GAGGAGACGg || ||:|||: ||||||: uucAAUAAUAGCUGAACCUCUGUu 2 21 88 111 [mm9:11:62366653-62366676:+] 0.5604 143 0 -18.58 -0.1580 MIMAT0000556 mmu-miR-324-3p 22187 Ubb ucGUCGUGGAC-CCCGUCACc || : || | |||||||| ugCAUUCCCAGUGGGCAGUGa 2 19 11 31 [mm9:11:62366576-62366596:+] 0.4137 153 7 -20.03 -1.0328 MIMAT0004640 mmu-miR-325 22187 Ubb aacUAUCCUCCACGAGUUAUUu || | || :||||||| gaaAUUACAAGU-UUCAAUAAu 2 20 76 96 [mm9:11:62366641-62366661:+] 0.5314 145 7 -6.24 -1.0728 MIMAT0000578 mmu-miR-337-3p 22187 Ubb ucCGUAGUAUAUCCUCGACUu |: ||| ||| |||||| aaGUUUCA-AUAAUAGCUGAa 2 20 84 103 [mm9:11:62366649-62366668:+] 0.5314 129 6 -12.87 -0.1605 MIMAT0004746 mmu-miR-409-5p 22187 Ubb uacguuuCAACGAGCCCAUUGGa ||||| : ||||| | agguuuuGUUGCAU-GGUAAGCa 2 17 127 148 [mm9:11:62366692-62366713:+] 0.4957 122 0 -12.67 -0.1027 MIMAT0004789 mmu-miR-450a-3p 22187 Ubb uacuuacguuucguaGGGGUUa |||||| cacucuagccacuugCCCCAAu 2 8 45 66 [mm9:11:62366610-62366631:+] 0.5314 120 6 -13.23 -0.2039 MIMAT0003373 mmu-miR-302b* 22187 Ubb ucUUUCG-UAAGGGUACAAUUUca | ||| : ||: ||||||| uaAUAGCUGAACCUCUGUUAAAaa 3 22 93 116 [mm9:11:62366658-62366681:+] 0.5604 136 0 -10.45 -0.1566 MIMAT0003375 mmu-miR-302c* 22187 Ubb cgUCCAUUGGGGUACAAUUUcg || |:| ||: ||||||| auAGCUGAACCUCUGUUAAAaa 3 21 95 116 [mm9:11:62366660-62366681:+] 0.5604 148 0 -15.70 -0.1507 MIMAT0003735 mmu-miR-672 22187 Ubb aguGUGUGUCAUGUGGUUGGAGu || |:| || : |||||| uuuCA-AUAAUAGCUGAACCUCu 2 21 87 108 [mm9:11:62366652-62366673:+] 0.5604 122 6 -12.58 -0.1541 MIMAT0003493 mmu-miR-703 22187 Ubb aagaaAGGAAGACUUCCAAAa | :| | ||||||| aaaaaUGUUAAUAAAGGUUUu 2 17 113 133 [mm9:11:62366678-62366698:+] 0.5502 144 7 -7.52 -0.7788 MIMAT0004839 mmu-miR-743b-5p 22187 Ubb acuaccuguggucaGACUUGu |||||| aguuucaauaauagCUGAACc 2 8 85 105 [mm9:11:62366650-62366670:+] 0.5314 120 6 -10.12 -0.1241 MIMAT0000224 mmu-miR-194 22187 Ubb agguguACCUCAACGACAAUgu || | | |||||| aauagcUGAACCU-CUGUUAaa 3 17 94 114 [mm9:11:62366659-62366679:+] 0.5604 122 0 -8.12 -0.1705 MIMAT0003168 mmu-miR-543 22187 Ubb uucuucacguggcgcUUACAAa |||||| gaaccucuguuaaaaAAUGUUa 2 8 101 122 [mm9:11:62366666-62366687:+] 0.5604 120 6 -4.57 -0.2879

DNA & RNA Element - TRANSFAC Accession AS Description Species Entrez Pubmed Binding Info G006859 Ubb Mus musculus 22187

DNA & RNA Element - RepTar Gene Name miRNA Begin End Profile Ubb mghv-miR-M1-6 beg:77 end:92 pic:3' TTTTGGTGGAGTGTGTCAAAGT 5'& |.||| ||||||| &5' ---------TTACA-AGTTTCA 3' Ubb mmu-miR-106a beg:35 end:59 pic:3' GATG-GACGTGACAATC-GTGAAAC 5'& ||| ||||||| ||| ||||| &5' -TACTCTGCACTC-TAGCCACTT-- 3' Ubb mmu-miR-1 beg:1 end:19 pic:3' TATGTATGAAGAA--ATGTAAGGT 5'& ||| |.|||||| &5' --------TTCGGTCTGCATTCC- 3' Ubb mmu-miR-1970 beg:4 end:25 pic:3' GTTTCGGA--TAGGGGTCACTGTGT 5'& .|.|| ||.|||||||. &5' ---GGTCTGCATTCCCAGTGG---- 3' Ubb mmu-miR-20a beg:35 end:59 pic:3' GATG-GACGTGATATTCGTGAAAT 5'& ||| ||||||| ||. ||||| &5' -TACTCTGCACTCTAGCCACTT-- 3' Ubb mmu-miR-31star beg:125 end:145 pic:3' CTACCGTTATACAACCGTATCGT 5'& ||. |||| ||||.|.| &5' ---GGTTT--TGTT-GCATGGTA 3' Ubb mmu-miR-324-3p beg:9 end:31 pic:3' TCGTCGTGGAC-CCCGTCACC 5'& ||| || | |||||||| &5' -GCATTCCCAGTGGGCAGTG- 3' Ubb mmu-miR-337-3p beg:83 end:104 pic:3' TCCGTAGTATATCCTCGACTT 5'& |. ||| ||| ||||||| &5' --GTTTCA-ATAATAGCTGAA 3' Ubb mmu-miR-345-3p beg:56 end:77 pic:3' CAGAGGTCTGGGGA-----TCAAGTCC 5'& .|||| ||||.|| &5' --------GCCCCAATTTAAGTTTAG- 3' Ubb mmu-miR-450a-3p beg:5 end:23 pic:3' TACTTACGTTTCGTAGGGGTTA 5'& |. ||||.||||.| &5' ------GTCT-GCATTCCCAGT 3' Ubb mmu-miR-450b-3p beg:5 end:23 pic:3' TACGTACGTTTTACAAGGGTTA 5'& |. |||| ||||||.| &5' --GTCTGCA-----TTCCCAGT 3'

DNA & RNA Element - miRNAMap Gene Name Mature miRNA Target Start Target End miRNA 3-5 Alignment Target 5-3 Ubb mmu-miR-106a 37 60 -AUG-GACGUGACAAUC-GUGAAAC ||| ||||||| ||| ||||| UUACUCUGCACUC-UAGCCACUUG- Ubb mmu-miR-141 5 32 -GGUAGAAAU--GG----UCUGUCACAAU | :||| || :|:||||| UCGGUCUGCAUUCCCAGUGGGCAGUGA-- Ubb mmu-miR-155 15 41 -GGGGAUAGU-GUUA--AUCGUAAUU :||| :| : ||:| |:|||||| UUCCCAGUGGGCAGUGAUGGCAUUAC Ubb mmu-miR-17-5p 35 60 -UGAUG-GACGUGACAUUCGUGAAAC |:||| ||||||| ||: ||||| CAUUACUCUGCACUCUAGCCACUUG- Ubb mmu-miR-19a 25 49 AGUCAAAA-CGUAUCUAAACGUGU |||| |||| ||||| GCAGUGAUGGCAUUACUCUGCACU Ubb mmu-miR-19b 18 49 AGUCAAAACGU----ACC-UAA----ACGUGU |||| ||| ||| ||| ||||| CCAGUGG-GCAGUGAUGGCAUUACUCUGCACU Ubb mmu-miR-200b 4 32 CAGUA----GUAAUGG---UCCGUCAUAAU ||: |||| || :||||||: UUCGGUCUGCAUUCCCAGUGGGCAGUGA-- Ubb mmu-miR-20a 37 60 GAUG-GACGUGAUAUUCGUGAAAU ||| ||||||| ||: ||||| UUACUCUGCACUCUAGCCACUUG- Ubb mmu-miR-217 2 32 -UAGGUCAGUC--AAGG---ACUACGUCAU- ||:|:||| | |||| ||: |||||: UAUUCGGUCUGCAUUCCCAGUGG-GCAGUGA Ubb mmu-miR-24* 7 29 UGACUAUAGUCGA----GUCAUCCGUG :|| || ||||:|||| -----GGUCUGCAUUCCCAGUGGGCAG Ubb mmu-miR-290 57 79 UUUUUCACGGGGGUA---UCAAA-CUC |||||| ||||| || -----UUGCCCCAAUUUAAGUUUAGAA Ubb mmu-miR-298 93 113 CCUUCUUGUCGGGA-GGAGACGG- ||:|||: ||||||:: ----UAAUAGCUGAACCUCUGUUA Ubb mmu-miR-301 31 50 CGAAACUGUUAUGAUAACGUGAC ||:|| |||| |||||| ---AUGGCAUUACUC-UGCACUC Ubb mmu-miR-301b 27 50 ACGAAACUGUUAUGGUAACGUGAC |: ||:|| |||: |||||| AGUGAUGGCAUUACUC-UGCACUC Ubb mmu-miR-302c* 95 116 -GUCGUCCAUUGGGGUACAAUUU- :||| ||||:| ||||||| AUAGCUG--AACCUC-UGUUAAAA Ubb mmu-miR-31 23 56 GUCGAUACGGUCGU-----------AGAACGGA :|| :|| :||| ||| ||| GGGCAGUGAUGGCAUUACUCUGCACUCUAGCCA Ubb mmu-miR-324-3p 4 32 -GGUCGU-CGU---GGAC-CCCGUCACC :|:|: ||| || | |||||||| UUCGGUCUGCAUUCCCAGUGGGCAGUGA Ubb mmu-miR-326 6 26 UGACCUCCUUCCCGGGUCUCC- || ||||| || --CGGUCUGCAUUCCCAGUGGG Ubb mmu-miR-331 8 28 AAGAUCCUAUCCGGGUC-CCCG- |||: ||||| |||| GUCUGCAUU---CCCAGUGGGCA Ubb mmu-miR-339 11 33 ACUCG--AGGACCUCCUGUCCCU- || ||| | ||:||| || --UGCAUUCCCAGUGGGCAGUGAU Ubb mmu-miR-346 6 33 UCUCCGUCCGUGAG-----CCCGUCUGU- ||: |||:|| |||||| | --CGGUCUGCAUUCCCAGUGGGCAGUGAU Ubb mmu-miR-370 6 28 UUGGUCCAAGGUG---GGGUCGUCCG- || ||::| |||||::||| ----CGG-UCUGCAUUCCCAGUGGGCA Ubb mmu-miR-449b 17 56 -GGUCGAUCGUU--------------ACGUGA---CGGA ||||: :|||: |||||| ||| CCCAGUGGGCAGUGAUGGCAUUACUCUGCACUCUAGCCA Ubb mmu-miR-666 39 65 CCGAGA-GUG---UCGAC--ACGGGCGA |||| ||| ||| ||||| | -ACUCUGCACUCUAGCCACUUGCCC-CA Ubb mmu-miR-674 9 32 AUGUGGUGAGGGUAGA--GUCACG | ||:||||| ||||| -UCUGCAUUCCCAGUGGGCAGUGA Ubb mmu-miR-675-3p 21 42 UGACUCGCCAAUCCCGU-AUGUC ||:|| || |||| ||| -GUGGGCAGUGAUGGCAUUACU- Ubb mmu-miR-675-5p 20 50 UGACACCCGGG--------AA--AGGCGUGGU |||||| || ||:||||: --AGUGGGCAGUGAUGGCAUUACUCUGCACUC Ubb mmu-miR-695 3 24 -AAGUCAGUGGAUACGGGUUAGA |||:||| | || ||||:| AUUCGGUCUGC-AUUCCCAGUG- Ubb mmu-miR-703 98 135 AAGAAA-GGAAGAC--U--------------UCCAAAA- || ||| ||| | ||||||| -GCUGAACCU-CUGUUAAAAAAUGUUAAUAAAGGUUUUG Ubb mmu-miR-707 20 43 GCAUCCGUU-C-GCCGUACUGAC ||:||||: | :||||| ||| AGUGGGCAGUGAUGGCAUUACUC Ubb mmu-miR-709 46 65 AGGAGGACGGA-GACGGAGG- |||: ||| :|||| || -ACUCUAGCCACUUGCC-CCA Ubb mmu-miR-742 16 37 AAAUGGGUCG-----UACCACCGAAAG |||||: :|| |||| ---UCCCAGUGGGCAGUGAUGGCA--- Ubb mmu-miR-744 49 65 CGACAAUCGG-GAUCGGGGCGU ||||| || ||||| ----CUAGCCACUUGCCCCA-- Ubb mmu-miR-759 42 55 CAGUUUUAACAAACGUGAGA-CG- |||||||| || -----------CUGCACUCUAGCC Ubb mmu-miR-762 39 65 CGAGAC---AGGGCCGG-GGUCGGGG- ||||| ||: ||| |: ||||| ACUCUGCACUCUA-GCCACUUGCCCCA Ubb mmu-miR-763 1 27 CGGUGA-CCAAG---AAGGGUCGACC- ::|:| ||| |||||||: || -UUAUUCGGUCUGCAUUCCCAGUGGGC Ubb mmu-miR-801 4 34 CAGCUAAGGCGU-------GCGUGUCGUUAG |||: ||:||| :| :|||::|| UUCGG-UCUGCAUUCCCAGUGGGCAGUGAUG Ubb mmu-miR-302c* 117 124 --------------GUCGUCCAUUGGGG---------UACAAUUU :||| ||||:| ||||||| ACAAGUUUCAAUAAUAGCUG--AACCUCUGUUAAAAAAUGUUAAU Ubb mmu-miR-703 126 133 AA------GAAA-GGAAGAC----------------UUCCAAAA || ||| ||| |||||||| AAUAAUAGCUGAACCU-CUGUUAAAAAAUGUUAAUAAAGGUUUUG Ubb mmu-miR-106a 38 60 AUG-GACGUGACAAUC-GUGAAac ||| ||||||| ||| ||||| TACTCTGCACT-CTAGCCACTTgc Ubb mmu-miR-141 6 33 GGUAGA---AAUGGU---CUGUCACAAu | :||| || ||| |:||||| | CGGTCTGCATTCCCAGTGGGCAGTGATg Ubb mmu-miR-155 16 40 gGGGAUA-GUGUUA--AUCGUAAUu ||| :| :||:| |:|||||| tCCCAGTGGGCAGTGATGGCATTAc Ubb mmu-miR-17-5p 36 60 UGAUG-GACGUGACAUUCGUGAAac |:||| ||||||| ||: ||||| ATTACTCTGCACTCTAGCCACTTgc Ubb mmu-miR-19b 25 48 aGUCA-AAACGUACCUAAACGUGu |||| | |||| | ||||| gCAGTGATGGCATTACTCTGCACt Ubb mmu-miR-200b 8 33 CAGUAGUAAUGGU---CCGUCAUAAu ||| |||| ||| ||||||: | GTCTGCATTCCCAGTGGGCAGTGATg Ubb mmu-miR-20a 37 60 gAUG-GACGUGAUAUUCGUGAAau ||| ||||||| ||: ||||| tTACTCTGCACTCTAGCCACTTgc Ubb mmu-miR-217 3 30 UAGGUCAGUC--AA-GGAC-UACGUCAu ||:|:||| | || || | : ||||| ATTCGGTCTGCATTCCCAGTGGGCAGTg Ubb mmu-miR-24* 9 28 uGACUAUAGUCGAGUCAUCCGUg ||| ||: | ||||:|||| tCTG-CATT--CCCAGTGGGCAg Ubb mmu-miR-290 52 78 uuuuucACGGGGGUA---UCAAA-CUc |||||| || ||||| || gccactTGCCCCAATTTAAGTTTAGAa Ubb mmu-miR-298 89 111 ccUUCUUGUCGG-GAGGAGACgg || ||:|||: |||||| tcAATAATAGCTGAACCTCTGtt Ubb mmu-miR-301 28 49 cgaaACUGUUAUGAUAACGUGAc ||:|| |||| |||||| gtgaTGGCATTACT-CTGCACTc Ubb mmu-miR-302c* 96 124 gUCGUCCAUUGGGG---------UACAAUUu ||| | ||||:| ||||||| tAGCTG--AACCTCTGTTAAAAAATGTTAAt Ubb mmu-miR-31 42 62 GUCGAUACGGUCGUAGAACGGa | || | |:||| |||||| CTGC-ACTCTAGCCACTTGCCc Ubb mmu-miR-324-3p 9 31 gGUCGUCGUGGAC-CCCGUCACc | ||| : || | |||||||| tCTGCATTCCCAGTGGGCAGTGa Ubb mmu-miR-326 4 24 ugaccuccuucccGGGUCUCC ||||| || ttcggtctgcattCCCAGTGG Ubb mmu-miR-346 4 31 ucuCCGUCCGUGAG-----CCCGUCugu ||: |||:|| |||||| ttcGGTCTGCATTCCCAGTGGGCAGtga Ubb mmu-miR-370 2 26 uUGGUCCA-AGGU-GGGGUCGUCCG |:: ||| | || :|||||::||| tATTCGGTCTGCATTCCCAGTGGGC Ubb mmu-miR-449b 45 62 ggucGAUCGUUACGUG-ACGGa ||||| ||| |||| cactCTAGC----CACTTGCCc Ubb mmu-miR-666 45 65 ccGAGAGUGUCGACACGGGcga |||| :| || ||||| caCTCTAGCCACT-TGCCCcaa Ubb mmu-miR-674 3 24 augugguGAGGGUAGAGUCACg || | || ||||| attcggtCTGCATTCCCAGTGg Ubb mmu-miR-675-3p 20 42 UGACUCGCCAAUCCCGU-AUGuc | ||:|| || | |||| ||| AGTGGGCAGTGATGGCATTACtc Ubb mmu-miR-675-5p 25 49 uGACAC--CCGGGA-AAGGCGUGgu | ||| ||| :| ||:|||| gCAGTGATGGCATTACTCTGCACtc Ubb mmu-miR-695 4 24 AAGUCAGUGGAUACGGGUUAga |||:||| | || ||||:| TTCGGTCTGC-ATTCCCAGTgg Ubb mmu-miR-705 33 57 aCG-GGUGGGGUG-GAG---GGUGg || ::||:|::| ||| |||| gGCATTACTCTGCACTCTAGCCACt Ubb mmu-miR-709 31 50 aggaGGACGGAGACG-GAGg | | |||||| ||| atggCATTACTCTGCACTCt Ubb mmu-miR-742 13 39 aaAUGGGU----CGU-ACCACCGAAAg | |||| ||| || |||| || caTTCCCAGTGGGCAGTGATGGCATTa Ubb mmu-miR-744 44 66 CGACA-AUCGG-GAUCGGGGcgu || | ||||| || ||||| GCACTCTAGCCACTTGCCCCaat Ubb mmu-miR-759 21 45 CAGUUUUAACAAAC---GUGAGACG || :: | || | | :||||||| GTGGGCAGTGATGGCATTACTCTGC Ubb mmu-miR-801 8 33 CAG-C-UAAGGCGUGCGUGUCGUUAg ||| | ||||| ::| :|||::|| GTCTGCATTCCCAGTGGGCAGTGATg

DNA & RNA Element - RAID2 Gene Name RAID ID Interactor 1 Category 1 ID 1 Interactor 2 Category 2 ID 2 Methods Score Ubb RAID01433235 mmu-miR-194-5p miRNA MIMAT0000224 Ubb mRNA 22187 CLIP-seq//Prediction 0.6308 Ubb RAID02557081 mmu-miR-6999-3p miRNA MIMAT0027901 Ubb mRNA 22187 Prediction 0.1828 Ubb RAID02660936 mmu-miR-5120 miRNA MIMAT0020628 Ubb mRNA 22187 Prediction 0.1828 Ubb RAID03772829 mmu-miR-543-3p miRNA MIMAT0003168 Ubb mRNA 22187 CLIP-seq//Prediction 0.6478