DNA & RNA Element - AREsite Gene Name Motif CDS Area ARE Area Evidence Rrp9; Rnu3ip2; U3-55k ATTTA 31-1458 1470-1474 Identification of a target RNA motif for RNA-binding protein HuR.#Proc Natl Acad Sci U S A 2004; 101(9): 2987-92.!

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 MIMAT0004187 mmu-miR-744 27966 Rrp9 acgacaaucGGGAUCGGGGCGu :|| :||||||| uaagugacuUCCAGGCCCCGCc 2 14 15 36 [mm9:9:106387691-106387712:+] 0.5887 149 7 -22.00 -0.5926 MIMAT0003895 mmu-miR-764-3p 27966 Rrp9 ugucAACGGUGAUACCGGAGGa ||| :|:|| |||||| ucuuUUG-UAUUAAAGCCUCCu 2 19 44 64 [mm9:9:106387720-106387740:+] 0.5530 128 6 -17.42 -0.3672 MIMAT0003499 mmu-miR-709 27966 Rrp9 aggaGGACGGAGAC-GGAGg || ||| ||| |||| aggcCCCGCCCCUGUCCUCu 2 16 27 46 [mm9:9:106387703-106387722:+] 0.5708 123 0 -23.32 -0.4691 MIMAT0004842 mmu-miR-879 27966 Rrp9 ccGAAUCUCGAUAUUCGGAGa :|| | :|| ||||||| ucUUUUGUAUUA-AAGCCUCc 2 20 44 63 [mm9:9:106387720-106387739:+] 0.5530 149 7 -12.92 -1.2176 MIMAT0009435 mmu-miR-1962 27966 Rrp9 uacacagggucacggUCGGAGa |||||| ccucuuuuguauuaaAGCCUCc 2 8 42 63 [mm9:9:106387718-106387739:+] 0.5530 120 6 -13.03 -0.3494 MIMAT0013803 mmu-miR-2861 27966 Rrp9 ggcgggcGGCGGUCCGGGg |: |||||||| uaagugaCUUCCAGGCCCc 2 13 15 33 [mm9:9:106387691-106387709:+] 0.5887 148 7 -23.82 -0.6029 MIMAT0000671 mmu-miR-224 27966 Rrp9 uugccuuggugaUCACUGAAu |||||||| cucccuuauuuaAGUGACUUc 2 10 5 25 [mm9:9:106387681-106387701:+] 0.5887 145 7 -11.61 -0.3467 MIMAT0003128 mmu-miR-485 27966 Rrp9 cuuaaguagugccggUCGGAGa |||||| ccucuuuuguauuaaAGCCUCc 2 8 42 63 [mm9:9:106387718-106387739:+] 0.5530 120 6 -11.95 -0.3523

DNA & RNA Element - TRANSFAC Accession AS Description Species Entrez Pubmed Binding Info G065991 Rrp9 Mus musculus 27966

DNA & RNA Element - RepTar Gene Name miRNA Begin End Profile Rrp9 mmu-miR-2861 beg:16 end:34 pic:3' GGCGGGC-GGCGGTCCGGGG 5'& .| |. ||||||||| &5' -----TGACTTCCAGGCCCC 3' Rrp9 mmu-miR-224 beg:14 end:25 pic:3' TTGCCTTGGTGATCACTGAAT 5'& |||||||| &5' ------------AGTGACTT- 3' Rrp9 mmu-miR-188-5p beg:0 end:22 pic:3' GGGAGGTGGTACGTTCCCTAC 5'& |.|||| ..|| .||| || &5' CTCTCCCTTATTTAAGTGA-- 3' Rrp9 mmu-miR-2145 beg:22 end:42 pic:3' TTGGTCC-GGGCTGGGACGA 5'& ||||| |||| |||||. &5' --CCAGGCCCCGCCCCTGT- 3' Rrp9 mmu-miR-744 beg:15 end:36 pic:3' ACGACAATC-GGGATCGGGGCGT 5'& || .|| .||||||| &5' ----GTGACTTCCAGGCCCCGC- 3'

DNA & RNA Element - miRNAMap Gene Name Mature miRNA Target Start Target End miRNA 3-5 Alignment Target 5-3 Rrp9; Rnu3ip2; U3-55k mmu-miR-298 27 44 CCUUCUUGUCGGGA-GGAGACGG- :|||| || |||:| -------AGGCCCCGCCCCUGUCC Rrp9; Rnu3ip2; U3-55k mmu-miR-490 16 31 GUCGUACCUCAGGAGGUCCAAC ||: || |:|||||| AAGU---GA--CUUCCAGGC-- Rrp9; Rnu3ip2; U3-55k mmu-miR-491 7 43 -GGAGUA----C-CU-----UCCCAA--GGGGUGA- |||:|| | || ||| |||| | CCCUUAUUUAAGUGACUUCCAGGCCCCGCCCCUGUC Rrp9; Rnu3ip2; U3-55k mmu-miR-540 24 46 -GGUCCUA-GCUGGAGACUGGA- ||||| || || ||| ||| UCCAGGCCCCGCCC-CUGUCCUC Rrp9; Rnu3ip2; U3-55k mmu-miR-542-5p 17 36 GCACUGUACUACUAGGGGCUC ||||| ||||| AGUGACUUCCAGG-CCCCGC- Rrp9; Rnu3ip2; U3-55k mmu-miR-615 16 36 UUCUCCCUCUGGGUCCGA-GCCU || || :|||||| || --AAGUGACUUCCAGGCCCCGC- Rrp9; Rnu3ip2; U3-55k mmu-miR-665 14 42 -AUUCCCUGGAG--UCGGA----GGACCA |||| |||:|| :||| |||| UUAAGUGACUUCCAGGCCCCGCCCCUGU- Rrp9; Rnu3ip2; U3-55k mmu-miR-671 21 46 -GGAGGU-CGGGGAGGUCCCGAAGGA- |:|||| ||||| || |||| ACUUCCAGGCCCCGCCCCUG--UCCUC Rrp9; Rnu3ip2; U3-55k mmu-miR-675-5p 17 40 UGACAC-------CCGGGAAAGGCGUGGU ||| ||||| ||| || --AGUGACUUCCAGGCCC----CGCCCCU Rrp9; Rnu3ip2; U3-55k mmu-miR-709 34 65 AGGAGGAC-GGAGA-----------CGGAGG- || |||| ||||| |||||| GCC-CCUGUCCUCUUUUGUAUUAAAGCCUCCU Rrp9; Rnu3ip2; U3-55k mmu-miR-714 17 44 -CGCUGG----CUGGC-CGGGAGCAGC |:|||: |:|| |||| :||| AGUGACUUCCAGGCCCCGCCCCUGUCC Rrp9; Rnu3ip2; U3-55k mmu-miR-744 17 37 CGACAAUC-GGGAUCGGGGCGU || :|| :||||||| --AGUGACUUCCAGGCCCCGCC Rrp9; Rnu3ip2; U3-55k mmu-miR-762 21 40 CGAGACAGGGCCGGGGUCGGGG- || ||| |||||| ||||| --ACU-UCCAGGCCCC-GCCCCU Rrp9; Rnu3ip2; U3-55k mmu-miR-764-3p 25 66 UGUCAA---CGG---------------UGAUACCGGAGGA ||| ||| |:|| ||||||| CCAGGCCCCGCCCCUGUCCUCUUUUGUAUUAAAGCCUCCUA Rrp9; Rnu3ip2; U3-55k mmu-miR-770-3p 1 36 GGUC-GAGG------------UGCA-GUCCGGGUGC- || |||| || ||||||| || -CACUCUCCCUUAUUUAAGUGACUUCCAGGCCC-CGC Rrp9; Rnu3ip2; U3-55k mmu-miR-298 25 49 ccUUCUUGUCGGG---AGGAGAcgg |:| | |||| |||||| ccAGGCCCCGCCCCTGTCCTCTttt Rrp9; Rnu3ip2; U3-55k mmu-miR-490 11 32 gucguacCUCAGGAGGUCCaac | | |:|||||| tatttaaGTGACTTCCAGGccc Rrp9; Rnu3ip2; U3-55k mmu-miR-491 8 36 GGAGUACCUUC---------CCAAGGGGUGa |||:|| ||| || ||||:| CCTTATTTAAGTGACTTCCAGG--CCCCGCc Rrp9; Rnu3ip2; U3-55k mmu-miR-540 25 44 GGUCCUAGCUGGAGACUGGA ||||| | :|| ||| ||| CCAGGCCCCGCCCCTGTCCT Rrp9; Rnu3ip2; U3-55k mmu-miR-542-5p 17 36 gCACUGUA-CUACUAGGGGCuc ||||| | | | ||||| aGTGACTTCCAGG--CCCCGcc Rrp9; Rnu3ip2; U3-55k mmu-miR-615 14 35 uucUCCCUCUGGGUCCGAGCCu || || :|||||| | | ttaAGTGACTTCCAGGCCCCGc Rrp9; Rnu3ip2; U3-55k mmu-miR-665 15 42 AUUCCCUGGAG--UCG----GAGGACca |||| |||:|| :|| | |||| TAAGTGACTTCCAGGCCCCGCCCCTGtc Rrp9; Rnu3ip2; U3-55k mmu-miR-671 2 27 gGAGGUCGGG---GAGGUC-CCGAAGGa |||: ||| :|: || | ||||| aCTCT--CCCTTATTTAAGTGACTTCCa Rrp9; Rnu3ip2; U3-55k mmu-miR-675-5p 22 39 ugacacCCGGGAAAGGCGUGGu |||| |||| || cttccaGGCC----CCGCCCCt Rrp9; Rnu3ip2; U3-55k mmu-miR-700 17 38 cCACCUGA--GCCAAGGGCGcac || |||| | | ||||| aGT-GACTTCCAGGCCCCGCccc Rrp9; Rnu3ip2; U3-55k mmu-miR-709 24 46 AGG---AGGACGGAGAC-GGAGg ||| || ||| ||| |||| TCCAGGCCCCGCCCCTGTCCTCt Rrp9; Rnu3ip2; U3-55k mmu-miR-714 18 43 CGCU---GG--CUGGCCGGGAGCAGc |:|| || | || |||| :||| GTGACTTCCAGGCCCCGCCCCTGTCc Rrp9; Rnu3ip2; U3-55k mmu-miR-744 16 36 cgacaaucgGGAUCGGGGCGu || :||||||| aagtgacttCCAGGCCCCGCc Rrp9; Rnu3ip2; U3-55k mmu-miR-762 19 38 cgaGACAGGGCCGGGGUCGGGG || ||| || ||| ||||| tgaCT-TCCAGG-CCCCGCCCC Rrp9; Rnu3ip2; U3-55k mmu-miR-764-3p 44 64 ugucAACGGUGAUACCGGAGGA ||| :|:|| ||||||| tcttTTG-TATTAAAGCCTCCT Rrp9; Rnu3ip2; U3-55k mmu-miR-770-3p 13 35 ggucgaggUGCA-GUCCGGGugc || | ||||||| tttaagtgACTTCCAGGCCCcgc

DNA & RNA Element - RAID2 Gene Name RAID ID Interactor 1 Category 1 ID 1 Interactor 2 Category 2 ID 2 Methods Score Rrp9 RAID00265692 mmu-miR-374c-5p miRNA MIMAT0014953 Rrp9 mRNA 27966 Prediction 0.1828 Rrp9 RAID02066796 mmu-miR-485-5p miRNA MIMAT0003128 Rrp9 mRNA 27966 Prediction 0.1828 Rrp9 RAID03790324 mmu-miR-224-5p miRNA MIMAT0000671 Rrp9 mRNA 27966 Prediction 0.1828