# STOCKHOLM 1.0 #=GF ID Actino-pnp #=GF AC RF01688 #=GF DE Actino-pnp RNA #=GF AU Weinberg Z; 0000-0002-6681-3624 #=GF GA 47.7 #=GF NC 47.6 #=GF TC 47.7 #=GF SE Published; PMID:20230605; #=GF SS Published; PMID:20230605; #=GF TP Cis-reg; #=GF BM cmbuild -F CM SEED #=GF CB cmcalibrate --mpi CM #=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 2958934 CM SEQDB #=GF DR SO; 0005836; regulatory_region; #=GF RN [1] #=GF RM 20230605 #=GF RT Comparative genomics reveals 104 candidate structured RNAs from bacteria, #=GF RT archaea and their metagenomes. #=GF RA Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR #=GF RL Genome Biol. 2010;11:R31. #=GF WK Actino-pnp_RNA_motif #=GF SQ 77 AACY023426552.1/759-700 AUUGGUCCUCGGUAGUGGU-UUCCGG-G--------------------CAGUUAUA---------------------CCCGUGA-ACUUCGAUCGAAGAU-CC-AU AACY020708686.1/419-480 CGUGGUCCUCGGUAGUGGUUCA-CAC-A----A-C-------------UUUUCU-----------------G---U-UGUG-UGUGCUUCGAUCGAUGAU-CA-UC AACY023352938.1/798-727 GAUGGUCCUCGGUAGUGGU-UUCCGC-GAA--C-A-------------GAUAUAAGUAUUUG---------U---G-CGCGUGA-ACUUCGAUCGAAGAC-UC-UU AACY020665672.1/306-242 AUUGGUCCUCGGUGGUGGC-UUACGG-A----U-U--U-U--------UACA-----------------AGA---ACGCCGUGG-GCUUCGAUCGAAGAU-CC-AU CP000850.1/1544689-1544762 ACCGGUCUCCGGUAGUGGCCCC-CGG-G----CAU--CCGGC------AGCAC--------------GCCGACCCG-CCCG-GGCGCUUCGAUCGAAGAC-CG-GC CP000667.1/1548720-1548793 ACCGGUCUCCGGUAGUGGCCUC-CGG-GCAUCC-G--GCAUC------UCGCC--------------GAUCC---G-CCCG-GGCGCUUCGAUCGAAGAC-CG-GC CP000431.1/7150693-7150751 GUCGGUCUUCGGUAGUGGU-CUUCCG-G----A-C-------------ACG--------------------G---U-CCGGGGG-ACUUCGAUCGACGGC-CG-CC AL583920.1/13687-13757 GGCGGUCUUCGGUAGUGGCUGU-CGG-G----C-U----CUCCG----GAUC-------------UGGAGCA---G-GUCG-GCCGCUUCGAUCGAUGGC-CG-UA AACY020163669.1/593-531 AUUGGUCCUCGGUAGUGGU-UUCCGGGG----U-U--U----------UACA------------------AG---A-CCCGUGA-ACUUCGAUCGAAGAU-CC-AU CP000384.1/2248687-2248748 GGCGGUCUUCGGUAGUGGCUGC-CGG-U----G-A--C----------GCGA------------------GU---C-CCCG-GCCGCUUCGAUCGACGGC-CG-UA CP000656.1/4277016-4276958 CGCGGUCUUCGGUAGUGGC-UGCCGG-A----G---------------AGAGA----------------------C-UCCGACA-GCUUCGAUCGACGGC-CG-UC AACY023292770.1/648-584 GAUGGUCCUCGGUAGUGGU-UUCCGC-G----C---------------UUGAAUACUU-----------------G-CGCGUGA-ACUUCGAUCGAAGAU-UCAUU AACY020924984.1/409-479 UUUGGUCCUCGGUAGUGGU-UUCCGG-A----A-A--G-UUUG-----UUAAU-------------UAAAUU---U-GCCGUGA-ACUUCGAUCGAUGAU-CC-AA AACY020053120.1/1600-1521 AAUGGUCCUCGGUAGUGGU-UUCCGC-G----CACGACAUCCUU----ACU--------------AAGGAAACAAGUCGCGUGA-ACUUCGAUCGAAGAUUCA-UU AACY020571544.1/471-413 UGGGGUCCUCGGUAGUGGC-UCUCGGAU----A---------------UUUA-----------------------U-GCCGACG-GCUUCGAUCGAUGAU-CU-CC AACY021246509.1/305-247 AUUGGUCCUCGGUAGUGGU-UUCCGG-A----A-A-------------UGA--------------------U---U-UCCGUGA-ACUUCGAUCGAAGAU-CC-AU CP000820.1/1413476-1413546 GCCGGUCCUCGGUCGUGGC-CGCCGG-GA---C-G--A-GCGCC----GUC--------------GGUGC-C---G-CCCGGAG-ACUUCGACUGAGCAC-CG-GC AACY021521465.1/225-297 AAUGGUCCUCGGUAGUGGC-UCACGA-A----A-UGCUGAUU------CAGAA--------------AAUAA---U-UUCGUGG-ACUUCGAUCGAAGAU-UCAUU CP000481.1/1705830-1705770 GCCGGUCCUCGGUCGUGGU-CU-CCG-GG---A-G--C----------GCAA------------------GC---U-GCGG-AG-GCUUCCAUCGAAGAC-CG-GC AE016822.1/918955-919031 GCUGGUCCUCGGUGGUGGU-AUCCGG-A----U-G----CG-UUCGCCGUCA---------GGC-AAUCGGC---A-GCCGUGU-AUUUCUACUGAUGGC-CA-GA AL939124.1/278624-278683 GCCGGUCCUCGGUAGUGGCCCC-CGG-G----G-G-------------CAGA-------------------U---C-CCCG-GGUGCUUCGAUCGAAGAC-CG-GC AACY023439687.1/1346-1402 ACUGGUCCUCGGUGGUGGC-UUACGG----------------------AUGAUUG-----------------------CCGUGG-GCUUCGAUCGAAGAU-CC-AU AACY023300562.1/827-768 UUUGGUCCUCGGUAGUGGU-UUCCGG-A----A-A-------------ACGU-------------------U---U-UCCGUGA-ACUUCGAUCGAAGAU-CC-AU AE017283.1/1592080-1592022 AUGGGUCCUCGGUAGUGGC-CACCGG-G----G---------------CGCGA----------------------U-CCCGGCG-GCUUCGAUCGAAGAC-CG-GU AAGP01000012.1/38273-38199 UUCGGUCCUCGGUAGUGGC-UUCCGG-AAGA-G-C--ACGCAU-----GCGC--------------AUGCUGA--U-UCCGUGG-GCCCCGAUCGAUGAC-CG-GC AACY023309503.1/1286-1224 AAUGGUCCUCGGUAGUGGU-UUCCGC-A----C-A-------------AAUUAA-----------------U---G-UGCGUGA-ACUUCGAUCGAAGAU-UCAUU CP000511.1/2507941-2507999 CGCGGUCUUCGGUAGUGGC-UGCCGG-A----G---------------AGACA----------------------C-UCCGGCA-GCUUCGAUCGACGGC-CG-UC BX248343.1/231827-231757 GGCGGUCCUCGGUAGUGGCUGC-CGG-G----C-U----CUCCG----GAUC-------------UGGGGCA---G-GUCG-GCCGCUUCGAUCGAUGGC-CG-UA AACY023326738.1/962-904 GUCGGUCCUCGGUAGUGAA-GUUCGG-C----U-C-------------GAU--------------------G---A-GCCGCGC-UUCUCGAUCGAAGAU-CG-AC AACY022754660.1/110-50 UUUGGUCCUCGGUAGUGGU-UUCCGG-A----A-U-------------CGGAU------------------A---U-UCCGUGA-ACUUCGAUCGAAGAU-CC-AU AACY024006489.1/767-823 AUUGGUCCUCGGUGGUGGC-UUCCGG-A--------------------AUAAA------------------------UCCGUGA-GCUUCGAUCGAAGAU-CC-AU AE016958.1/3223271-3223201 GGCGGUCUUCGGUAGUGGCUGC-CGG-G----C-U----CUCCG----GAUC-------------UGGAGCA---G-GUCG-GCCGCUUCGAUCGAUGGC-CG-UA AACY023441057.1/1068-995 CAUGGUCUCCGGUAGUGGU-UUUCAG-A----U-AAUUAGAUUU----AAU--------------AAAUC-U---A-UCUGAGA-ACUUCGAUCGUAGAUUCA-UU AACY020790955.1/80-142 AUUGGUCCUCGGUAGUGGU-UUCCGGGG----U-U--U----------UACA------------------AG---A-CCCGUGA-ACUUCGAUCGAAGAU-CC-AU CP000509.1/3377420-3377345 CUCGGUCCUCGGUAGUGGC-UCUCAGCA----U-C-----CGGCCGGCUCU----------GCCG--CGCAG---A-UCUGCGG-GCCUCGAUCGAAGAC-CG-GC CP000854.1/2339435-2339506 GGCGGUCUUCGGUAGUGGCUGC-CGG-G----CAC--C-CCG------GAUC---------------UGGGGAAAG-UCCG-GCCGCUUCGAUCGACGGC-CG-UA CP000249.1/4254111-4254042 GCCGGUCCUCGGUCGUGGU-CGCCGG-GA---U-G--G--GU------ACGG---------------GCACCGG-A-CCCGGGG-ACUUCGACUGAGCAC-CG-GC AACY023436648.1/995-922 CAUGGUCUCCGGUAGUGGU-UUUCAG-A----U-AAUUAGAUCU----AAU--------------AAAUC-U---A-UCUGAGA-ACUUCGAUCGUAGAUUCA-UU BX842580.1/319742-319672 GGCGGUCCUCGGUAGUGGCUGC-CGG-G----C-U----CUCCG----GAUC-------------UGGGGCA---G-GUCG-GCCGCUUCGAUCGAUGGC-CG-UA AP006618.1/4102358-4102295 GUCGGUCUUCGGUAGUGGCCUCUCGA-G----U-G--G----------ACAU------------------CC---G-CCCGUCGGGCUUCGAUCGAUGAC-CG-CC AACY023313868.1/759-819 UUUGGUCCUCGGUAGUGGU-UUCCGG-A----A-A--A----------CGA-------------------UU---U-UCCGUGA-ACUUCGAUCGAAGAU-CC-AU AACY023437808.1/532-468 AUUGGUCCUCGGUGGUGGC-UUACGG-A----U-U--U-U--------UACA-----------------AGA---ACGCCGUGG-GCUUCGAUCGAAGAU-CC-AU AACY023308296.1/1399-1470 AUCGGUCCUCGGUUGUGGC-UUCCGG-G----CCU--A-AAUU-----UUUU--------------AAUU-AAAU--CCCGUGG-GCUUCCAUCGAAGAU-CC-GU AACY023341077.1/765-703 AAUGGUCCUCGGUAGUGGU-UUCCGC-A----C-A-------------AAUUAA-----------------U---G-UGCGUGA-ACUUCGAUCGAAGAU-UCAUU AACY020051675.1/2004-2064 UUUGGUCCUCGGUAGUGGU-UUCCGG-A----A-A--A----------CGA-------------------UU---U-UCCGUGA-ACUUCGAUCGAAGAU-CC-AU AACY020529213.1/353-293 GUCGGUCCUCGGUAGUGGC-UUCCGG-G----C-A-------------GAUGA------------------U---G-CCCGUGG-GCCUCGAUCGAAGAC-CG-GC AACY023353825.1/1157-1215 GUCGGUCCUCGGUAGUGAA-GUUCGG-C----U-C-------------AAU--------------------G---A-GCCGCGC-UUCUCGAUCGAAGAU-CG-AC AACY020470050.1/941-881 UUUGGUCCUCGGUAGUGGU-UUCCGG-A----A-A--A----------CGA-------------------UU---U-UCCGUGA-ACUUCGAUCGAAGAU-CC-AU AACY020174452.1/327-265 AUUGGUCCUCGGUAGUGGU-UUCCGGGG----U-U--U----------UACA------------------AG---A-CCCGUGA-ACUUCGAUCGAAGAU-CC-AU AACY020946272.1/515-457 ACUGGUCCUCGGUGGUGGC-UUACGG-A----G-A-------------UGA--------------------U---C-UCCGUGG-GCUUCGAUCGAAGAU-CC-AU CP000454.1/1593772-1593848 CGCGGUCCUCGGUAGUGAU-UCCCGG-GAA--C-G----GCUUCG---AAGAA-----------UGAAGCCC---GGCCCGUGG-GUCUCGAUCGAUGAC-CG-GG CP000474.1/1715342-1715414 CGCGGUCCUCGGUAGUGAU-UCCCGG-GAA--A-C--C-AUC------UGUGAC-------------GAUGA---UGCCCGUGG-AUCUCGAUCGAUGAC-CG-GG CT573213.2/6238131-6238064 GCCGGUCCUCGGUCGUGGU-CGCCGG-G----A-GCGG-GC-------UUC-----------------GUCC---UCCCCGGGG-GCUUCGACUGAGCAC-CG-GC AACY023331383.1/842-771 AUCGGUCCUCGGUUGUGGC-UCCCGG-GCCAAA-U--U-UA-------UUAAUU--------------UAAA---U-CCCGUGG-GCUUCCAUCGAAGAU-CC-GU AM420293.1/6641639-6641570 GCCGGUCCUCGGUAGUGGC-UCCCGG-GCG--G-A--C-CUC------GCAG---------------GAGGU---U-CCCGAGG-GCUUCGAUCGAUGGC-CG-GC AACY020057517.1/1019-1083 UUUGGUCCUCGGUGGUGGC-UUACGG------A-U--U-U--------AAACAA---------------GAA---U-GCCGUUG-GCUUCGAUCGAAGAU-CC-AU AACY023344935.1/1046-983 UUCGGUCCUCGGUAGUGAU-GUCCGG-A----A-A--A----------AAGUUC----------------UU---U-UCCGUGC-GUCUCGAUCGAUGAC-CG-GG AACY023336117.1/1190-1249 AAUGGUCCUCGGUAGUGGU-UUCCGG-A----U-G-------------AUU--------------------C---A-UCCGUGA-ACUUCGAUCGAAGAUACA-UU CP000750.2/752310-752240 ACCGGUCCUCGGUAGUGGC-CUCCGG-A----A-G--C----------AGCACGACCACCA---------GC---U-UCCGUGG-GCCUCGAUCGAAGGC-CG-GG CP000479.1/3804947-3804877 GGCGGUCUUCGGUAGUGGCUGC-CGG-G----C-U----CUCCG----GAUC-------------UGGAGCA---G-GUCG-GCCGCUUCGAUCGAUGGC-CG-UA AACY023306957.1/1382-1311 AAUGGUCCUCGGUAGUGGU-UUCCGG-AG---A-U--U-U-CU-----UUCGU-------------AGAAAAG--U-UCCGUGA-ACUUCGAUCGAAGAU-UC-AU BA000030.3/3089217-3089156 GCCGGUCCUCGGUAGUGGCCCC-CGG-G----G---------------GAAGUGAG-------------------C-CCCG-GGUGCUUCGAUCGAAGAC-CG-GC AACY022757199.1/365-309 GCUGGUCCUCGGUGGUGGC-UUACGGAU--------------------GAUU-------------------------GCCGUGG-GCUUCGAUCGAAGAU-CC-AU AACY023297464.1/53-112 UUUGGUCCUCGGUAGUGGU-UUCCGG-A----A-A-------------ACGU-------------------U---U-UCCGUGA-ACUUCGAUCGAAGAU-CC-AU AACY023333656.1/840-769 AUCGGUCCUCGGUUGUGGC-UUCCGG-GCC--U-A--A-AUU------CUUU---------------AAUUUA--AUCCCGUGG-GCUUCCAUCGAAGAU-CC-GU CP000088.1/925836-925906 GCCGGUCUUCGGUAGUGGU-UCUCCG-AC---A-CG-C-CC-------GCACCA--------------GGGG---UCUCGGGGA-ACUUCGAUCGAUGGC-CG-GC AACY023311107.1/673-600 UAUGGUCCUCGGUAGUGGU-UUCCAG-A----U-G--U-AUGCA----CCAGA------------UGUAUAU---A-GCUGUGA-ACUUCGAUCGAAGAUUCA-UU AACY023312886.1/602-542 AAUGGUCCUCGGUAGUGGU-UUCCAG-A----U-G-------------UUUG-------------------C---A-UCUGUGA-ACUUCGAUCGAAGAU-UCAUU AACY023445683.1/836-893 AAUGGUCUCCGGUAGUGGU-UUACGA-A--------------------AUUGA------------------------UUCGUGA-ACUUCGAUCGUAGAUUCA-UU AACY020469612.1/870-946 AAUGGUCCUCGGUAGUGGU-UUCCGC-AGA--G-C--G-CGA------UUAAAUUCGC---------UUGCG---U-UGCGUGA-ACUUCGAUCGAAGAUUCA-UU AACY023308618.1/1250-1184 AAUGGUCCUCGGUAGUGGU-UUCCGC-A----A-G--G-C--------GCCAAA---------------GUU---U-UGCGUGA-ACUUCAAUCGACGAUUCA-UU AACY020164649.1/1734-1676 ACUGGUCCUCGGUGGUGGC-UUACGG----------------------AUAACGAUG---------------------CCGUUG-GCUUCGAUCGAAGAU-CC-AU CP000480.1/2735853-2735921 GGCGGUCUUCGGUAGUGGC-UGCCGG-GA---A-UCCA-AA-------CAGG----------------UUUA---U-CCCGACA-GCUUCGAUCGACGGC-CG-UA AACY023314755.1/1127-1062 AAUGGUCCUCGGUAGUGGU-UUCCGCAA----G-AC-G-C--------UUUC-----------------GUU---C-UGCGUGA-ACUUCGAUCGACGAU-UC-AU AACY023816550.1/761-687 GUCGGUCCUCGGUAGUGGC-CCUCGAAGGGAUU-C----GCGC-----CCA---------------GCGC-GAG-AACCCGGGG-GCCUCGAUCGAAGAC-CG-CC AACY020554846.1/2493-2429 AUUGGUCCUCGGUGGUGGC-UUACGG-A----U-U--U-U--------UACA-----------------AGA---ACGCCGUGG-GCUUCGAUCGAAGAU-CC-AU AACY023344307.1/624-697 AAUGGUCCUCGGUAGUGGU-UUCCAG-A----U-G----CAAGCA---CUAGA-----------UGUUUGGC---A-UCUGUGA-ACUUCGAUCGAAGAU-UC-AU #=GC SS_cons <<<<<<<-<<<<<---<<<.<<<<<<.<....<.<..<..........____................._>>...>.>>>>>>>.>>>--->>>>>->>>.>>.>> #=GC RF accGGUCCUCGGUAGUGGc.uccCGG.g....c.c..c..........aaua.................ugg...g.cCCGgga.gCUUCGAUCGAaGAC.Cg.gu //