# STOCKHOLM 1.0
#=GF ID snoZ196
#=GF AC RF00134
#=GF DE Small nucleolar RNA Z196/R39/R59 family
#=GF AU Daub J; 0000-0001-6022-563X
#=GF GA 55.0
#=GF NC 54.9
#=GF TC 55.0
#=GF SE Griffiths-Jones SR
#=GF SS Predicted; PFOLD
#=GF TP Gene; snRNA; snoRNA; CD-box;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 31.25 -Z 2958934 CM SEQDB
#=GF CL CL00054
#=GF DR SO; 0000593; C_D_box_snoRNA;
#=GF DR GO; 0006396; RNA processing;
#=GF DR GO; 0005730; nucleolus;
#=GF RN [1]
#=GF RM 12477388
#=GF RT Experimental RNomics. Identification of 140 Candidates for Small
#=GF RT Non-Messenger RNAs in the Plant Arabidopsis thaliana.
#=GF RA Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P,
#=GF RA Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL Curr Biol 2002;12:2002-2013.
#=GF RN [2]
#=GF RM 12007400
#=GF RT Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT cellular functions.
#=GF RA Kiss T
#=GF RL Cell 2002;109:145-148.
#=GF RN [3]
#=GF RM 10024243
#=GF RT A computational screen for methylation guide snoRNAs in yeast.
#=GF RA Lowe TM, Eddy SR
#=GF RL Science. 1999;283:1168-1171.
#=GF RN [4]
#=GF RM 12215523
#=GF RT Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT 2'-O-methylation of target RNA in vitro.
#=GF RA Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL Mol Cell Biol. 2002;22:6663-6668.
#=GF CC This family includes plant snoRNA snoZ196 and yeast snoRNAs R39 and R59.
#=GF CC Members of this family belong to the C/D box class of snoRNA which contain
#=GF CC C (UGAUGA) and D (CUGA) box motifs. Most of the members of the box C/D
#=GF CC family function in directing site-specific 2'-O-methylation of substrate
#=GF CC RNAs. snoZ196 acts as a methylation guide for 18S ribosomal RNA in plants
#=GF CC [1].Although the selection of the target nucleotide requires the antisense
#=GF CC element and the conserved box D or D' of the snoRNA, the methyltransferase
#=GF CC activity is supposed to reside in one of the protein components [4].
#=GF WK Small_nucleolar_RNA_Z196/R39/R59_family
#=GF SQ 22

AC140545.26/107249-107163      UGCAAUCUAUGAUGC-AAUUUUUAUAU--CCUUACUAUU--CUG-AU-UUCCGUGA--UUAUUCAGAA-----AUAUCACCAUCUUUCG--GCUGAGA-UUGCA
AC150706.4/102309-102395       UGCAAUCUAUGAUGC-AAUUAAUAU----CCUUACUAUU--AUGAUUUCCCCGUGA--UUAAUAAAAU-----AUAUCACCAUCUUUCG--ACUGAGA-UUGCA
Z70229.1/1-81                  ---AGCCUGUGAUGC-AAAAGG-------ACCCAUGAAA--CUGAAU-UACACUGAAUUAAUUCCAAAC----AAAUCACCAUCUUUCGG-GCUGAGG-UU---
AP006687.1/73908-73825         UGCAAUCAAUGAUGA-AAUUUC-------CUUAAUAUA---AUGAAUAUAUUGUGA--UUAUUAUACC-A---AGAUCACCAUCUUUCG--GCUGAGA-UUGCA
X67711.2/2410-2494             UGCAGCCUGUGAUGGCAAAAGU-------ACCCAUUAAA--CUGAAU-UACACUGA--UUAUUCCAAAC----AAAUCACCAUCUUUCG--GGCGAGG-UUGGC
AC068667.6/43175-43262         UGCAAUCAGUGAUGA-AAUUAUG------UCAAAUUCA---AUGAUUAUACAAUGA--UUAUUAUAAUCACU-AGAUCACCAUCUUUCG--GCUGAGA-UUGCU
Z70693.1/1-77                  ---AACCUGUGAUGU-AAAUUA-------ACCCAUUUA---CUGAAC-UACGUUGA--UUAUUUCAGU-A---AAAUCACCAUCUUUCG--GCUGAGG-UU---
AC068667.6/51559-51646         UGCAAUCAGUGAUGA-AAUUAUG------UCAAAUUCA---AUGAUUAUACAAUGA--UUAUUAUAAUCACU-AGAUCACCAUCUUUCG--GCUGAGA-UUGCA
AJ490449.1/1-82                -GCAGCCUGUGAUGC-AAAAGU-------ACCCAUUAAA--CUGAAU-UACACUGA--UUAUUCCAAAC----AAAUCACCAUCUUUCG--GCUGAGG-UUGC-
AC134045.2/133476-133559       UGCAGCCUGUGAUGC-AAAAGU-------ACCCAUUAAA--CUGAAU-UACACUGA--UUAUUCCAAAC----AAAUCACCAUCUUUCG--GCUGAGG-UUGCU
AJ490447.1/1-83                UGCAACCUGUGAUGU-AAAUUA-------ACCCAUUUA---CUGAAC-UACGUUGA--UUAUUUCAGU-A---AAAUCACCAUCUUUCG--GCUGAGG-UUGCA
AJ490452.1/1-84                UGCAACCUGUGAUGC-AAAACU-------ACCCAUUAAA--CUGAAU-UACACUGA--UUAUUACAAAC----AAAUCACCAUCUUUCG--GCUGAGG-UUGCA
AY220647.1/3-86                UGCAAUCUAUGAUGC-AAAUAA-------UCCCAUUUG---CUGAAU-CACUGUGA--UUAUUGCAAUAA---AAAUCACCAUCUUUCG--GCUGAGA-UUGCA
AJ490445.1/2-85                UGCAAUCUAUGAUGC-AAAUAA-------UCCCAUUUG---CUGAAU-CACUGUGA--UUAUUGCAAUAA---AAAUCACCAUCUUUCG--GCUGAGA-UUGCA
AY220646.1/6-89                UGCAAUCUGUGAUGC-AAAUAA-------UCCCAUUUG---CUGAAU-CACUGUGA--UUAUUGCAAUCA---AAAUCACCAUCUUUCG--GCUGAGA-UUGCA
AJ490442.1/2-85                UGCAAUCUGUGAUGC-AAAUAA-------UCCCAUUUG---CUGAAU-CACUGUGA--UUAUUGCAAUCA---AAAUCACCAUCUUUCG--GCUGAGA-UUGCA
D25232.1/916-1003              CUUUCUUAAUGAUGA-AAACUAU------UCCUUAUUC---UCGACUAGUCUUUGA--CAAUGCUGUCGUU--UAAUCACCAUCUUUCG--GCUGACUAGUAAA
X53575.1/491-574               AUAUGAAAAAGAUGA-ACCUUU-------CACUCUUGGA--UUG-CU-AGUUUCGA--CGAUGCUGCUCC---AAAAUACCAUCUUUCG--GCUGAUU-CAUAU
Z73554.1/1068-1155             CUUUCUUAAUGAUGA-AAACUAU------UCCUUAUUC---UCGACUAGUCUUUGA--CAAUGCUGUCGUU--UAAUCACCAUCUUUCG--GCUGACUAGUAAA
AAFW02000099.1/355930-355833   CUCAUUUUAUGAUGA-AAAUCCAUUGUAUCCCAAUACAUAUUCGACUAGUCAUUGA--CGAUGCUGUCGUAACUUAUCACCAUCUUUCG--ACUGAUU-AUAAG
X62627.1/916-1013              CUCAUUUUAUGAUGA-AAAUCCAUUGUAUCCCAAUACAUAUUCGACUAGUCAUUGA--CGAUGCUGUCGUAACUUAUCACCAUCUUUCG--ACUGAUU-AUAAG
AACU03000099.1/1424175-1424089 UCAAGGAAAUGAUGG-ACAACA-------UACCCUUUG---C-GACUAGACUCUGU--CGAUGCUGUUGCA--AAAUUACCAUCUUUCGGGUCUGACC-CUUGA
#=GC SS_cons                   <<<<<<<________.______......._________...______.________..____________...________________.._____>>.>>>>>
#=GC RF                        ugcagccuAUGAUGa.AAAuua.......uCCcAUUua...cUGAaU.uaCuuUGA..UuAUucuaauca...AAAUCACCAUCUUUCG..GCUGAgg.cugca
//
