# STOCKHOLM 1.0
#=GF ID SNORD42
#=GF AC RF00150
#=GF DE Small nucleolar RNA SNORD42
#=GF AU Moxon SJ; 0000-0003-4644-1816
#=GF GA 39.0
#=GF NC 38.8
#=GF TC 39.1
#=GF PI U42
#=GF SE Griffiths-Jones SR
#=GF SS Predicted; PFOLD; Daub J
#=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 26.00 -Z 2958934 CM SEQDB
#=GF DR SO; 0000593; C_D_box_snoRNA;
#=GF DR GO; 0006396; RNA processing;
#=GF DR GO; 0005730; nucleolus;
#=GF DR snoopy; Mus_musculus300937;
#=GF DR snoopy; Danio_rerio300150;
#=GF RN [1]
#=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 RN [2]
#=GF RM 11387227
#=GF RT RNomics: an experimental approach that identifies 201 candidates for
#=GF RT novel, small, non-messenger RNAs in mouse.
#=GF RA Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA Bachellerie JP, Brosius J
#=GF RL EMBO J 2001;20:2943-2953.
#=GF RN [3]
#=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 CC snoRNA U42 is found in intron 3 of the ribosomal protein L23a (RPL23a)
#=GF CC gene in humans and is also present in mice. U42 is a member of the C/D
#=GF CC class of snoRNA which contain C (UGAUGA) and D (CUGA) box motifs. Most of
#=GF CC the members of the box C/D family function in directing site-specific
#=GF CC 2'-O-methylation of substrate RNAs. Although the selection of the target
#=GF CC nucleotide requires the antisense element and the conserved box D or D' of
#=GF CC the snoRNA, the methyltransferase activity is supposed to reside in one of
#=GF CC the protein components [1].
#=GF WK Small_nucleolar_RNA_SNORD42
#=GF SQ 7

AJ224023.1/1-67           GUGCA-UAUGAUGGA-AAAGUUUUAA-UCUCC-U-----GACACUUGUGAUGUCUUCAAAGGAACCACU--GAUGCAC
AC004807.1/1740-1672      GUGCA-UAUGAUGGAAAAAAUCUGAAGUCUCC-U-----GAGACCUGUGAUGUCUUCAAAGGAACCACU--GAUGCAC
AC124016.3/72783-72715    UAGCA-UAUGAUGGA-AAAAUCUUAA-UCUUC-U-----GAGACUUGUGAUGUCUUCAAAGGAACCACUUCAAUGCAA
Z75890.1/1272-1207        -AGCCCUAAAAUGGAAAAAAUUUAAA-AUUAC-UUA---GACAA-UGUGAUGUCAUCAAAGGAACC-CU--AA-GUA-
AL591070.19/168628-168690 -UGCA-AAUGAUGGA-AAA--CUCAA-UGUUU-G-----GAAAAGAAUGACACCAACAAAGGAACCACU--GAUGCU-
X96641.1/1-62             -GGCU-AAUGAUGGAAAAA-----------UCAUUAUUGGAAAAGAAUGACAUGAACAAAGGAACCACU--GAAGUG-
AF001689.1/3146-3209      GGGGU-AAUGAUGGAAAAA-----------UCAUUAUUGGAAAAGAAUGACAUGAACAAAGGAACCACU--GAAGUGC
#=GC SS_cons              <<<<<.____________________._____._.....______________________________..__>>>>>
#=GC RF                   guGCa.uAUGAUGGAAAAAAUcUuAA.UcUuC.U.....GAaAauugUGAugUcauCAAAGGAACCACU..GAuGCac
//
