# STOCKHOLM 1.0
#=GF ID SCARNA17
#=GF AC RF00492
#=GF DE small Cajal body-specific RNA 17
#=GF AU Daub J; 0000-0001-6022-563X
#=GF GA 75.0
#=GF NC 74.7
#=GF TC 75.6
#=GF PI snoU12-22
#=GF SE Moxon SJ
#=GF SS Published;PMID:15556860
#=GF TP Gene; snRNA; snoRNA; scaRNA;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 26.32 -Z 2958934 CM SEQDB
#=GF DR GO; 0006396; RNA processing;
#=GF DR GO; 0015030; Cajal body;
#=GF DR GO; 0005730; nucleolus;
#=GF DR SO; 0002095; scaRNA;
#=GF RN [1]
#=GF RM 15556860
#=GF RT Guide RNAs with 5' Caps and Novel Box C/D snoRNA-like Domains for
#=GF RT Modification of snRNAs in Metazoa.
#=GF RA Tycowski KT, Aab A, Steitz JA
#=GF RL Curr Biol 2004;14:1985-1995.
#=GF RN [2]
#=GF RM 12032087
#=GF RT Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation
#=GF RT and pseudouridylation guide RNAs.
#=GF RA Darzacq X, Jady BE, Verheggen C, Kiss AM, Bertrand E, Kiss T
#=GF RL EMBO J. 2002;21:2746-2756.
#=GF RN [3]
#=GF RM 16381836
#=GF RT snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT snoRNAs.
#=GF RA Lestrade L, Weber MJ
#=GF RL Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC scaRNAs are a specific class of small nuclear RNAs which localise to the
#=GF CC Cajal bodies and guide the modification of RNA polymerase II transcribed
#=GF CC spliceosomal RNAs U1, U2, U4, U5 and U12 [1]. The complete human
#=GF CC U12-22/U4-8 scaRNA is composed of two tandem C/D box domains (termed
#=GF CC U12-22 and U4-8). The 5' and 3' C/D domains are predicted to guide the
#=GF CC 2'O-ribose methylation of residue U22 in U12 (RFAM:RF00007) and residue C8
#=GF CC in U4 (RFAM:RF00015) snRNAs respectively [1]. This family only includes
#=GF CC only the 5' C/D box domain (U12-22) as the 3' C/D box is represented by
#=GF CC RFAM:RF00283. The 3' C/D domain (U4-8) was also cloned previously by
#=GF CC Darzacq [2] and called U91. Both the doublet (U12-22/U4-8) and singlet
#=GF CC (U4-8) forms of this snRNA have been purified from Hela cells [1]. The
#=GF CC doublet form U12-22/U4-8 has been shown to localise to the nucleoplasm and
#=GF CC is proposed to reside in the Cajal bodies whereas the U4-8 single domain
#=GF CC appears to accumulate in the nucleolus [1]. In humans the genomic location
#=GF CC of U12-88/U4-8 is intergenic and the purified transcript has been shown to
#=GF CC possess a methylated guanosine cap suggesting it is independently
#=GF CC transcribed by RNA pol II [1].
#=GF WK Small_Cajal_body_specific_RNA_17
#=GF SQ 6

AC090227.10/15587-15444   CUUUCGGGUCCCCAUUGCAGCCCCCGGAUGAGCCCGCAGUAUUUUCCUUAUAUGAUCAGGUCCCAUUGCGGGCG-GCGCCGCUUGCCCGGAGCCUGAGAGGAUUAUGAAAACGUGGCGAGCGAAAUGGGGCCAGGGGACCUGGAG
AC129097.27/183442-183585 UUCUCAGGUCCCCAGUGCAGCCCCCAGAUAAGACUGCAGUAUUUUCCUUAUAUGAUCUGGUCCCACCGUGGGCA-GCACUGCAUGCCCAGAGCCUGAGAGGAUUAUGAAAACAUGGCAAGGGAAGUGAGGCCAGGGAACCCAGCA
AC018751.30/166114-165972 UUCUCAGGUCCCCAGUGCAGCCCCAAGAUGAGCCUGCAGUAUUUUCCUUACAUGAUCUGGUCCUACUGUGGGCA-GCGCUGC-UGCCCAGAGCCUGAGAGGAUUAUGAAAACAUGGCAACGGAAGUGAGGCCAGGGGACACAGCA
AC125020.7/181527-181661  CGCAUGGGUCCCCGAGGCAG-CCCUGAGUGAGCCCCGUGUAUUUUCCUUAUGUGAUCAGGC-CUCUCAU-AGUG-GGGCUGCUGGUUUGGAGCCUGAGAGGAUUAUGAAAAUGGGGCAG------UGUUACCAGCUGUUCUUGAC
AC127289.4/19294-19156    CACCUGGGUCCCCGAGGC-AUCCCGGAGUGAGCCCGGUGUAUUUUCCUUAUAUGAUUAGGC-CUCUCAU-A-CAGGCGCUGCUGGUUUGGAGCCUGAGAGGAUUAUGAAAACGUGGCAGGUGA--UGGAGUCAGGGGACCUGGAG
AC023490.5/121842-121984  UUCUCAGGUCGCCAGUGCAGCCCCAAGAUGAGCCUGCAGUAUUUUCCUUACAUGAUCUGGUCCUACUGUGGGCA-GCGCUGC-UGCCCAGAGCCUGAGAGGAUUAUGAAAACAUGGCAACGGAAGUGAGGCCAGGGGACACAGCA
#=GC SS_cons              <<<-<<<<<<<<<------<<<<<-------------------------------<<<<<<-<<---<<<<<<<.____>>>>>>>-->>->>>>>>----------------------------->>>>>-->>>>>>>>>>>>
#=GC RF                   ccCucggGuCcCCaauGCAGcccCaagaUGAGcCugcaGUAUUUUCCUUAuAUGAUcaGGcCCcauugugaGca.GcGCugCuugcccgGAgCCugAGAGGAUUAUGAAAAcauGGCAaggGAAgUGgggCCAGGgGaCccgGgg
//
