# STOCKHOLM 1.0
#=GF ID snoU109
#=GF AC RF01233
#=GF DE Small nucleolar RNA U109
#=GF AU Wilkinson A; 0000-0001-7406-0151
#=GF GA 43.0
#=GF NC 42.9
#=GF TC 43.0
#=GF SE Predicted; WAR; Wilkinson A
#=GF SS Predicted; WAR; Wilkinson A
#=GF TP Gene; snRNA; snoRNA; HACA-box;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 33.32 -Z 2958934 CM SEQDB
#=GF DR snoRNABase; U109;
#=GF DR GO; 0006396; RNA processing;
#=GF DR GO; 0005730; nucleolus;
#=GF DR SO; 0000594; H_ACA_box_snoRNA;
#=GF RN [1]
#=GF RM 16361266
#=GF RT A novel experimental approach for systematic identification of box H/ACA
#=GF RT snoRNAs from eukaryotes.
#=GF RA Gu AD, Zhou H, Yu CH, Qu LH
#=GF RL Nucleic Acids Res. 2005;33:e194.
#=GF RN [2]
#=GF RM 7225127
#=GF RT Pseudouridine residues in the 5'-terminus of uridine-rich nuclear RNA I
#=GF RT (U1 RNA).
#=GF RA Reddy R, Henning D, Busch H
#=GF RL Biochem Biophys Res Commun. 1981;98:1076-1083.
#=GF RN [3]
#=GF RM 12912925
#=GF RT A common sequence motif determines the Cajal body-specific localization of
#=GF RT box H/ACA scaRNAs.
#=GF RA Richard P, Darzacq X, Bertrand E, Jady BE, Verheggen C, Kiss T
#=GF RL EMBO J. 2003;22:4283-4293.
#=GF WK Small_nucleolar_RNA
#=GF SQ 26

AM055742.1/1-134           UUGCAUGUGGAA---------AUGUCUGCUUCUCAUUCC-UUG--G-GAGCAGGAAUAUGUUCAUAACAUGCUACAUUA-AC-------AAAGGAGUUCUCAGGGCUGCCAACCUUCUAGUAAAGGUUGAGUGGUAGUAUAUUUCUCCAACAUAA
AAFC03012751.1/570-436     UCGCAUGUGGAA---------AUGUCUGCUUCUCAUUCCUUUG--G-AAGCAGGAAUACGUCCAUAACAUGCUACAUUA-AA-------AAAGGAGUUCUCAGGGCUGCCAACCUUCCAGUAGAGGUUGAGUAGUAGUAUAUUUCUCCUACAUAA
ABDC01105195.1/1988-2122   UUGCAUGUGGAA---------AUGUCUGCUCCUUAUUCC-UUC-GG-GAGCAGGAAUACAUUCAUAACAUGCUACAUUA-AA-------AAAGGAGUUCUCAGGGCUGCCAACCUUACAGUUGAGGUUGAGUGGUAGUAUAUUUCUCCUACAUAA
AADA01032425.1/12845-12711 UUGCAUGUGGUA---------AUGUCUGCUCUUCAUUCCUUUG--G-GAGCAGAAAUACAUCCAUAACAUGCUAAAUUA-AA-------AAAGGAGUUCUCAGGGCUGCCAACCUUACAGUAGAGGUUGAGUGGUAGUAUAUUACUCCUACAUAA
AAIY01155199.1/1916-1782   CUGCAUGUGGAA---------AUAUCUGCUCCUCAUUUC-GUU-AG-GAGCAGGAAGACAUCCAUAACAUGCUACAUUA-AU-------AAAGGAGUUCUCAGGGCUACCAACCUUACAGUAGAGGUUGAGUAGUAGUAUAUUUCUCUUACACAA
AAQQ01025945.1/7271-7137   UUGCAUGUGGAA---------AUGUCUGCCCCUCAUUUC-UUC-AG-GGGCAGGAAUGCAUCCAUAACAUGCUACAUUA-AC-------AAAGAGGUUCUCAGGGCUGCCAGCCUUAUAGUAGAGGCUGAGUGGUAGUAUAUUUCUCCUACAUAA
AACN010521667.1/155-289    CUGCAUGUGGAA---------AAGUCUGCUCCUCAUUCU-UUG-GG-GAGCAAGAAUACAUCCAUUACAUGCUACAUUA-AA-------AAAGGAGUUCUCAGGGCUACCAGCCUUACAGUAGAGGUUGAGUAGUAGUAUAUUUCUCCUACAUAU
AANG01809596.1/3729-3863   UGGCAUGUGGAA---------AUGUCUGCUCCUCAUUCCUUUG--G-GAGCAGGAAGACAUCCAUUACAUGCUACAUUG-AA-------AAAGGAGUUCUCAGGGCUGCCAGCCUUACAGUAGAGGCUGAGUAGUAGUAUAUUUCUCCUACAUAG
AAPY01288712.1/832-964     UUGCAUGUGGAA---------ACGUCUGUUCUGCAUUCU-UUU--G-GAGCAGGAAUACAUCCAUCACAUGCUACAUUG-AG--------AAGGAGUUCUCAGGGCUGCCGACCUUACAGUAGAGGUUGAGUAGUAGUAUAUUUCUCCUACAUAA
AL592403.6/87724-87858     UUGCAUGUGGAA---------AUACCUUCUCCUCAUUCUAUUU--G-GAGCAGGAAUGCAUCCAGAACAUGCUACACUA-AA-------AGAGGAGUUCUCAGGGCUGCCAACCUUACAGUAGAGGUUGAGUAGUAGUAUAUUUCUCCUACAGAA
AAHX01075576.1/2850-2716   UUGCAUGUGGAA---------AUACCUUCUCCCCAUUCUCUUU--G-GAGUAGGAAUGUAUCCAGAACAUGCUACACUA-AA-------AGAGGAGUUCUCAGGGCUGCCAGCCUUCUAGUAGAGGUUGGGUGGUAGUAUAUUUCUCCUACAGAA
AANU01221802.1/12812-12946 UUGCAUGAGGAA---------GUAUCUGCUCUUCAUUCCUUUG--G-GGGCAGAAAUACAUCUAUCACAUGCUAAAUUA-CA-------AAAGGAGGUCUCAGGGCCGCCAACGUUUCAAUAGAGGUUGAGUGGUAGUAUAUUACUCCUAUAUAA
AALT01635921.1/820-679     UUGCAUGUGAAA---------AUGCCUGCUUCUCAUUCC-UUU-AG-GGGCAGGAAUACAUCCAUAACAUGCUACAUUA-AAAAGGAAAAAAGGAGUCUUCAAGGCUACCAAACUUACAUUAGAGGUUGAGUAGUAGUAUAUUUCUCCUACACAA
AANN01279194.1/758-890     UUGCAUGUGGAA---------ACGUCUUCUGCUCAUUCCUUUG--G-GCGCAGG-AUAUAUCC-UUACAUGCUACAUUA-AG-------AAAGGAGUUCACAGGGCUGCCAACCUUACAGUAGAGGUUGAGUAGUAGUAUAUUUCUCCUACAAAA
AAFR03013540.1/37441-37297 CUGCAUGUUGGACUUUUUAA-AGUCAUACUUCUUAAUGCAAUA--G-AAGUAUGAAUAUAACCAGUACAUGCUAUAUAA-AAAU-----AUAGGAGUUUUCAGGGCUGCCAACCUUGCAGUAAAGGUUGAGUAGUAGUAUAUUUCUCCUACAUCA
AAYZ01413806.1/796-664     UUGCAUGUGGAAG--------UUUCUUUCUCCUCACUCC-UGU--G-GAGGAGGAAUGCAUCCAUUACAUGCUACAUUA-GC---------AGGAGUUCUCAGGGCUGCCGGCCUGCCAGGAGAGGCUGGGCAGUAGUAUAUUGCUCCAACACAA
AAPN01018558.1/7732-7871   UUGCAUGAUGGAAACCAA---UUUUCAGCUCUUUGUUCU-UUA-AG-GAGCAUGAAUAUAUCCAUAACAUGCUACAUAA-AU--------GAGGAGCUGUCAGGGCUGCCAGCCUUUUAGUUAAGGCUGUGUGGUAGUAUAUUUCUCCAACACUG
AAKN02019979.1/23970-23835 UGGCAUGUGGAA---------AUGCCUUCUCCUCAUUCC-UUG-UG-GAGCAGGAAUAUAUCCAUGACAUGCUACAUUA-AAA------AAAGGAGUUGUCAGGGCUGCCAACCUUACAGUAGAGGUUGAGUGGUAGUAUAUUUCUCCUACAUUA
AAWR02003035.1/86430-86564 UUGCAUGUGGAA---------AUGUCUGCUCCUCAUUCCUUUG--G-GGGCAGGAACACAUCCGUAUCAUGCUACAGUA-AA-------AAAGGAGUUCUCAGGGCUGCCAACCUUACAGUAGAGGUUGAGUAGUAGUAUAUUUCUCCUACAUAA
AAGV020307937.1/641-507    UUGCAUGUGGAA---------AUGUCUGCUCCUCAUUCU-UUU-AG-GAGCAGGAAUAUAGCCAUAACAUGCUACAUUA-AA-------AUAGGAGUUCUCAGGGCUGCCAAUCUUGCAGAAGAGGUUGAGUGAUAGUAUAUUUCUCUUACAUUA
AAWZ02032644.1/10370-10504 CUGCAUGAUGGAAACU-----UGUCAUUCUUCUUUCUUC-UG---G-GAGAAUGAAUAUUCCUUCA--AUGCUAUAAAA-AU-------CAAGGAGUUUUCAGGGCCACCUGCCUUGGAGUAGAGGCUGAGUGGUAGUAUAUUUCUCCUACAUUA
AAGU03001560.1/48063-48198 UGACAUGUGGAA---------AGGUCUGCUCCUCAUUCC-UUU-AG-GAGCAGGAAUACAUCUAUAACAUGCUACACUAUAA-------AAAGGGGUUUUCAGGACUGACAACUUUACAGUAGAGUUUGAGUGGUAGUAUAUUUCUCCUACAUUA
AAPE02000595.1/29599-29732 UUGCAUGUGGAAAU-------AUGUCUGUUCCUCAUUCCUUUG--G-GAGCAGGAAUACCUCCAUAACAUGCUACAUAA-----------AAGGAGUUCUCAGGGCUGCCAACCUUACAGUAGAGGUUGAGUAGUAGUAUAUUUCUCCUACAUAG
AAQR03037363.1/5502-5637   UUGCAUGUGGAA---------AUGUCUGCUCCUCAUUCC-UUU--GAGAGCAGAAAUACGUCCAUAACAUGCUACAUUA-AAA------AGAGGAGUUCUCAGGGCUGCCAACCUUACAGUAGAGGUUGAGUAGUAGUAUAUUACUCCUACAGAA
AAGW02054189.1/12164-12297 UUGCAUGUGGAA---------AUGCCUUCUCCUCAUUCC-UUU--G-GAGCAGGACAACAUCCAUAACAUGCUAUAUUA-AC-------AAAGGAGUUCUCAGGGCUGCCAACCUUACAGUAGAGGUUGAGUGGUAGUAUAUUUCUCCUACACAA
AADN03004144.1/23237-23093 CUGCAUGUUUCAAAAAAACACAAUUCUGCUCCUUAUUCC-CUUAAG-GAGCAUGAAUAUAUCUAUAACAUGCUACAGAA-AA-------CAAGGAGUCUUCAGGGCUGCCAGUCUUCAAGUAAAGGCUGAGUGGUAGUAUAUGCCUCCUACAUUC
#=GC SS_cons               ::<<<<<<----.........---<<<<<<<<_______.___..>.>>>>>>>------------>>>>>>:::::::.::.......:::<<<<--------<<--<<<<<<<<______>>>>>>>->-->>--------->>>>:::::::
#=GC RF                    UUGCAUGugGaA.........AugccugCucCUcAUUcc.UUu..G.gaGcaggAAUAcAUCcAUaaCAUGCUAcAuuA.Aa.......AaAGGaGUUcUCAGGgCUGCCagcCUcacAGUAgAGgcuGAGUaGuAGUAUAUUuCuCCUACAuaA
//
