# STOCKHOLM 1.0
#=GF ID snR43
#=GF AC RF01256
#=GF DE Small nucleolar RNA snR43
#=GF AU Wilkinson A; 0000-0001-7406-0151
#=GF GA 60.0
#=GF NC 58.9
#=GF TC 60.2
#=GF SE Predicted; WAR; Wilkinson A
#=GF SS Published; PMID:18332121; 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 26.53 -Z 2958934 CM SEQDB
#=GF CL CL00027
#=GF DR snornadb; snR43;
#=GF DR GO; 0006396; RNA processing;
#=GF DR GO; 0005730; nucleolus;
#=GF DR SO; 0000594; H_ACA_box_snoRNA;
#=GF RN [1]
#=GF RM 8797828
#=GF RT The RNA world of the nucleolus: two major families of small RNAs defined
#=GF RT by different box elements with related functions.
#=GF RA Balakin AG, Smith L, Fournier MJ
#=GF RL Cell. 1996;86:823-834.
#=GF WK Small_nucleolar_RNA
#=GF SQ 20

X59720.2/107708-107500       CACUCCUGUUUCUGCCUCAUGUCUU-----UUAAAACGCUUCCACGGGA-CA-UGGGUUCUAAUUAU-GGAGAAGAUCAAGCUUUGAAAUGGCCCGU-UUACACAUUUUGAUACAACCGUAG-A-CGGCGUCUCGUUUCAAAGACCGUGUGGUUGUCUAUCAGUAUAU-ACUCAUUG-----UGUUUUUCAA----AAAA
AABZ01000112.1/9647-9855     CACUCCUGUUUCUGCCUCAUGUCCUU----UUACAACGCUUCCACGGGA-CA-UGGGUUCUAAUUAU-GGAGAAGAUCAAGCUUUGAAAUGGCCCGU-AUACACAUUUUGAUACAACCGUAU-A-CGGCGUCUCGUUUCAAAGAUCGUGUGGUUGUCUAUCGAUAUAU-ACUCAUUG-----UGUUUUUAG-----AAAA
AABY01000162.1/1359-1151     CACUCCUGUUUCUGCCUCAUGUCCUU----UUACAACGCAUCCACGGGA-CA-UGGGUUCUAAUUAU-GGAGAAGAUCAAGCUUUGAAAUGGCCCGU-UUACACAUUUUGAUACAACCGUAU-A-CGGUGUCUCAUUUCAAAGAUCGUGUGGUUGUCUAUCAAUAUAU-ACUCACUA-----UGUUUUUCAA----AAAA
AACI02000137.1/4593-4383     CACUCCUGUUUCUGCCUCAUUUCCCC---UUUUAAACGCUUCCACGGGU-CA-UGGGUUCUAAUUAU-GGAGAAGAUCAAGCUUUGAAAUGGCCCGU-UUACACAUUUUGAUACAACCGUAG-A-CGGCGUCUCGUUUCAAAGAUCGUGUGGUUAUCUAUCGUUAUGU-ACUCAUUG-----UUUUCAAAAA----AUAA
AACG02000009.1/53495-53284   CACUCCUGUUUCUGCCUCGUGUCCU-----UUUAAACGCUUCCACGGGA-CA-UGGGUUCUAAUUAU-GGAGAAGAUCAAGCUUUGAAAUGGCCUGU-UCACACAUUUUGAUACAACCGUGA-A-CAGUGUUCCGUUUCGAAGAUCGUGUGGGUUUCUAUCGUUUCGU-ACUCAUUG-----UGUUUUCAAAA-AAAAAA
Z86109.1/3914-3708           CACUCCUGUUUCUGCCUCGUGUCCU-----UAGAAACGCUUCCACAGGA-CA-CGGGUUCUAAUUAU-GGAGAAGAUCAAGCUUUGAAAUGGCCUAU-UCACACAUUUUGAUACAACCGUGA-A-CAGUGUUCCGUUUCGGAGAUCGUGUGGGUUUCUAUCGUUACGU-ACUCAUUG-----UGUUUU--CA----AAAA
AACF01000094.1/6899-6696     CUCUCCGAUUUCUGCCUCAUUUUCUU----UU-----GCUUCAAUAGAUUCA-UGGGUUCUAAUUUUUGGAGAAGAAUAAGCUGUAUGACGACUCAAUUCACACAUUUUGAUACAACCGUGA-U-UGA-G---CGUGGUGCAGAUCGUGAGAUUACUUC---AUUCGA-CUUGAUUA-----AUUCAAUUUAU-UGUUUA
CR382121.1/752772-752561     CACUCCUGAUUCUGCCCCAUGUUCUU----U-----CUCUUCCAUAGAU-UAAUGGGUUCUGUUUAU-GGAGAAGAUAAAGCUGGUGAAUGGUGCGC-CUGCGC-CUUUGAUACAACAGUGG-GAUGC-ACUUCAUUUACCAGAUCGUGAGAACACAUU---AAACGA-CUUGUCUGA---CUUUAUUUUCG----AAUA
AAZN01000184.1/27875-28075   CACUCCUAUUUCUGCCCCAUAUUCCC----CU----UUCUUCUAUGGAU-UAAUGGG-UCUAACGAU-GGAGAAGAAAAAGCCAAUGAAUGGUUCAA-UUACAACUUUUGAUACAUCCGUAA-U-UGA-ACUUCAUUUGUUGGAUCGUGUAGUUGAGUU---GUACAA-UUUCUUAA-----UUCCAAUAUG----UUAA
AADM01000355.1/4342-4146     CCCUCCUAUUUCUGCCCCACAUUCUU----UA----CGCUACCAUAGAA-UAAUGGGUUCUAUUAAU-GGAGAAGAGAAAGCCUGCUAACGCAUUAC-CUACAC-UUUUGAUACAACCGUGG-G-UUUUUG--UGUUGACAGGAUCGUGUGUAAGGGCC---AAACAC-CUUUAAGA-----UUAGCU--------AAUU
AAPO01000014.1/230229-230440 CACUCCUGUUUCUGCCUCAAAUCCGU----UU----UGUUUCUAUAGGA-UUAUGGGUUCUGGUGAU-GGAGAAGAUCAAGCCAUGAAAUGGGCUUA-UACCAACUUUUGAUACAUCCGGUA-U-UUGUCU--UGUUUCAUGGAUCGUGUGGAUGAUUUUGUAUCCGU-UGUGUGGAGC-AAUAUCAAUAUAAAGUUUGA
AAVQ01000001.1/924370-924575 CACUCCUGUUUCUGCCCCAAAUUCUU----UU---ACACAGCCAUAGAA-UUAUGGGUUCUACUUAU-GGAGAAGAAAAAGCCAUUCAACGAACUUC-GGACAC-UUUUGAUACAACCGUCC-G-UUG-UU--UUUUGGGUGGAUCGGGUGGUUAGGCUUUGUAUCCU-UGCGUGACU--GACUCGGAACGU----UCCG
AAFM01000047.1/164975-164781 ACCUCCUGUUUCUGCCUCAAGUUCUU----UU-----UUCACCAUAGAA-UAUUGGGUUCUGUUUAG-GGAGAAGAUAAAGCUGGUUGAAG--ACAA-CGACAC-CUUUGAUACAACCGUCGCU-UGU-----UUUUGACCAGAUCGUGUGGACAGGCCCAACCUUGA-AGGCAU-A-----UCGGCUCAUU----GCCC
AACE03000004.1/744835-745036 CACUCCUGUUUCUGCCUCAUACUCUU----UC----UACUUCCAUAGAU-UAAUGGGUUCUAGUUAU-GGAGAAGAUAAAGCCAGGGGAUGACCUUU-CCACAA-CUUUGAUACACACGUGG-A-UGG-GCUUCAUUGUCUGGAUCGUGAGAACACAUU---GAAUGA-CUUCUUGC-----AAUUUCUAUA----AUUG
CR382139.2/961528-961315     CACUCCUGUUUCUGCCUCAGAUUCUU----AU-----GUUUCCAUAGAA-UUAUGGGUUCUGUUUAU-GGAGAAGAUUAAGCCUGUUAACGGAGCUU-GGACAC-UUUUGAUACAACCGUCC-A-UGU-UC--UUUUAGCAGGAUCGUGUGGUUAGAUUUGUCCGUGUGUGAUACACUCGAUAAUGGUUAGU----UCCA
AAFN02000078.1/177466-177681 AACUCCUGUUUCUGCCUCAGAUUCGUGCUUUCAUAUGGAAGCAAUGGGA-UUAUGGGUUCUGGUGAU-GGAGGAAAUCAAGCCAUCGAACAGACAAU-UGCUAC-CUUUGAUACAACCAGCU-U-UUGUUUUUUGUUUUAUGGAUCGUGUGG-UCGACUUGUAUCCGU-AGUUGGUU-----UGUUGUGUGAU--UACAA
AE016814.2/333453-333261     CACUCCUAUUUCUGCCCCAUCUUCUU----AU-----UACUCCAUAGAU-UAAUGGGUUCUAGUAAA-GGAGAAGAAAAAGCCGUGGAAUGGCUUCC-CG----CACUUGAUACUUCG--CG-G-UUUAGCUUCAUUCCGCGGAUCGUGUGUA-GUGGCAGGUUAU---CCGGCUGC-----AGCAUUU-------UAUG
HE576754.1/979444-979647     CUCUCCGAUUUCUGCCUCAUUUUCUU----UU-----GCUUCAAUAGAU-UCAUGGGUUCUAAUUUUUGGAGAAGAAUAAGCUGUAUGACGACUCAAUUCACACAUUUUGAUACAACCGUGA-U-UGA-G---CGUGGUGCAGAUCGUGAGAUUACUUC---AUUCGA-CUUGAUUA-----AUUCAAUUUAU-UGUUUA
U56644.1/1-209               CACUCCUGUUUCUGCCUCAUGUCUUU----UAA-AACGCUUCCACGGGA-CA-UGGGUUCUAAUUAU-GGAGAAGAUCAAGCUUUGAAAUGGCCCGU-UUACACAUUUUGAUACAACCGUAG-A-CGGCGUCUCGUUUCAAAGACCGUGUGGUUGUCUAUCAGUAUAU-ACUCAUUG-----UGUUUUUCAA----AAAA
AJ003086.1/1-207             CACUCCUGUUUCUGCCUCGUGUCCUU----AGA-AACGCUUCCACAGGA-CA-CGGGUUCUAAUUAU-GGAGAAGAUCAAGCUUUGAAAUGGCCUAU-UCACACAUUUUGAUACAACCGUGA-A-CAGUGUUCCGUUUCGGAGAUCGUGUGGGUUUCUAUCGUUACGU-ACUCAUUG-----UGUUUU--CA----AAAA
#=GC SS_cons                 ::<<<<---------<<<<<<<<<<_....__...._________>>>>.>>->>>>----------.>>>>:::::::::<<<<<<<<<<<<<<<<.<<<<________________>>>>.>.>>>->>-->>>>>>>>>>:::::<<<<--<<<<<---------.<<<<<--<.....-<<<<<____....>>>>
#=GC RF                      CACUCCUGUUUCUGCCuCAugucCuU....Uu....cgcuuCcAUaGga.caAUGgGUUCUAaUuAU.GGAGAAGAuaAAGCcggggaAcGgcccgc.ccaCACauUUUGAUACAACCGugg.g.cggugcuUCgUuccccgGAUCGUGuGguUgccucUuaauacgu.ccucauug.....ucuuuuuaua....aaaa

X59720.2/107708-107500       U--------CUCUGGGUUGUUUAGAU-GCCACUAUAUUU
AABZ01000112.1/9647-9855     C--------CUUUGGGUUGUUUAGAU-GCCACUAUAUUU
AABY01000162.1/1359-1151     C---------UCUGGGUUGUUUAGAU-GCCACUAUAUUU
AACI02000137.1/4593-4383     U--------CUCUGAGUUGUUUAGAU-GCCACUAUAUUU
AACG02000009.1/53495-53284   U--------CUUUGAGUUGUUUAGAU-GCCACUAUAUUU
Z86109.1/3914-3708           U--------CUCUGAGUUGUUUAGAU-GCCACUAUAUUU
AACF01000094.1/6899-6696     U--------UUUUCAAGAUUUGGAGU-GACUCUACAUUU
CR382121.1/752772-752561     UCCAAUAGCCUGACGAGACUUGAUGU-GCCUCUAUAUUU
AAZN01000184.1/27875-28075   U---------UAAGGAAACGCAAUUC-UCUUCUAUAUUC
AADM01000355.1/4342-4146     A--------UCUUAGAGAUAUGGUGC-UUCACUACAUUU
AAPO01000014.1/230229-230440 U-------AUUGA-GCCUGAUCGGUC--CCACUACAUUA
AAVQ01000001.1/924370-924575 G--------GAAAGUCUGAUCGGUCU--CCACUAUAUUU
AAFM01000047.1/164975-164781 G--------U--UGUCGGUUUGGUCU--CCACUACAUCU
AACE03000004.1/744835-745036 A--------GCAAGAAGACUCAAUGU-CUCUCUAUAUUC
CR382139.2/961528-961315     AAUG-ACGAGAAAAUCUGGCAAAUCU--CCACUACAUAU
AAFN02000078.1/177466-177681 U--------AUUCAAUGAACUGAUCGUCCCACUAUAUUU
AE016814.2/333453-333261     U--------GCAGUCGGGCU-GUCAU-UGCUCUAUAUUU
HE576754.1/979444-979647     U--------UUUUCAAGAUUUGGAGU-GACUCUACAUUU
U56644.1/1-209               U--------CUCUGGGUUGUUUAGAU-GCCACUAUAUUU
AJ003086.1/1-207             U--------CUCUGAGUUGUUUAGAU-GCCACUAUAUUU
#=GC SS_cons                 >........>-->>>>>---->>>>>.->>>>:::::::
#=GC RF                      g........cuuugaggauuUgaggc.gcCaCUAUAUUU
//
