# STOCKHOLM 1.0
#=GF ID SNORA41
#=GF AC RF00403
#=GF DE Small nucleolar RNA SNORA41
#=GF AU Moxon SJ; 0000-0003-4644-1816
#=GF GA 80.0
#=GF NC 79.6
#=GF TC 81.4
#=GF PI snoACA41
#=GF SE PMID:15199136, INFERNAL
#=GF SS Predicted; PFOLD; Moxon SJ
#=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 26.00 -Z 2958934 CM SEQDB
#=GF DR SO; 0000594; H_ACA_box_snoRNA;
#=GF DR GO; 0006396; RNA processing;
#=GF DR GO; 0005730; nucleolus;
#=GF DR snoopy; Mus_musculus300178;
#=GF DR snoopy; Loxodonta_africana300445;
#=GF RN [1]
#=GF RM 15199136
#=GF RT Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL Mol Cell Biol 2004;24:5797-5807.
#=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 CC ACA41 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC modification of uridines to pseudouridines [1]. The family also includes
#=GF CC the mouse sequence MBI-83 described in [2].
#=GF WK Small_nucleolar_RNA_SNORA41
#=GF SQ 31

AF357411.1/1-113           -------------------CAGCUGUCUUUA-UGGUAGCAGUUGUAGCAUUCC-UCUGUGGGAAAGAAA-CUGUU-ACACAA--UUUAAU-GCCU-CUUUCUUAGCCACACAGGAGG-AGG---AUUAUGUGUGACAGACACAA
AL645950.13/74028-74159    UUCCACAGCUACUGGUCUACAGCUGUCUUUA-UGGUAGCAGUUGUAGCAUUCC-UCUGUGGGAAAGAAA-CUGUU-ACACAA--UUUAAU-GCCU-CUUUCUUAGCCACACAGGAGG-AGG---AUUAUGUGUGACAGACACAA
AC121963.3/78058-77927     UUCCACAGCUACUGGUCUACAGCUGUUUUUA-UGGUAGCAGUUGUAGCAUUCC-UCUGUGGGAAAGAAA-CUGUU-ACACAA--UUUAAU-GCCU-CUUUCUUAGCCACACAGAAGG-AGG---AUUACGUGUGACAGACACAA
AC007383.4/101218-101349   UUCCACAGCUACUGGUCUGCAGCUGUUCUUA-UGGUAGCAGUUGUGGCAUUCC-UCUGUGGGAAAGAAA-CUGUUAACACA------AAC-ACCU-CUUUCUUAGCAAAACAGAAAGUGGGU-AUAUAUGUGUGACAGACACAA
AC090527.3/17174-17301     UUCCACCACUAUUGGUCUGCAGCUCUUCUUA-UGGUAGCAGUUGUUGCAUUUC-UCUGUGGGAAAGAAA-------AGAGGA--UUAAAC-ACCU-CUUUCUUAGCAAAACAGAGAGUAGG---CAUAUGUGUGACAGACACAA
AJ609464.1/1-132           UUCCACAGCUACUGGUCUGCAGCUGUUCUUA-UGGUAGCAGUUGUGGCAUUCC-UCUGUGGGAAAGAAA-CUGUUAACACA------AAC-ACCU-CUUUCUUAGCAAAACAGAAAGUGGGU-AUAUAUGUGUGACAGACACAA
AAQQ01276679.1/221-355     UUCCACAGCUACUGGUCUGCAGCUGUUCUAA-UGGUAGCAGUUGUAGCAUUCC-UCUGUGGGAAAUAAA-CUGUU-AUACAA--UUAUAU-GCCU-CUUUCUUAGCCAAAGAGAAAGUGGGC-ACAUGUGUGUGACAGACACAU
AAFC03055400.1/29161-29294 UUCCACAGCUACUGGUCUGCAGCUGUUCUUAAAGGUAGCAGCUGUGGCAUUCC-ACUGUGGGAAAGAAA-CUGUC-ACACAA--CUCAAC-ACCU-CUUUCUCAGCACAACAGAAAGUGGG---CAUGUGUGUGACAAACACAA
AAIY01152799.1/3962-4099   UUCCACAGCUACUGGUCUGCAGCUGUUUUUA-UGGUAGCAGUUGUGGCAUUCC-UCUGUGGGAAAGAAA-GUGUU-ACCCAAUGUGACAU-CCCU-CUUUCCCAGCAAAAUGGAAAGUUGGGCAUAUGUGUGUGACAGACACAG
AANG01689589.1/3219-3352   UUCCACAGCUACUGGUCUGCAGCCGCUCUUA-UGGUAGCAGUUGUGGCAUUCC-UCUGUGGGAAAGGAAACUGUC-ACACAA--UUAAAU-ACCU-CUUUCUUAGCACGACAGAAAGUGGG---CAUGUGAGUGACAAACAGAU
AAYZ01152970.1/1639-1769   UUCCACAGCUACUGGUCUGCAGCUGUUCUUA-UGGUAGCGGUUGUGGCAUUCC-ACUGUGGGAAAGCAA-CUGUC-ACAAU----UAAAC-ACCU-CUUUCUUGGCAAACCAGAAAGGGGG---CAUAUUUGUGACAGACAGGA
AAPY01235580.1/6370-6239   UUCCACAGCUACUGGUCUGCAGCUGUUCUUA-CAGUAGCACUUGUGGCAUUCC-UCUGUGGGAAAGAAA-CUGUU-A-ACGG--UUAAAU-ACCU-CUUUCUUAGUAAAAUAGAAAGUAGU---CAUGUGUGUUUCAGACAAAA
ABDC01218542.1/3016-3147   UUCCACAGCUACUGGUCUGCAGCUGUUCUUA-UG-UAGCAGUUGUGGCAUUCC-UCUGUGGGAAAGAAA-CUCAUGACACAG--UCAUAC-ACCU-CUUUCUUAGCAAA-CGGAAAGUGGG---UAUCAGGGUGACAGACACAA
AANN01478268.1/1238-1104   UUCCACAGCUAGUGAUAUGCAACUGUUCUUA-AGGUAGCAGUUGUGACAUUCU-UCUGUGAGAAAGAAA-UAAUG-ACACAAAUUUAAAU-ACCU-CUUGCCUAGCAAAACAGAAAGUUGG---CAUAUGUGUGACAAAUAAGA
AAFR03041977.1/27839-27705 UUCCACAGCUACUGGUCUGCAACUGUUCUCAUCUAUAGCAGUUGUUGUAUUCC-ACUGUGGGAAAGGAA-CUGUU-ACACUG--UUAAAUAACCU-CUUUCU-AAUAUAACAGAAAGUGGG--UUCUUUGUGUGACAGACACCU
AALT01533432.1/8901-8769   UUCCAUAGCAGCAGGUCUGCAAUUGCUCUUC-CUGUAGCAAUUGUGGCAGUCA-UCUGUGAGGAAGAAA-UUGUU-A-CUUG--GUUAAC-ACUG-CUUUCUUAGCAAAAUAGACAGUAAU--AGUGUAAUUUGUCAGGCUAGA
AAVX01259799.1/576-710     UUCCACAGAUACUGGUCUGGAAUUGCUUGCU-UGGUAGUAGUUUCAGUAUUCCUUCUGUGGAAUAAUAA-UUGUU-GCACUC--AGUUAU-CAGCUCUUUAUAAAUCACUAUCAAAGUGCU---UUAUGGUGUGACACACAUUU
AAKN02019509.1/9665-9798   GUCCACAGCUACUGGUCUGCAGCUGCUGUCAAUCGUAGCAGCUGUGGCAUUCC-ACUGUGGGAAAGGAA-GUGUU-ACACAG--UUAAAU-ACCU-CUUUCUUAUCCAAGAAGAAAGUGGG---CAUGUGUGUGACAGACAGUG
AAHX01054375.1/23514-23383 UUCCACAGCUACUGGUCUGCAGCUGUCCUUA-UGGUAGCAGUUGUAGCAUUCC-UCUGUGGGAAAGAAA-CUGUU-ACACAA--UUUAAU-GCCU-CUUUCUUAGCCACAUAGAAAG-AGG---AAUAUGCGUGACAGACACAA
AAWR02007092.1/1413-1544   CCCCACAGCUCCUGGGCCGCAGCUGUUCUCA-CGGCAGCAGCUGUGGCAUUCC-UCUGUGGGAGAGAAA-CUGUU-ACACGA--UUGAAA--CCG-CUUUCUUAGCAAAACAGAAAGCGGG---CAUGUGUGUGACAAACACAG
AAGV020028150.1/1950-2082  CUCCACAGCUACUGGUCUGCAGCUGUUCUUA-UGGUGGCAAUUGUGGCAUUCC-UCUGUGGUAAAGAAU-CUGUU-ACAUAA--UUAAAU-ACUU-CUUUCUUAGCAAAACAGAAAGUGGG---CAUGUGUGUGACAAAGUUAA
EU094007.1/3-137           UUCCACAGCUACUGGUCUGCAGCUGUUGUGCUCUGUAGCAGUUGCAGUAUUCCAUCUGUGGGAAAGAAACUUGUUGACACUG--UUCGUU-ACCC-CUUUCUCGGCAAC--AGAAUGGGGU---UUUCUGUGCGACAGACAAAU
EU240316.1/2-135           GUCCACAGUUACUGGUCUGAAACUGUUCAGGACUGUAGCAGUUGCAGUAUUCCCUCUGUGGAAGAUAAA-CUGUU-ACGUAG--UAUUAA-GCUC-CUUCUCAGAUCUUCUAAGAAG-GAC---UUUCUAUGUAACAAACAACG
FJ915969.1/1-130           UUCCACAGCUACUGGUCUGCAGCUGUUCUUA-UGGUAGCAGUUGUGGCAUUCC-UCUGUGGGAAAGAAA-CUGUUAACACA------AAC-ACCU-CUUUCUUAGCAAAACAGAAAGUGGG---CAUAUGUGUGACAGACAUAA
AAWZ02015247.1/62201-62072 UUCCACAGCUACUGGCCUGCAACUGUUCAGUAUUGUAGCAAUUGCAGUAUUCCAGCUGUGGGAGAUUAG-CAGUU-ACACC------UAU-AUGA-UUCUCCUUUCAAA-UGGGGAGAUAA---UUGACGUGUAACGGACAAGA
AAPE02003230.1/9283-9415   UUCCACAGCUACUGGUCUGCAGCUGUUCUCA-UGGUGGCAGUUGUGGCAUUCC-UCUGUGGGAAAGAAA-UUGUU-ACACGA--UUAAAC-ACCU-CUUUCUUAGCAAAACAGAAAGGGGG---CAUAUGUGUGACAAACAUGA
AACN011054043.1/216-348    UUCCACAGCUACUGGUCUGCAGCUGUUCUUA-CAGUAGCAGUUGUGGCAUUCC-UCUGUGGGAAAGAAA-CUGUU-AUGCAA--UUAAAC-ACCU-CUUUCUUAGCACAACGGAAAGUGGG---CAUAUGAGUAACAAACAUAA
AAQR03032350.1/9868-9736   AUCCACAGCUACUGGUCUGCAGCUGUUCUUA-UG-UAACAGUUGUGGCAUUCC-UCUGUGGGAAAGAAA-CUGUUAACACAG--UUAAAU-ACCU-CUUUCUUAGCAAAACAGAAAGUGGG---UAUACGUGUGACAGACAGAA
AADN03005226.1/24909-25042 GUCCACAGUUACUGGUCUGAAACUGUUCAGGACUGUAGCAGUUGCAGUAUUCCCUCUGUGGAAGAUAAA-CUGUU-ACGUAG--UAUUAA-GCUC-CUUCUCAGAUCUUCUAAGAAG-GAC---UUUCUAUGUAACAAACAAUG
AAGW02037058.1/8662-8794   UUCCGCAACUACUGGUCUGCAGCUGUUCUUA-UGGUAGCAGUUGUGGCAUUCC-ACCGUGGGAAAGAAA-CUGUU-AUACAA--UUAAAU-ACCU-CUGUCUUAGCAAAACAGAAAGUGGG---UAUAUGUGUGACACACAUGA
AAGU03009554.1/92378-92246 UUCCACAGCUACUGGUCUGCAACUGUCUUCA-UGGUAGCAGUUGCGGCAUUCC-UCUGUGGGAAAGAAA-CUGUU-ACGUGA--UUAAAC-ACCU-CUUUCUUAGCAAAACAGAAAGUGGG---CAUAUGUGUGACAGACAAGA
#=GC SS_cons               ::<<<<----------<<<<<<<<<______.______>>>>>>>>>------.--->>>>::::::::.:::::.<<<<<-..------.-<<<.<<<<<<_________>>>>>>->>>...---->>>>>:::::::::::
#=GC RF                    UUCCACAGCUACUGGUCugcAacUGUUcUua.ugGUAGCAguUgcaGcAUUCC.UCUGUGGGAAAGAAA.cUGUU.ACacaa..UuaaAu.accc.CUuucuUAgCAAaacagaaAGUggg...uaUauguGUGACAgACAaaa
//
