# STOCKHOLM 1.0
#=GF ID SNORD31
#=GF AC RF00089
#=GF DE Small nucleolar RNA SNORD31
#=GF AU Griffiths-Jones SR; 0000-0001-6043-807X
#=GF GA 40.0
#=GF NC 39.9
#=GF TC 40.0
#=GF PI U31
#=GF SE Griffiths-Jones SR, INFERNAL
#=GF SS Predicted; 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 25.85 -Z 2958934 CM SEQDB
#=GF CL CL00053
#=GF DR SO; 0000593; C_D_box_snoRNA;
#=GF DR GO; 0006396; RNA processing;
#=GF DR GO; 0005730; nucleolus;
#=GF DR snoopy; Mus_musculus300715;
#=GF DR snoopy; Loxodonta_africana300011;
#=GF RN [1]
#=GF RM 8559254
#=GF RT A mammalian gene with introns instead of exons generating stable RNA
#=GF RT products.
#=GF RA Tycowski KT, Shu MD, Steitz JA
#=GF RL Nature 1996;379:464-466.
#=GF RN [2]
#=GF RM 8962077
#=GF RT A small nucleolar RNA requirement for site-specific ribose methylation of
#=GF RT rRNA in Xenopus.
#=GF RA Tycowski KT, Smith CM, Shu MD, Steitz JA
#=GF RL Proc Natl Acad Sci U S A 1996;93:14480-14485.
#=GF CC U31 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC and D (CUGA) box motifs. U31 is encoded within the U22 snoRNA host gene
#=GF CC (UHG) in mammals [1] and is thought to act as a 2'-O-ribose methylation
#=GF CC guide for ribosomal RNA.
#=GF WK Small_nucleolar_RNA_SNORD31
#=GF SQ 26

U40580.1/2987-3057         CUCACCAG-UGAUGAGUUGAAU--ACCGCCCCAGUCUGAUCAAUGUGUGACUGAAA-GGUAU-UUUCUGAGCUGUG
U40654.1/2265-2331         CUCACCC--UGAUGAACUGAAU--ACCGCCCCAGUCUGAUAGC--UGUGGA-GAAA-GGUAU-UUUCUGAGUUGUG
U72868.1/1-67              AAGACC---UGAUGAUCUCUAUU-ACCGCCCCAGUCUGAUUA-UAUGUGACUGAAU-GGUAU-CUUCUGA--UUGC
U72869.1/1-64              AAGACC---UGA---UCUCUAUU-ACCGCCCCAGUCUGAUUA-UCUGUGACUGAAU-GGUAU-CUUCUGA--UUGC
ABDC01628854.1/541-473     CUCACCAG-UGAUGAGUUGAAU--ACCGCCCCAGUCUGAUCAC--UGUGACUGAAA-GGUAU-UUUCUGAACUGAG
AAQQ01114996.1/830-898     CUCACCAG-UGAUGAGUUGAAU--ACCGCCCCAGUCUGAUCAU--UGUGACAGAAA-GGUAC-ACUCUGAGUUGUG
AANG01643015.1/1946-1878   CUCACCAG-UGAUGAAUGCAAU--ACCGCCCCAGUCUGAACAC--UGUGACUGAAA-GGUAU-UCUCUGAGCUGUG
AAPY01121463.1/746-813     CUCACCAG-UGAUGAGUUGA-U--ACCGCCCCAGUCUGAUCAC--UGUGACUGAUA-GGUAU-UUUCUGAGCUGUG
AAFC03036502.1/30234-30167 CUCACCAA-UGAUGAGUUCAAU--ACCGCCCCAGUCUGAUCAC--UAUGACUGAAA-GGUAU--UUCUGAGCUGUG
CAAE01014779.1/63527-63596 CCCACCAAAUGAUGAGUACGUU--ACCGCCCCAGUCUGAUAA-CUCGUGACUGAUG-GGUAU-UUUCUGA-CUGAA
AAPN01030027.1/4732-4665   AAUAUUCUGUGAUGAA-UCUAU--ACCGCCCCAGUCUGAUCAU--UGUGACUGAAA-GGUA--AUUCUGAGCUGUC
AANU01261827.1/873-941     AUCACCAG-UGAUGAGAUGAAU--ACUGCCCCUUUCUGAUCAA--UAUGCGUGAAA-GAUAU-UUUCUGAGCUGUG
AANN01835099.1/8950-8883   AUUACUAG-UGAUGAAUUCAUU--GCCACCC-AGUCUGAUCGC--UGUGACUGAUA-GGUAU-UUCCUGAGCUGUG
AAFR03060925.1/33935-33869 CCCACCAG-UGAUGAGACGAUU--ACCGCCCCAGGCUGAUUCC--UGUGACUGAUA-GGUU--GUUCUGAG-UGGG
AAZX01004141.1/32507-32574 AUUUAUAA-UGAUGACAUCCAU--ACCGCCCCAGUCUGAGUUC--UGUGACUGAUU-CGGAU--UACUGAUAAAAA
AAJJ01000083.1/51812-51744 AACGUAACGUGAUGAUUUACUU--ACCGCCCCAGUCUGAAAUC--GGUGACUGAUU-GGUUU--UUCUGAUUUGUU
AAVX01289320.1/180-247     CUAAAUA--UGAUGAGCCUGUU--AUCGCCCCAGUCUGAUUG-UUGGUGACUGAAACGGUAA-CCUCUGA--UUCA
AANH01007201.1/24133-24067 UUUUGAUG-UGAUGA--UUAUU--ACCGCCCCAGUCUGAUAA-UUCAUGACUGAUU-GGUU--ACUCUGAUCAAAU
AAKN02039313.1/10431-10499 CUCACCAG-GGAUGAA-UUGAAU-ACCGCCCCAGUCUGAUCAC--UGUGACAGAAA-GGUAU-UUUCUGAGUUGAG
AAGV020553791.1/5789-5856  CUCACCAG-UGAUGAGUUGAAU--ACCGCCCCAGUCUGAAAAC--UAUGACUGAAA-GGUAU--UUCUGAGCUGUG
AL954715.13/177135-177065  AUAGGU-G-UGAUGAUUUUAGAUUACCGCCCCAGUCUGAUUUA--UCUGACUGAUU-GGUACCCCUCUGAACCUUU
AAWR02037725.1/16273-16205 CUCACCAG-UGAUGAGUUCAAU--ACCGCCCCAGUCUGAUUAC--UGUGACUGAAA-GGUAU-UCUCUGAGCUGUG
AAGU03076505.1/711-778     AUCACCAG-UGAUGAGUUGAAU--ACCGCCCCAGUCUGAUCAC--UGUGACUGAAA-GGUAU--UUCUGAGCUGUG
AAGW02063721.1/8086-8154   CUCACUAG-UGAUGAGUCUGAU--ACCGCCCCAGUCUGAUCAC--UGUGACUGAAA-GGUAU-UUUCUGACCUGUG
AL138914.9/114073-114005   ACCACCAG-UGAUGAGUUGAAU--ACUGCCCCAGUCUGAUCAA--CAUGCGUGAAA-GAUAU-UUUCUGAGCUGUG
AAQR03118152.1/8663-8595   UUUACCAG-UGCUGAGUUGAAU--ACCACCCCAGUCUGAUAAC--UGUGACUGAAA-AGUAU-UUUCUGAACUGAG
#=GC SS_cons               ::<<____._____________..___________________..___________._____._________>>::
#=GC RF                    aUcaccAG.UGAUGAguUuaaU..ACCGCCCCAGUCUGAUcac..UGUGACUGAaA.GGUAU.uUUCUGAgCugug
//
