snR48-SNORD60

  • snR48-SNORD60_intronic-boxCDsnoRNA-127nt

  • Within spliced transcript as CNAG_12216

 C. neoformans Tremellomycetes snR48

../../_images/snr48_h99_igb.png

 

../../_images/snR48-r2r-opt.svg

  • Putative target in 25S rRNA: gaggTgccag

  • In yeast multiple modification by snR48 is linked to an irregular D’ box (auguua) acting as two, partially overlapping cuga motifs, affecting the positioning of Nop1/fibrillarin so that two nucleotides, separated by one base, get methylated in the same target sequence [van.Nues-2016]. In Tremellomycetes, if the putative D’ box (uuga) controls positioning of Nop1/fibrillarin, 2’-O-methylation of the ‘in-between’ nucleotide could be expected. The 5’ U in the motif, however, could be part of the guide region that base-pairs to the target sequence, and this, combined with an irregular C’ box (putatively ugcucu) might change the organization of the proteins and the positioning of the methylase. Thus, a different modification pattern might occur which can only be determined experimentally.

  • Orthologue of yeast snR48, human SNORD60

../../_images/snR48-SNORD60-aligned.png

>AE017343.1:34182-34301 Cryptococcus neoformans var. neoformans JEC21 chromosome 3 sequence
ATAAGTGAAGAGTGGTTTATTACCCCATGGCACCTCTTGACCCAGGGTCTCGTCCTGTCCTTGTCTACGA
GACTTGACATTAAGGACGCAGGCCGCTGCTCTAAACGGACAATCTGATAC







  • Image source alignment:

# STOCKHOLM 1.0
#=GF RW van Nues, June 2023
#=GF https://coalispr.codeberg.page/paper
Annot/1-46                  --GTGrGT-----------------------------------------RTGATGA-------------------------GACCGUGGAGA-CTGA-------------------------------------------------------------------------------------------------------RTGATGA----------------CTGA-------------------------------------------------CTGA--------------YAG---
#=GS snR48-SNORD60/1-127 DE intronic-boxCDsnoRNA-as-CNAG_12216-127nt ncrna 3:34179:34306:1
snR48-SNORD60/1-127         -------------------------------------------GTATAAGTGAAGAGTGGTTTAT---------TACCCC-ATGGCACCTC--TTGACCCAGGGTCT--CGTCCT---------GTC------CTT----GTCT-----ACG----AGAC-----TT----GAC-----ATTA---AGGACGC-AGGCCGCTGCTCTAAACGGACAA-----TCTGATACCTGAT-----------------------------------------------------------------
#=GS CNAG_12216/48-282 DE XR_001045514.1 Cryptococcus neoformans var. grubii H99 hypothetical RNA (CNAG_12216), ncRNA
CNAG_12216/48-282           TTGTGAGTCCTTTTCCTATCCTATCCTACCCTTTGAGCTCCAACTATAAGTGAAGAGTGGTTTAT---------TACCCC-ATGGCACCTC--TTGACCCAGGGCCT--CGTCCT---------GTC------CTT----GTCT-----ACG----AGAC-----TT----GAC-----ATTA---AGGACGC-AGGCCACTGCTCTAAACGGACAA-----TCTGATACATGATACTTCTCCCGCCACTGCTTTGAAACTGCATGTGGACAAGAGCTGATCGTTTGTTTTATTTAGTTG
#=GS H99/1-126 DE CP003822.1:40536-40661 Cryptococcus neoformans var. grubii H99 chromosome 3, complete sequence
H99/1-126                   --------------------------------------------TATAAGTGAAGAGTGGTTTAT---------TACCCC-ATGGCACCTC--TTGACCCAGGGCCT--CGTCCT---------GTC------CTT----GTCT-----ACG----AGAC-----TT----GAC-----ATTA---AGGACGC-AGGCCACTGCTCTAAACGGACAA-----TCTGATACATGAT-----------------------------------------------------------------
#=GS WM276/1-121 DE CP000288.1:c1929602-1929482 Cryptococcus gattii WM276 chromosome C, complete sequence
WM276/1-121                 -------------------------------------------TCATAAGTGAAGAGTGGTTTAT---------TACCCC-ATGGCACCTC--TTGACCCAGGGTCT--CGTCCT---------GTC------CT-----GTCT-----ACG----AGAC-----TT----GAC-----ATTA---AGGACGT-AGGCCGCTGCTCTAAACGGACAA-----TCTGATAC----------------------------------------------------------------------
#=GS R265/1-122 DE CP025759.1:c2167906-2167785 Cryptococcus gattii VGII R265 chromosome 1, complete sequence
R265/1-122                  -------------------------------------------TCATAAGTGAAGAGTGGTTTAT---------TACCCC-ATGGCACCTC--TTGACCCAGGGTCT--CGTCCT---------GTC------CTT----GTCT-----ACG----AGAC-----TT----GAC-----ATTA---AGGACGT-AGGCCACTGCTCTAAACGGACAA-----TCTGATAC----------------------------------------------------------------------
#=GS CryWin/1-128 DE CP034262.1:c34308-34181 Cryptococcus wingfieldii strain CBS7118 chromosome 2, complete sequence
CryWin/1-128                -------------------------------------------GTTTAAATGAAGAGTGGTTTT----------TACCCCTATGGCACCTC--TTGTACCAGGGTCT--CCTCCTT-------TGTCA------T----TGTCT-----GC-----GGACG----T----TGACG-----CC---AAGGTTG--AGGCCGATGCTCTAAACGGACAA-----TCTGATACCAGAT-----------------------------------------------------------------
#=GS KocImp/1-130 DE NBSH01000009.1:29466-29595 Kockovaella imperatae strain NRRL Y-17943 BD324scaffold_9, whole genome shotgun sequence
KocImp/1-130                --------------------------------------------TATAAATGAAGAGCGGCACATT--------TGCCCCATTGGCACCTC--TTGACCCAGGGCTATCCGAC-------------------GTCTC---ATGC----TCAGC---GCAT---------------------A------GTCG-ATAGCCGCTGCTCTCAACGGACA------TCTGATATCACACCATCCTATCCCA-----------------------------------------------------
#=GS SaiPod/1-131 DE RSCD01000006.1:c1221770-1221640 Saitozyma podzolica strain DSM 27192 scaffold_6, whole genome shotgun sequence
SaiPod/1-131                ---------------------------------------------CTGAATGAAGAGCGGCGAAA---------CGCCCCATTGGCACCTC--TTGACCCAGGGTCC--CGTCT-----C--TCGTCCAC----CC---TCCGG-----CTT----TCGGG----TCGA-GTGGGTGG---A----AGGGCG--GGGCCACTGCTCTCAACGGACAA-----TCTGACGTA---------------------------------------------------------------------
#=GS CryFla/1-131 DE CAUG01000273.1:15-145 Cryptococcus flavescens NRRL Y-50378 WGS project CAUG00000000 data, contig NODE_398_length_17465_cov_44_579216, whole genome shotgun sequence
CryFla/1-131                ---------------------------------------TCCCCCTCAAGTGAAGAGTGGTACTCA--------TACCCCATTGGCACCTC--TTGTTCCAGGGTGT--TGCAGC---AAGACCTC-------ATT----CACT------TC----GGTG-----TTC------GAGG---CG---GCTGCA--ACATCGATGCTCGCACCGGACA------TCTGATAAT---------------------------------------------------------------------
#=GS CrySki/1-139 DE BCHT01000008.1:c30508-30370 Cryptococcus skinneri DNA, scaffold: scaffold_7, strain: JCM 9039, whole genome shotgun sequence
CrySki/1-139                -----------------------------------------TCGCTTAAGTGAAGAGCGGCATGTCA-------TGCCCCATTGGCACCTC--TTGACCCAGGGTCC--ATCGTC---AACACCTCGCTTT----T----GCTT----AAGAC---AAGT---------AGAGTGAGG---GG---GGCGAT--GGGCCGTTGCTCTCAACGGACTA-----TCTGATGAG---------------------------------------------------------------------
#=GS PasPL2/1-122 DE JAMFRE010000005.1:323569-323690 Pascua sp. PL2904B ctg_5, whole genome shotgun sequence
PasPL2/1-122                --------------------------------------------TATATATGAAGAGTGGAAAATC--------TTCCCCATTGGCACCTC--TTGACCCAGGGTCC--GGCG-----ATGACC----------GC---CAGCA----CGTGT---TGCTG----C----------GG---CG-----CGCC--GGGTCGATGCTCTCACTGGAC-A-----TCTGATATCTT-------------------------------------------------------------------
#=GS KwoDej/1-127 DE ASCJ01000006.1:34246-34372 Kwoniella dejecticola CBS 10117 cont1.6, whole genome shotgun sequence
KwoDej/1-127                -------------------------------------------GTATAAATGAAGAGCGGCAAAAT--------TGCCCCATTGGCACCTC--TTGACCCAGGGTCC--GTCATC----C------------------GATATC----CCACAC--GATATC----------------ATACGA--GATGAC--GGGCCATTGCTCTCACCGGACTA-----TCTGATAACAACA-----------------------------------------------------------------
#=GS CryFag/1-133 DE BCHU01000010.1:63421-63553 Cryptococcus fagi DNA, scaffold: scaffold_9, strain: JCM 13614, whole genome shotgun sequence
CryFag/1-133                --------------------------------------------TATAAGTGAAGAGCGGCATGTCA-------TGCCCCATTGGCACCTC--TTGACCCAGGGTCC--ATGAAAT--CCA--TTTTT-----TTC----ATCAT-----TC----GTGAT----AGTC--AAAAA---------GTTTCAT--GGGTCGTTGCTCTCAACGGACTA-----TCTGATAACT--------------------------------------------------------------------
#=GS DioHun/1-127 DE JAMRJJ010000001.1:c5970089-5969963 Dioszegia hungarica strain Y1 Contig1, whole genome shotgun sequence
DioHun/1-127                -------------------------------------------GCTCGAATGAAGAGTTGCGATAT--------TGCACCATTGGCACCTC--TTGACCCAGGGTCT--GTCCTC----CA---AT------CTTC---CTCTGC-----TT----GCAGAG---TA-----AT------------GGGGAT--GGGCCGCTGCTCTCAACGGAC-A-----TCTGATATATACC-----------------------------------------------------------------
#=GS KwoHev/1-133 DE ASQC01000254.1:c3842-3710 Kwoniella heveanensis CBS 569 cont2.254, whole genome shotgun sequence
KwoHev/1-133                -----------------------------------------TATTATAAATGAAGAGCGGCAAAAT--------TGCCCCATTGGCACCTC--TTGACCCAGGGTCC--GTC-CTAC--C-----------------GTCTTCCATTC--AC--GAATGGAGGACATCC----------AGC--GTAGCGAT--GGGCCACTGCTCTCAACGGACTA-----TCTGATA-----------------------------------------------------------------------
#=GS BulAlb/1-130 DE CAMYTR010000051.1:c149119-148990 Bullera alba genome assembly, contig: jcf7180000012145, whole genome shotgun sequence
BulAlb/1-130                --------------------------------------------TATAAGTGAAGAGCGGCAAATA--------TGCCCCATTGGCACCTC--TTGACCCAGGGAAC--GACTC---TGCAC-TCCA----TCATC---GTTTC-----GAC----GAC-AC----T----TGGA------AC----GAGTC--GGACCGCTGCTCTCAACGGACAA-----TCTGATGCAC--------------------------------------------------------------------
#=GS KwoSha/1-128 DE NQVO01000053.1:c9362-9235 Kwoniella shandongensis strain CBS 12478 scaffold00053, whole genome shotgun sequence
KwoSha/1-128                ----------------------------------------------CGAATGAAGAGCGGCAATTA--------TGCCCCATTGGCACCTC--TTGACCCAGGGTCT--TGGCGTC-CAGCA-TCTTTT----AC----GAAAG-----TTG----CTTTT-----C--AAAGGA------C---GAT-CCG--AGGCCACTGCTCTCACCGGACTA-----TCTGATA-----------------------------------------------------------------------
#=GS NaeEnc/1-122 DE MCFC01000021.1:c76117-75996 Naematelia encephala strain 68-887.2 BCR39scaffold_21, whole genome shotgun sequence
NaeEnc/1-122                --------------------------------------------TATAAGTGAAGAGCGGCACATC--------TGCCCCATTGGCACCTC--TTGACCCAGGGTTC--GTCCT----GTA---CGT----------GCCCACC----CTTGA---GGTGGGC---T----ACG-------------GGGAC--GGGCCGCTGCTCTCAACGGAC-A-----TCTGATAC----------------------------------------------------------------------
Annot-SacCer-A/1-36         -------------------------------------------------RTGATGA----------------------AAAGACCGUGGAGA-CTGA----------------------------------------------------------------------------------------------------RTGATGA-------------------CTGA----------------------------------------------------------------------------
Annot-SacCer-B/1-36         -------------------------------------------------RTGATGA----------------------AAAGACCGUGGAGA---CTGA--------------------------------------------------------------------------------------------------RTGATGA-------------------CTGA----------------------------------------------------------------------------
#=GS Tree-snR48/5-95 DE Trichoderma reesei or Hypocrea jecorina from https://doi.org/10.1038/emboj.2011.148
Tree-snR48/5-95             -----------------------------------------------TTATGATGACACGAACACA---TTTTGTTTTATTTTGGCACCTCTTATGTTA---GGCC----------T---------------------CCT------TC----GGG----------------------T-------------GGTC---AATGAATGGACC-GGACT-----TCTGATC--------------------------------------------------------------------------
#=GS SacCer-snR48/1-110 DE Saccharomyces cerevisiae snR48 from https://doi.org/10.1038/emboj.2011.148
SacCer-snR48/1-110          -----------------------------------------------TAATGATGATTTCACTTATACCTATATGTTTTTTCTGGCATCTCTAATGTTA---GGATG---------T----GA---------------AGT----TTAAGT--ACT-------C--------TC-----------------CATTC---AATGAATACAATTTTTGACAATATCTGATT--------------------------------------------------------------------------
#=GS HumSap-SNORD60/1-80 DE Home sapiens U60 from https://doi.org/10.1038/emboj.2011.148
HumSap-SNORD60/1-80         -----------------------------------------------CTGTGATGAA------TTGCTT------TGACTTCTGACACCTCGTATGAAAA--CTGCA----------------------------------------CG------------------------------------------TGCAGTCTGATTATTTAGCAAGA---------CTGAGGCTT-----------------------------------------------------------------------
#=GC SS_cons                ---------------------------------------------------<<<<--------------------------------------<<<<-----((((((.((((((((.....(((((((((......(((((((((((......)))))))))))....)))))))))......)))))))).))))))--->>>>----------------->>>>----------------------------------------------------------------------------
//

  • Image source R2R-model:

# STOCKHOLM 1.0
#=GF RW van Nues, June 2023
#=GS snR48-SNORD60/2-122 DE intronic-boxCDsnoRNA-as-CNAG_12216-127nt ncrna 3:34179:34306:1
snR48-SNORD60/2-122         TATAAGTGAAGAGTGGTTTAT--TACCCC-ATGGCACCTCTTGACCCAGGGTCT--CGTCCT---------GTC------CTT----GTCT-----ACG----AGAC-----TT----GAC-----ATTA---AGGACGC-AGGCCGCTGCTCTAAACGGACAATCTGATAC
#=GS CNAG_12216/92-212 DE XR_001045514.1 Cryptococcus neoformans var. grubii H99 hypothetical RNA (CNAG_12216), ncRNA
CNAG_12216/92-212           TATAAGTGAAGAGTGGTTTAT--TACCCC-ATGGCACCTCTTGACCCAGGGCCT--CGTCCT---------GTC------CTT----GTCT-----ACG----AGAC-----TT----GAC-----ATTA---AGGACGC-AGGCCACTGCTCTAAACGGACAATCTGATAC
#=GS H99/1-121 DE CP003822.1:40536-40661 Cryptococcus neoformans var. grubii H99 chromosome 3, complete sequence
H99/1-121                   TATAAGTGAAGAGTGGTTTAT--TACCCC-ATGGCACCTCTTGACCCAGGGCCT--CGTCCT---------GTC------CTT----GTCT-----ACG----AGAC-----TT----GAC-----ATTA---AGGACGC-AGGCCACTGCTCTAAACGGACAATCTGATAC
#=GS WM276/2-121 DE CP000288.1:c1929602-1929482 Cryptococcus gattii WM276 chromosome C, complete sequence
WM276/2-121                 CATAAGTGAAGAGTGGTTTAT--TACCCC-ATGGCACCTCTTGACCCAGGGTCT--CGTCCT---------GTC------CT-----GTCT-----ACG----AGAC-----TT----GAC-----ATTA---AGGACGT-AGGCCGCTGCTCTAAACGGACAATCTGATAC
#=GS R265/2-122 DE CP025759.1:c2167906-2167785 Cryptococcus gattii VGII R265 chromosome 1, complete sequence
R265/2-122                  CATAAGTGAAGAGTGGTTTAT--TACCCC-ATGGCACCTCTTGACCCAGGGTCT--CGTCCT---------GTC------CTT----GTCT-----ACG----AGAC-----TT----GAC-----ATTA---AGGACGT-AGGCCACTGCTCTAAACGGACAATCTGATAC
#=GS CryWin/2-123 DE CP034262.1:c34308-34181 Cryptococcus wingfieldii strain CBS7118 chromosome 2, complete sequence
CryWin/2-123                TTTAAATGAAGAGTGGTTTT---TACCCCTATGGCACCTCTTGTACCAGGGTCT--CCTCCTT-------TGTCA------T----TGTCT-----GC-----GGACG----T----TGACG-----CC---AAGGTTG--AGGCCGATGCTCTAAACGGACAATCTGATAC
#=GS KocImp/1-113 DE NBSH01000009.1:29466-29595 Kockovaella imperatae strain NRRL Y-17943 BD324scaffold_9, whole genome shotgun sequence
KocImp/1-113                TATAAATGAAGAGCGGCACATT-TGCCCCATTGGCACCTCTTGACCCAGGGCTATCCGAC-------------------GTCTC---ATGC----TCAGC---GCAT---------------------A------GTCG-ATAGCCGCTGCTCTCAACGGACA-TCTGATAT
#=GS SaiPod/1-130 DE RSCD01000006.1:c1221770-1221640 Saitozyma podzolica strain DSM 27192 scaffold_6, whole genome shotgun sequence
SaiPod/1-130                -CTGAATGAAGAGCGGCGAAA--CGCCCCATTGGCACCTCTTGACCCAGGGTCC--CGTCT-----C--TCGTCCAC----CC---TCCGG-----CTT----TCGGG----TCGA-GTGGGTGG---A----AGGGCG--GGGCCACTGCTCTCAACGGACAATCTGACGT
#=GS CryFla/6-130 DE CAUG01000273.1:15-145 Cryptococcus flavescens NRRL Y-50378 WGS project CAUG00000000 data, contig NODE_398_length_17465_cov_44_579216, whole genome shotgun sequence
CryFla/6-130                CTCAAGTGAAGAGTGGTACTCA-TACCCCATTGGCACCTCTTGTTCCAGGGTGT--TGCAGC---AAGACCTC-------ATT----CACT------TC----GGTG-----TTC------GAGG---CG---GCTGCA--ACATCGATGCTCGCACCGGACA-TCTGATAA
#=GS CrySki/4-138 DE BCHT01000008.1:c30508-30370 Cryptococcus skinneri DNA, scaffold: scaffold_7, strain: JCM 9039, whole genome shotgun sequence
CrySki/4-138                CTTAAGTGAAGAGCGGCATGTCATGCCCCATTGGCACCTCTTGACCCAGGGTCC--ATCGTC---AACACCTCGCTTT----T----GCTT----AAGAC---AAGT---------AGAGTGAGG---GG---GGCGAT--GGGCCGTTGCTCTCAACGGACTATCTGATGA
#=GS PasPL2/1-119 DE JAMFRE010000005.1:323569-323690 Pascua sp. PL2904B ctg_5, whole genome shotgun sequence
PasPL2/1-119                TATATATGAAGAGTGGAAAATC-TTCCCCATTGGCACCTCTTGACCCAGGGTCC--GGCG-----ATGACC----------GC---CAGCA----CGTGT---TGCTG----C----------GG---CG-----CGCC--GGGTCGATGCTCTCACTGGAC-ATCTGATAT
#=GS KwoDej/2-122 DE ASCJ01000006.1:34246-34372 Kwoniella dejecticola CBS 10117 cont1.6, whole genome shotgun sequence
KwoDej/2-122                TATAAATGAAGAGCGGCAAAAT-TGCCCCATTGGCACCTCTTGACCCAGGGTCC--GTCATC----C------------------GATATC----CCACAC--GATATC----------------ATACGA--GATGAC--GGGCCATTGCTCTCACCGGACTATCTGATAA
#=GS CryFag/1-131 DE BCHU01000010.1:63421-63553 Cryptococcus fagi DNA, scaffold: scaffold_9, strain: JCM 13614, whole genome shotgun sequence
CryFag/1-131                TATAAGTGAAGAGCGGCATGTCATGCCCCATTGGCACCTCTTGACCCAGGGTCC--ATGAAAT--CCA--TTTTT-----TTC----ATCAT-----TC----GTGAT----AGTC--AAAAA---------GTTTCAT--GGGTCGTTGCTCTCAACGGACTATCTGATAA
#=GS DioHun/2-122 DE JAMRJJ010000001.1:c5970089-5969963 Dioszegia hungarica strain Y1 Contig1, whole genome shotgun sequence
DioHun/2-122                CTCGAATGAAGAGTTGCGATAT-TGCACCATTGGCACCTCTTGACCCAGGGTCT--GTCCTC----CA---AT------CTTC---CTCTGC-----TT----GCAGAG---TA-----AT------------GGGGAT--GGGCCGCTGCTCTCAACGGAC-ATCTGATAT
#=GS KwoHev/4-133 DE ASQC01000254.1:c3842-3710 Kwoniella heveanensis CBS 569 cont2.254, whole genome shotgun sequence
KwoHev/4-133                TATAAATGAAGAGCGGCAAAAT-TGCCCCATTGGCACCTCTTGACCCAGGGTCC--GTC-CTAC--C-----------------GTCTTCCATTC--AC--GAATGGAGGACATCC----------AGC--GTAGCGAT--GGGCCACTGCTCTCAACGGACTATCTGATA-
#=GS BulAlb/1-128 DE CAMYTR010000051.1:c149119-148990 Bullera alba genome assembly, contig: jcf7180000012145, whole genome shotgun sequence
BulAlb/1-128                TATAAGTGAAGAGCGGCAAATA-TGCCCCATTGGCACCTCTTGACCCAGGGAAC--GACTC---TGCAC-TCCA----TCATC---GTTTC-----GAC----GAC-AC----T----TGGA------AC----GAGTC--GGACCGCTGCTCTCAACGGACAATCTGATGC
#=GS KwoSha/1-128 DE NQVO01000053.1:c9362-9235 Kwoniella shandongensis strain CBS 12478 scaffold00053, whole genome shotgun sequence
KwoSha/1-128                --CGAATGAAGAGCGGCAATTA-TGCCCCATTGGCACCTCTTGACCCAGGGTCT--TGGCGTC-CAGCA-TCTTTT----AC----GAAAG-----TTG----CTTTT-----C--AAAGGA------C---GAT-CCG--AGGCCACTGCTCTCACCGGACTATCTGATA-
#=GS NaeEnc/1-122 DE MCFC01000021.1:c76117-75996 Naematelia encephala strain 68-887.2 BCR39scaffold_21, whole genome shotgun sequence
NaeEnc/1-122                TATAAGTGAAGAGCGGCACATC-TGCCCCATTGGCACCTCTTGACCCAGGGTTC--GTCCT----GTA---CGT----------GCCCACC----CTTGA---GGTGGGC---T----ACG-------------GGGAC--GGGCCGCTGCTCTCAACGGAC-ATCTGATAC
#=GC SS_cons                -------<<<<-----------------------------<<<<-----((((((.((((((((.....(((((((((......(((((((((((......)))))))))))....)))))))))......)))))))).))))))--->>>>------------>>>>---
#=GF R2R keep allpairs
//