U18-SNORD18

../../_images/u18_h99_igb.png

  • U18-SNORD18_intronic-boxCDsnoRNA

  • Within 1st intron of CNC03420 (CNAG_02714) mRNA for elongation factor 1-beta_EF1-beta

  • Predicted target in 25S rRNA: (gtctt)aaacAcggaccaagg

  • Orthologue of yeast U18, human SNORD18A

  • In yeast, modification was supported by the accessory guide while the A at the 5’ end of the C’ box and the G insertion in the D’ box played a role in multiple modification [van.Nues-2016], not seen in human nor expected for Cryptococcus.

../../_images/u18-aligned.png

>AE017343.1:1081077-1081180 Cryptococcus neoformans var. neoformans JEC21 chromosome 3 sequence
TTTCCTATGATGATATTTTGTTTTGGTCCGTGTTTCCGAGCTCAGCGGCGTAAGACCCCGCGACTTATGG
CGTTGAAGATACAACCTTTCCAAACCCTCTGATA







  • Image source:

# STOCKHOLM 1.0
#=GF RW van Nues, June 2023
#=GF https://coalispr.codeberg.page/paper
#=GS U18-SNORD18/1-121 DE intronic-boxCDsnoRNA-in-CNC03420 ncrna 3:1081077:1081184:1
U18-SNORD18/1-121              TTCTTGCTTTCCTATGATGATATT---TTGTTTTGGTCCGTGTTT-CCGA-GCTCAGCGGCGTAAGACCCCGCGACTTATGGCGTTGA-AGATACAACC---TTTCCAAACCCT--------CTGATACTTTCATCTT-
#=GS H99/1-119 DE CP003822.1:c934939-934821 Cryptococcus neoformans var. grubii H99 chromosome 3, complete sequence
H99/1-119                      ---CCGCCTTTCTGTGATGATATT---TTGTTTTGGTCCGTGTTT-CCGA-GCTCAGCGGCGTAAGACCCCGCGACTTATAGCGTTGA-AGATACAACC---TTTCCAAACCCT--------CTGATACTTCTCATCTT
#=GS CryWin/1-113 DE AWGH01000002.1:308062-308174 Cryptococcus wingfieldii CBS 7118 supercont1.2, whole genome shotgun sequence
CryWin/1-113                   --------TTTCTATGATGATCTA---CCGTTTTGGTCCGTGTTT-CCGA-GCTCAGCGGCTTAAGACCCCGCGCCTTTC-GCATTGA-AGATACAACCA---TTCCAAACCCA--------CTGACCCTTATCACCTT
#=GS R265/1-121 DE CP025759.1:1305605-1305725 Cryptococcus gattii VGII R265 chromosome 1, complete sequence
R265/1-121                     -TCTCGCCTTTCTATGATGATATT---TTGTTTTGGTCCGTGTTT-CCGA-GCTCAGCGGCGTAAGACCCCGCGACTTATAGCGTTGA-AGATACAACC---TTTCCAAACCCT--------CTGATTCTTCTCATCTT
#=GS KwoDej/1-101 DE ASCJ01000005.1:302519-302619 Kwoniella dejecticola CBS 10117 cont1.5, whole genome shotgun sequence
KwoDej/1-101                   ------------TATGATGATCTA---CCGTTTTGGTCCGTGTTT-CCGA-GCGCAGCGGCTTAAGACCCCGCGACTCAT-GCATTGA-AGATAAAAAC---TTTCCAAACTCA--------CTGATTCTT--------
#=GS KwoBes/1-104 DE ASCK01000010.1:c382429-382326 Kwoniella bestiolae CBS 10118 cont1.10, whole genome shotgun sequence
KwoBes/1-104                   -----------TCATGATGATATA---CCGTTTTGGTCCGTGTTT-CCGA-GCGCAGCGGCTTAAGACCCCGCGACTCAATGCATTGA-AGATAAAATA---TTTCCAAACTCA--------CTGATTCTTT-------
#=GS CutDas/1-103 DE BEDX01000001.1:3979302-3979404 Cutaneotrichosporon daszewskae DNA, scaffold: scaffold_1, strain: JCM_11166, whole genome shotgun sequence
CutDas/1-103                   --------TCTCTATGATGAACCA----TGTTTTGGTCCGTGTTT-CCGA-GCGTAGCGGCTTAAGACCCCGCGCCTTAA-GCGTTGA-AGACAACACCC--TTTCCAAACCCT--------CTGATCT----------
#=GS CrySki/1-107 DE BCHT01000003.1:c50503-50397 Cryptococcus skinneri DNA, scaffold: scaffold_2, strain: JCM 9039, whole genome shotgun sequence
CrySki/1-107                   ---------TTTTGTGATGATCTA---CCGTTTTGGTCCGTGTTT-CCGA-GCGCAGCGGCTTAAGACCCCGCGCCTTTAAGCATTGA-AGATAATAA-T-TTTTCCAAACCCA--------CTGACCCTTT-------
#=GS KocImp/1-103 DE NBSH01000009.1:c173312-173210 Kockovaella imperatae strain NRRL Y-17943 BD324scaffold_9, whole genome shotgun sequence
KocImp/1-103                   ----------TTCTTGATGATCTA---CCGTTTTGGTCCGTGTTT-CCGA-GCTCAGCGGCTTAAGACACCGCGCCTTTTGGCACTGA-AGACAACATC---TTTCCAAACTCA--------CTGACCAC---------
#=GS TakKor/1-105 DE BCKT01000003.1:c1856617-1856513 Takashimella koratensis DNA, scaffold: scaffold_2, strain: JCM 12878, whole genome shotgun sequence
TakKor/1-105                   ----------TCTCGGATGAACC----TTGTTTTGGTCCGTGTTT-CCGACGCTCAGCGGATTAAGACCCCGCGCCTTATAGCAGTGA-AGATACACCCA-TTTTCCAAACTAT--------CTGATCTC---------
#=GS VanFra/1-107 DE BEDY01000002.1:2429061-2429167 Vanrija fragicola DNA, scaffold: scaffold_2, strain: JCM 1530, whole genome shotgun sequence
VanFra/1-107                   ---------TCTCCTGATGAACC----TTGTTTTGGTCCGTGTTT-CCGA-GCGCAGCGGCTTAAGACCCCGCGACTCA-AGCATTGA-AGATAAACCCA-TTTTCCAAACTAT--------CTGATCCTATC------
#=GS TriFae/1-105 DE JXYK01000001.1:3999209-3999313 Trichosporon faecale strain JCM 2941 scaffold_0001, whole genome shotgun sequence
TriFae/1-105                   ---------TTTCATGATGAACAT---TTGTTTTGGTCCGTGTTT-CCGA-GCT--GCGGATTAAGACCCCGCGACTATG-GCGTTGA-CGACAACACCT--CTTCCAAACTAT--------CTGACTCTTTC------
#=GS KwoPin/1-103 DE ASCL01000006.1:353456-353558 Kwoniella pini CBS 10737 cont1.6, whole genome shotgun sequence
KwoPin/1-103                   ----------TTTATGATGATCTA---CCGTTTTGGTCCGTGTTT-CCGA-GCGCAGCGGCTTAAGACCCCGCGACTCAT-GCATTGA-AGATAAAATTA--TTTCCAAACTCA--------CTGATCTC---------
#=GS KwoMan/1-108 DE ASQD01000040.1:c172279-172172 Kwoniella mangroviensis CBS 10435 cont2.40, whole genome shotgun sequence
KwoMan/1-108                   ---------TACTATGATGATCTA---CCGTTTTGGTCCGTGTTT-CCGA-GCGCAGCGGCTTAAGACCCCGCGACTCAATGCATTGA-AGATAAAATTA--TTTCCAAACTCA--------CTGATTCTCTC------
#=GS VanPse/1-102 DE CP086715.1:c2041037-2040936 Vanrija pseudolonga isolate DUCC4014 chromosome 2
VanPse/1-102                   --------TCACCATGATGAACC----TTGTTTTGGTCCGTGTTT-CCGA--GGTAGCGGATTAAGACCCCGCGCCTTT--ACATTGA-AGATACAACCT--TTTCCAAACTAT--------CTGATCCC---------
Annot/1-44                     -------------RTGATGA---------AGGAACCAGGCACAAA-CTGA------------GUUCUG----------------RTGA-TGA------------------------------CTGA-------------
#=GS SacCer-snR18-U18/1-102 DE Saccharomyces_cerevisiae U18
SacCer-snR18-U18/1-102         ---------GTGAATGATGAATTTA--ATTCTTTGGTCCGTGTTT-ATGA--------------TGGGAAGTAAGACCCCCGATATGAGTGACAAAAGAGATGTGGTTGACTATCACAGTATCTGACG-----------
#=GS HomSap-SNORD18A/1-70 DE Homo_sapiens SNORD18A
HomSap-SNORD18A/1-70           --------CAGTAGTGATGAAATTCCACTTCATTGGTCCGTGTTT-CTGA--------ACCACATGATTTTCTC-----------GGA-TGTT-----------------------------CTGATG-----------
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