snR62-SNORD34

../../_images/snR62_h99_igb.png

  • snR62_intronic-boxCDsnoRNA-81nt-in-CNE03520 (CNAG_02185)

  • Within 1st intron of CNE03520 for RCM1, 28S rRNA (Cytosine-C(5))-Methyltransferase that modifies C2278 in yeast [Sharma-2013]

../../_images/Nop2-Rcm1-targets-opt.svg

  • Putative CNE03520 target is in 25S rRNA: ggtagcCaAAtgcc

  • Predicted target of snR62 in 25S rRNA: (atgga)acaaTgtagataag

  • Accessory base-pairing is provided for sequence in between round brackets by conserved motif upstream of the D box.

  • Orthologue of yeast snR62, human SNORD34

../../_images/snR62-align.png

>AE017345.1:994452-994532 Cryptococcus neoformans var. neoformans JEC21 chromosome 5 sequence
TGTCATGATGTTTGTAAATCTTATCTACATTATCAGAACAACACATGTTGTACACTTTATCCATTCTTAC
ACCTGAACTCT







  • Image source snR62:

# STOCKHOLM 1.0
#=GF RW van Nues, July 2023
#=GF https://coalispr.codeberg.page/paper
Annot/1-41                       -----RTGATGA---------------GAAUAGAUGUAAcACTGA----------------------RTGATGA--------AGGUA--------CTGA-----
#=GS snR62/1-81 DE intronic-boxCDsnoRNA-81nt-in-CNE03520 ncrna 5:994451:994532:1
snR62/1-81                       -TGTCATGATGTTTGTAAA-------TCTTATCTACATTATCAGA--ACAACA-----CA-----TGTTGTACACTTTA---TCCATTCTTACACCTGAACTCT
#=GS snR62-in-CNAG_02185/1-81 DE CP003825.1:959466-959546 Cryptococcus neoformans var. grubii H99 chromosome 6, complete sequence
snR62-in-CNAG_02185/1-81         -TGTCATGATGTTTGTAAA-------TCTTATCTACATTATCAGA--ACAACA-----CA-----TGTTGTACACTTTA---TCCATTCTTACACCTGAACTCT
#=GS WM276/1-80 DE CP000290.1:893025-893105 Cryptococcus gattii WM276 chromosome E, complete sequence
WM276/1-80                       -TGTCATGATGTTTGTAAA-------TCTTATCTACATTATCAGA--ACAACA-----CA-----TGTTGTACA-TTTA---TCCATTCTTACACCTGAACTAT
#=GS R265/1-81 DE CP025764.1:c440698-440618 Cryptococcus gattii VGII R265 chromosome 6, complete sequence
R265/1-81                        -TGTCATGATGTTTGTAAA-------TCTTATCTACATTATCAGA--ACAACA-----CA-----TGTTGTACAATTTA---TCCATCCTTACACCTGAACCCT
#=GS KwoHev/2-85 DE ASQC01000122.1:20619-20703 Kwoniella heveanensis CBS 569 cont2.122, whole genome shotgun sequence
KwoHev/2-85                      -CGTCATGATGCCTTGAAAA------ACTTATCTACATTATCAGAATACAACA-----AA-----TGTTGTACAACCAAT--TCCAT-TTTCAACCTGAACAAA
#=GS KwoSha/2-79 DE NQVO01000022.1:170148-170230 Kwoniella shandongensis strain CBS 12478 scaffold00022, whole genome shotgun sequence
KwoSha/2-79                      -CGTCGTGATGCTTTACAA-------TCTTATCTACATTATCAGAA-ACAAC-----CAAT-----GTTGTACACCATA---TCCAT----GTAACTGAACTCC
#=GS KwoMan/1-82 DE ASQF01000015.1:c4634-4553 Kwoniella mangroviensis CBS 8886 cont1.15, whole genome shotgun sequence
KwoMan/1-82                      -CGTCATGATGTCAAAATA-------TCTTATCTACATTATCAGAA-CTTAA----ATAATG----TTAAGACAACTTAT--TCCAT---GTTAACTGAACTAT
#=GS CryAmy/1-80 DE MEKH01000006.1:621994-622073 Cryptococcus amylolentus CBS 6273 supercont2.6, whole genome shotgun sequence
CryAmy/1-80                      -TGTTATGATGTCTGCAA--------TCTTATCTACATTGTCAGAA-CCTAC------AT------GTTTGACAATCATTTTTCCAT--ATATATCTGAACTCT
#=GS CryFlo/1-80 DE RRZH01000004.1:c1074335-1074256 Cryptococcus floricola strain DSM 27421 chromosome 4, whole genome shotgun sequence
CryFlo/1-80                      -TGTTATGATGTCTACAA--------TCTTATCTACATTGTCAGAA-CCTAC------AT------GTTTGACAATCATTTTTCCAT--ATATATCTGAACTCT
#=GS CryWin/1-80 DE AWGH01000049.1:46783-46862 Cryptococcus wingfieldii CBS 7118 supercont1.49, whole genome shotgun sequence
CryWin/1-80                      -TGTTATGATGTCTACAA--------TCTTATCTACATTGTCAGAA-CCTAC------AT------GTTTGACAATCATTTTTCCAT--ATATATCTGAACTCT
#=GS SacCer-snR62/1-100 DE 25S:U1888 Saccharomyces_cerevisiae snR62 http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi?mode=sno_info&id=Saccharomyces_cerevisiae300066
SacCer-snR62/1-100               -TTTTATGATGAATTTATGTTTTCAATCTTATCTACATTATCTGAATTAATAGCTAACAATAGTTATAATGGAAGATATACGACTATCAACAATTCTGAAA---
#=GS SNORD34/1-66 DE Homo_sapiens SNORD34 28S:U2824  http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi?mode=sno_info&id=Homo_sapiens300565
SNORD34/1-66                     CGTCCATGATGTT---------CCGCAACTACCTACATTGTTTGA--TCCTCA------------TGAAAGCAGCAC---------------TGGCTGAGACGC
#=GC SS                          ((((-------------------------------------------(((((--------------)))))--------------------------))))---
//