snR76-SNORD88

../../_images/snR76_h99_igb.png

  • snR76_intronic-boxCDsnoRNA-118nt-in-CNL04010

  • Within 1st intron of CNL04010 (CNAG_05228) for U3 small nucleolar ribonucleoprotein LCP5

  • Predicted target in 25S rRNA: (tttctg)ccCagtgct

  • Orthologue of yeast snR76, human SNORD88A

  • Conserved stem-loop near D-guide with ability to provide accessory base-paring via tagaaa to extend the complimentarity (in brackets) with the sequence targeted by the D’ guide

../../_images/snR76-align.png

>AE017352.1:c99100-98983 Cryptococcus neoformans var. neoformans JEC21 chromosome 12 sequence
ATCCGATGATGCTACCGCACTGGGCACTGAGCACCTCCAAAAGAGAGGTGTACAGATTACACGCCTATTC
CACCTTAGGAGGGTGGAGCGAGCCTAGAAAACTCGCGACTGAGGATTC







  • Image source snR76:

# STOCKHOLM 1.0
#=GF RW van Nues, August 2023
#=GF https://coalispr.codeberg.page/paper
Annot/1-39                  -----------RTGATGA-----UCGUGACCCGUCTGA----------------------------------RTGATGA------------------------------------------GUCUUU----------CTGA----------
#=GS snR76/1-118 DE intronic-boxCDsnoRNA-118nt-in-CNL04010 ncrna 12:98982:99100:-1
snR76/1-118                 ------ATCCGATGATGCT--ACCGCACTGGGCACTGAGCAC-CTC----CAAAAGA-------GAGGTGTACAGATTACA-CGCCTA-----TTCC-ACCTTAGGAGGGTGGAGCGAGCCTAGAAAACTCGCGA--CTGAGGATTC----
#=GS R265/1-119 DE CP025772.1:247803-247921 Cryptococcus gattii VGII R265 chromosome 14, complete sequence
R265/1-119                  ------ATCCGACGATGCT--ACCGCACTGGGCACTGAGTACCCTC----AAAAAGA-------GAGGTATACAGATTACA-CGCCTA-----TTCC-ACCTTAGGAGGGTGGAGCGAGCCTAGAAAACTCGCGA--CTGAGGATTC----
#=GS WM276/1-119 DE CP000295.1:c245065-244947 Cryptococcus gattii WM276 chromosome J, complete sequence
WM276/1-119                 ------ATCCGACGATGCT--ACCGCACTGGGCACTGAGTACCCTC----AAAAAGA-------GAGGTATACAGATTACA-CGCCTA-----TTCC-ACCTTAGGAGGGTGGAGCGAGCCTAGAAAACTCGCGA--CTGAGGATTC----
#=GS in-CNAG_05228/1-116 DE CP003823.1:783345-783460 Cryptococcus neoformans var. grubii H99 chromosome 4, complete sequence
in-CNAG_05228/1-116         ------ATCCTATGATGCT--ACCGCACTGGGCACTGAGCAC-CT-----CAAAAAA--------GGGTGTACAGATTACA-CGCCTA-----TTCC-ACCTTAGGAGGGTGGAGCGAGCCTAGAAAACTCGCGA--CTGAGGATTC----
#=GS KwoSha/1-125 DE NQVO01000023.1:c297760-297636 Kwoniella shandongensis strain CBS 12478 scaffold00023, whole genome shotgun sequence
KwoSha/1-125                ----ATTCCCGATGATGCT--ACTGCACTGGGCACTGAGCTC-CTC-----CAAAGA------GAGCGAGTATAGATTATA-CGCCAATTTGAATCC-ACTTTAGGAGAGTGGAGCGAGCCTAGAAAACTCGTGA--CTGAGGGAAT----
#=GS BulAlb/1-122 DE CAMYTR010000156.1:c747756-747635 Bullera alba genome assembly, contig: jcf7180000012257, whole genome shotgun sequence
BulAlb/1-122                ----ACTCCCGATGATGCT--ACTGCACTGGGCACTGAGTCCTTCC------AAAGA-------GGAGGAC-CTGATTAGA-CGCCA-TTTGAATCC-ACTTTAGTAGAGTGGAGCGAGCCTAGAAAACTCGTGA--CTGAGGGAAC----
#=GS CryWin/1-116 DE CP034264.1:c1230547-1230432 Cryptococcus wingfieldii strain CBS7118 chromosome 4, complete sequence
CryWin/1-116                ----GTATGCTGTGATGTTT--CCGCACTGGGCACTGAG-CACT-------CAAAGA--------AGTGACATAGATTACA-CGCCTA-----TTCC-ACCTTAGTAGGGTGGAGCGAGCCTAGAAACCTCGCGA--CTGAGCATAC----
#=GS CryFlo/1-116 DE RRZH01000006.1:c1223616-1223501 Cryptococcus floricola strain DSM 27421 chromosome 6, whole genome shotgun sequence
CryFlo/1-116                ----GTATGCTGTGATGTTT--CCGCACTGGGCACTGAG-CACT-------CAAAGA--------AGTGACATAGATTACA-CGCCTA-----TTCC-ACCTTAGCAGGGTGGAGCGAGCCTAGAAACCTCGCGA--CTGAGCATAC----
#=GS CryAmy/1-116 DE MEKH01000004.1:339812-339927 Cryptococcus amylolentus CBS 6273 supercont2.4, whole genome shotgun sequence
CryAmy/1-116                ----GTATGCTGTGATGTTT--CCGCACTGGGCACTGAG-CACT-------CAAAGA--------AGTGACATAGATTACA-CGCCTA-----TTCC-ACCTTAGCAGGGTGGGGCGAGCCTAGAAACCTCGCGA--CTGAGCATAC----
#=GS CrySki/1-114 DE BCHT01000010.1:336663-336776 Cryptococcus skinneri DNA, scaffold: scaffold_9, strain: JCM 9039, whole genome shotgun sequence
CrySki/1-114                ----GATCCCAATGATGTTT--CCGCACTGGGCACTGAG-CTC---------AAAAA---------GAGCCATTGATTATAA-GCCTC----AATCC-TCCTTAGAAGGGTGGAGCGAGCCTAGAAAACTCGTGA--CTGAGGGATC----
#=GS KwoHev/1-135 DE ASQC01000028.1:c165278-165144 Kwoniella heveanensis CBS 569 cont2.28, whole genome shotgun sequence
KwoHev/1-135                ----TACCCCAAAGATGCT--ACCGCACTGGGCACTGAAAACCCTGTCCCGTCAAGTTTACGAGGACTTGGTCAGATTATAACGCCTA---TTATCC-ACCTTAGGAGGGTGGAGCGAGCCTAGAAAACTCGTGA--CTGAGGGGTA----
#=GS CryFla/1-123 DE CAUG01000471.1:c32949-32827 Cryptococcus flavescens NRRL Y-50378 WGS project CAUG00000000 data, contig NODE_1025_length_46991_cov_46_464535, whole genome shotgun sequence
CryFla/1-123                ----TCCATTCATGATGCT--ACCGCACTGGGCACTGAACGAGCATCA-----AAGAA---TGA--CTCGTGTAGCTTATAACGCCAT-----ATCC-ACCTTAGCAGGGTGGAGCGAGCCTAGAAAACTCGTGA--CTGACTACTT----
#=GS PapTer/1-123 DE JAHXHD010001494.1:1570-1692 Papiliotrema terrestris strain LS28 scaffold-1493, whole genome shotgun sequence
PapTer/1-123                ----CCCTCTCATGATGCT--ACCGCACTGGGCACTGAACGAGCATCG-----AAGAA---TGA--CTCGTGCTGCTTATAACGCCTT-----ATCC-ACCTTAGCAGGGTGGAGCGAGCCTAGAAAACTCGTGA--CTGATCACTA----
#=GS PapLau/1-126 DE JAAZPW010000040.1:c8478-8353 Papiliotrema laurentii strain IF7SW-B5 scaffold96_cov184, whole genome shotgun sequence
PapLau/1-126                ----TTTATTCGTGATGCT--ACCGCACTGGGCACTGAGCTTCATGGT--CAAAAGA-----ACCTTGAGCTTTGATTATAACGCCAT-----GACC-ACCTTAGTAGGGTGGTGCGAGCCTAGAAAACTCGTGA--CTGAACAATA----
#=GS CryGC4/1-118 DE JALPCA010001158.1:2592-2709 Cryptococcus sp. GC_Crypt_4 iso00_46_1196, whole genome shotgun sequence
CryGC4/1-118                ----ACTCCCTATGATGTT--ACCGCACTGGGCACTGAG-CACTC-----AAAAA---------GAGTGACTTTGATTATA-CGCTTA---ATATCC-ACTGTAGTA-GGTGGAGCGAGCCTAGAAAACTCGTGG--CTGAGGGGCT----
#=GS TreFuc/1-117 DE LBGW01000442.1:c20667-20551 Tremella fuciformis strain tr26 contig442, whole genome shotgun sequence
TreFuc/1-117                ----ACACCCGAAGATGAA---ACGCACTGGGCACTGAGCCGGC------CAAAAGA--------GCCGAGCTTGATTA-GACGCAAC-----ATCC-TCCTTAGTAGGGAGGAGCGAGCCTAGAAAACTCGCGA--CTGAGGGCAC----
#=GS TriInk/1-102 DE QAEE01003685.1:c878-777 Trichosporon inkin strain ATCC 18020 NODE_3737_length_1852_cov_5.00282_ID_84190, whole genome shotgun sequence
TriInk/1-102                ----GACCCCGATGATGCTT--CCGCACTGGGCACTGAG--------------AC----------------CATGATTACACTGCCTG------TCC-ACCTTAGGAGGGTGGAGCGAGCCTAGAAAACTCGTGA--CTGAGGGGAA----
#=GS TriAsa/1-102 DE JAMALV010000017.1:307540-307641 Trichosporon asahii strain M6011 ctg_17, whole genome shotgun sequence
TriAsa/1-102                ----GTCCCCGATGATGTTT--CCGCACTGGGCACTGA---------------ATA----------------ATGATTACAACGCCTA------TCCAACCTTAGGAGGGTGGAGCGAGCCTAGAAAACTCGTGA--CTGAGGGGAA----
#=GS TriOvo/1-111 DE JXYN01000007.1:c1593840-1593730 Trichosporon ovoides strain JCM 9940 scaffold_0007, whole genome shotgun sequence
TriOvo/1-111                ----TTCCCCGATGATGTTT--CCGCACTGGGCACTGAGTGT-----------AACT-----------ATCCAAGATTACAACGCCTA------TCCAACCTTAGGAGGGTGGAGCGAGCCTAGAAAACTCGTGA--CTGAGGGGTT----
#=GS SacCer-snR76/1-109 DE 25S:C2197 Saccharomyces_cerevisiae snR76 http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi?mode=sno_info&id=Saccharomyces_cerevisiae300013
SacCer-snR76/1-109          ----AATGGAAATGAGGATCCACAGCACTGGGCACTGAGGGGGA-------AACAAAT----ATCCTTTCAAATGAGTGACAATGCTTT------------------------AGCGGGCCTAGAAAACCCGCGCAACTGATCCATTG---
#=GS SNORD88A/1-97 DE 28S:C3680  Homo_sapiens SNORD88A http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi?mode=sno_info&id=Homo_sapiens300570
SNORD88A/1-97               CCGGGGCCTCCATGATGT---CCAGCACTGGGCTCCGACT-------------GCC---------------ACTGAGGACA-----------------------CGGTGCCCCCCGGGACCTTTGACACCCGGGGGTCTGAGGGGCCCTGG
#=GC SS                     -------((((---------------------------((((.(((-----------------)))))))------------------------(((-(((-------))))))(((((.........)))))--------))))------
//