snR66¶
snR66_processed-boxCDsnoRNA-118nt-as-URS000035E911_235443
Processed from dedicated transcript (as CNAG_12022)
Predicted target in 25S rRNA: (ctgttg)agctTgactcta
Orthologue of yeast snR66
Various conserved segments could be accessory guides [van.Nues-2011], with tgacag just upstream of the D-box extending the modification guide (brackets).
These sections could determine different snoRNA conformations or interact in trans with (pre-)rRNA; complimentary regions are:
>AE017341.1:c347820-347703 Cryptococcus neoformans var. neoformans JEC21 chromosome 1, complete sequence CGCCCAGTGATGAGAATTGCCAACACAATAGAGTCAAGCTCGGAGACCCTAGTCGCCTCTTCGGATGGTG CTGGTCTATGTCGAGCACTGGCCTGTTTGACAGTTACTGAGGGTTCAT
Image source:
# STOCKHOLM 1.0
#=GF RW van Nues, June 2023
#=GF https://coalispr.codeberg.page/paper
Annot/1-58 ---------------------------------------------------------------------------------------------------------------------------------------------------------RTGATGA---GGUGGUUG-----AUCUCAGUUCGACTGA-------------------------------------------RTGATGA-aCUGGGCAG-GTTGTC-----CTGA--------------------------------------------------------------------------------------------------------------------------------------------------------------
#=GS snR66/6-123 DE processed boxCDsnoRNA-120nt-as-URS000035E911_235443 ncrna 1:347702:347818:-1
snR66/6-123 ---------------------------------------------------------------------------------------------------------------------------------------------------CGCCCAGTGATGAGAATTGCCAACACA-ATAGAGTCAAGCTCGGAGACCCTAGTCGCCTCT----TC---GGATGGTGCTGGTCTATGTCGAGCACTGGCCTGTT-TGACAGTT--ACTGAGGGTTCAT------------------------------------------------------------------------------------------------------------------------------------------------------
#=GS H99/1-414 DE CNAG_12022 ENA|CP003820.1:382584..382997:ncRNA|CP003820.1:382584..382997:ncRNA.1 Cryptococcus neoformans var. grubii H99 hypothetical RNA
H99/1-414 AAACATCTCTATTTTACAAGTTAGAGACGAATCAACAGGGCTACAGGACACAGCAAGCCAGGTGGCACATCATGTGGCGCAAGGTCGGTCGTGTCTTGTATTCTTGTTGCTCTTCATCTACCTTTCCTTTTCGTCTTTTTTCTTTCACGCCCGGTGATGAGAATTGCCAACACA-ATAGAGTCAAGCTCGGAGACCCTAGTCGCCTCT----TC---GGATGGTGCTGGTCTATGTCGAGCACTGGCCTGTT-TGACAGTT--ACTGAGGGTTCATCTTTTTCGTGTCTTTCATCATGTCGCTCCTTATCTTGGATCCATCAAACAACCTGTCAACATTTTGGTTCCAAGGTCTCATTTATTATGAAAATATATGCATGTATTGCAGATCAACTGAACAT-GTTTCTGCCAATCAATCCCAAATAG
#=GS H99-snR66/148-263 DE CNAG_12022 ENA|CP003820.1:382584..382997:ncRNA|CP003820.1:382584..382997:ncRNA.1 Cryptococcus neoformans var. grubii H99 hypothetical RNA
H99-snR66/148-263 ---------------------------------------------------------------------------------------------------------------------------------------------------CGCCCGGTGATGAGAATTGCCAACACA-ATAGAGTCAAGCTCGGAGACCCTAGTCGCCTCT----TC---GGATGGTGCTGGTCTATGTCGAGCACTGGCCTGTT-TGACAGTT--ACTGAGGGTTC--------------------------------------------------------------------------------------------------------------------------------------------------------
#=GS R265/1-393 DE ENA|CP025762.1:341899..342291:ncRNA|CP025762.1:341899..342291:ncRNA.1 Cryptococcus gattii VGII R265 hypothetical RNA
R265/1-393 -TCACAAGTCACAACACAGATCGGCGATCAACCAACTGGACTACAGGACACAGCAAGCTAGGTGGCACTTTATGTGGCGCAAAGCCGGTTGTGTCTTGTATTCTTGTTGCTCTTCATCTACTCTTTTTTTTTATCTTTTTATTTTTATGCCCAGTGATGAGAATTGCCAACACA-ATAGAGTCAAGCTCGGAGACCCTAGTCGCCTCT----TC---GGATGGTGCTGGTCTATGTCGAGCACTGGCCTGTT-TGACAGTT--ACTGAGGGTTCATCTTTTTCGTGTCTTTTT--ATGTC-TTCCT------TTGTCTAGCATCCACCAAACAAGCTGCCAAAGTTCGAGGTCATTTATC--ATGAACACCTATGCATGTATTGCAAATCAACTGAACATTGATTCTGCCAATCAA----------
#=GS CutCut/1-119 DE LTAL01000688.1:c26738-26620 Cutaneotrichosporon cutaneum strain ACCC 20271 contig688, whole genome shotgun sequence
CutCut/1-119 ------------------------------------------------------------------------------------------------------------------------------------------------CTCCACCCTATGATGAGAATTGCCAACAAAT-TAGAGTCAAGCTCGGAGACCCTAGTCGCGACCT---TC----GGGCGTGCTGGTTAATGCCGAGTGTCGGCCTGTC-TGACAGTT-CGCTGAGGGCT---------------------------------------------------------------------------------------------------------------------------------------------------------
#=GS Nae/1-116 DE MCFC01000009.1:c77628-77513 Naematelia encephala strain 68-887.2 BCR39scaffold_9, whole genome shotgun sequence
Nae/1-116 -------------------------------------------------------------------------------------------------------------------------------------------------TTCACCCAGTGATGAGACTTGCCAACACA-ATAGAGTCAAGCTCTTAGACCCTAGTCGCCTT-----TT-------GGTGCTGGTCAGAGACGAGCACTGGCCTGTTTTGACAGTT-TACTGAGGGATAT-------------------------------------------------------------------------------------------------------------------------------------------------------
#=GS CryWin/1-121 DE AWGH01000001.1:c1175943-1175823 Cryptococcus wingfieldii CBS 7118 supercont1.1, whole genome shotgun sequence
CryWin/1-121 --------------------------------------------------------------------------------------------------------------------------------------------------ACGCCCTATGATGAGAGTTGCCAACAC--ATAGAGTCAAGCTCGGAGACCCTAGTCGCTTTCT---TC---GGATCGTGCTGGTCATTGTCGAGTGTCGGCCTGTT-TGACAGTAAAACTGAGGGCTCAT------------------------------------------------------------------------------------------------------------------------------------------------------
#=GS CrySki/1-121 DE BCHT01000002.1:c1897-1777 Cryptococcus skinneri DNA, scaffold: scaffold_1, strain: JCM 9039, whole genome shotgun sequence
CrySki/1-121 ------------------------------------------------------------------------------------------------------------------------------------------------ATATCCCCTATGATGAGAATTGCCAACAC--ATAGAGTCAAGCTCGGAGACCCTAGTCGCCCGTT---TC--GACGGTGTGCTGGTCCATGTCGAGGTCTGGCCTGTT-TGACAGTT-TACTGAGGGTCT--------------------------------------------------------------------------------------------------------------------------------------------------------
#=GS CryFagi/1-114 DE BCHU01000002.1:574810-574923 Cryptococcus fagi DNA, scaffold: scaffold_1, strain: JCM 13614, whole genome shotgun sequence
CryFagi/1-114 -----------------------------------------------------------------------------------------------------------------------------------------------------CCCAGTGATGAGAATTGCCAACAA--ATAGAGTCAAGCTCGGAGACCCTAGTCGCATCCT---TC--GGGATTGTGCTGGTCATTGTCGAGGTCTGGCCTGTC-TGACAGTT-TACTGAGGGT----------------------------------------------------------------------------------------------------------------------------------------------------------
#=GS KwoShan/1-123 DE NQVO01000063.1:c20954-20832 Kwoniella shandongensis strain CBS 12478 scaffold00063, whole genome shotgun sequence
KwoShan/1-123 ---------------------------------------------------------------------------------------------------------------------------------------------------CGCCCAACGATGAGAATTGCCAACAAA-ATAGAGTCAAGCTCGGAGACCCTAGTCGCCTTTCCT-TC-GGGGGAGGTGCTGGTTAATGTCGAGCACTGGCCTGTTATGACAGTT-TACTGAGGGTTC--------------------------------------------------------------------------------------------------------------------------------------------------------
#=GS TakKor/2-415 DE BCKT01000006.1:c1137184-1136770 Takashimella koratensis DNA, scaffold: scaffold_5, strain: JCM 12878, whole genome shotgun sequence
TakKor/2-415 CTCATGCAGCAGTATCCCCTTCACCCGTGTTAGCTTCTGGCGGTTTTTAGCATCTACTCATGTCCTCTCTCAACATTGACGTCTGCCCCGACCGCCTCCCAACCCTCCCCCCTTCTAACCCCTGTCCCCCTACCCCCCTCCCCTCCTCCCCCTGTGATGAGAATTGCCAACACATATAGAGTCAAGCTCGTAGACCCTAGTCGCCCT-----TC-----GGGGTGCTGGTCTATGCCGAGCACTGGCCTGTTTTGACAGTT-TACTGAGGGCTCAACTACCTAGTCTCCCAATGCACCCATTACTGTTATGTCCCTGCTGCATGATGCCGGATCCCTTTCACGGCAGTATCCCTGATAGGTATAAAGGTATAAAAGATAGAAAGACCAAAGATGAAAGTAATAGGAAGAGCCAATGTTCGTTTTG-
#=GS VanHum/7-421 DE QKWK01000001.1:457854-458274 Vanrija humicola strain CBS 4282 CBS4282_scaffold01, whole genome shotgun sequence
VanHum/7-421 TGCCAGGCGATACTCACCGCGGCCTACGCACACCTTCCTCCCCAGCTCCACACCGCTCCCCTCCCCTCCCCTCCCCTCCCCTCCCCTCCTCGTCCCAGTCCCGTCCTTCTTCCGCCTCTCCTCCTCTCCCCATCCCATCCCCTTCCCTACCCGATGATGAGAGTTGCCAACACAA-TAGAGTCAAGCTCGGAGACCCTAGTCGCTACCT---TC---GGGA-GTGCTGGTTAATGCCGAGTGTCGGCCTGTT-TGACAGTAACACTGAGGGCTCTTCTTTCTCCATTCTTTCCTATCTTCCAGCTATCTCCTCCCCTGTGCGGGCGCGGTGTTCGTAGCATATCTCATTACTTGACATGCACATGGTGTTTGGGCGTTTTTGGGTGCTTTATGGTGTTCTACACAGAAACAGGAAGATGACGCG--
#=GS TriGue/1-409 DE BCJX01000001.1:3202421-3202835 Trichosporon guehoae DNA, scaffold: scaffold_0, strain: JCM 10690, whole genome shotgun sequence
TriGue/1-409 ----AAAGATGCTGGCCCTAACACTCCCCGCATCTTTTCACCACCAACCGTCCGCGACAGTGCCGGCGCGATGAGGCGGCGCAAACCCGTCCCCTCGTCGTCTGGCCAAGTGTCTCTCTTCCCCTCATCTCCCCTCCTTTCCCCATCCACCTCATGATGAGAATTGCCAACAAAT-TAGAGTCAAGCTCGGAGACCCTAGTCGCCGC-----TT-----GCGGTGCTGGTTAATGCCGAGTGTCGGCCTGTC-TGACAGTT-CACTGAAGGTCTTTCATCCTTGTCCTTTTCCGTTGTCTACTAGTGTTTTGTCCCTTGTCCTGCTATGAATATTATGGAAATCGAAAGCGAAAAGGAGATGGAGTTGCATTACACTTACGACGATGGAGGCTGACTGGCAAATTGAAGTGACCAAGGGCAAGGGC
#=GR SS ---------------------------------------------------------------------------------------------------------------------------------------------------------------------<<<---------------------------------((((((------------))))))------------------->>>((((----))))-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
#=GR SS ------------------------------------------------------------------------------------------------------------------------------------------------------------------<<<<-<<--------------------------------((((((------------))))))---------------------------->>->>>>----------------------------------------------------------------------------------------------------------------------------------------------------------------------
#=GC SS -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------<<<<-<<---------------((((((------------))))))------------------------>>-->>>>-------------------------------------------------------------------------------------------------------------------------------------------------------------------------
#=GS SacCer-snR66/1-85 DE http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi?mode=sno_info&id=Saccharomyces_cerevisiae300061
SacCer-snR66/1-85 -----------------------------------------------------------------------------------------------------------------------------------------------------TCAAATGATGAAATACCAATGCAA---CAGAGTCAAGCTCTGA----------GTTTC---AAAAA----GAAAC----------ATGGACGAGA---TTGCTT-TTTT--ATTACTGACC------------------------------------------------------------------------------------------------------------------------------------------------------------
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