• Within intron of CNH01600 (CNAG_07884) for mitochondrial 37S ribosomal protein S35

../../_images/snR88_h99_igb.png

snR88

  • snR88_intronic-boxCDsnoRNA-84nt-in-CNH01600

../../_images/snR88-align.png

  • Predicted target D’ guide in 18S rRNA: aacgAaggt

  • Targeted nt is in a Cryptococcus specific 18S rRNA sequence and close to that of a conserved A modified by yeast snR54, or human SNORD59 (with an overlapping guide).

  • D’ guide is controlled by a canonical cuga motif, which makes it unlikely that actually the same nt is methylated as in yeast, human or plant.

  • An alternative target for the D’ guide is in 25S rRNA: ggcgGgggt but this relies on weaker G-U base pairs.

  • Predicted target D guide in 25S rRNA: gaagTggagaaa and (atgtc)aaagTggagaaa

  • Orthologue of fission yeast snR88 (D guide).

  • Accessory guide (t)gacat could extend base pairing of the D-guide with the second 25S rRNAtarget (atgtc)aaagTggagaaa

  • SnoR29 (see SnoR29 in UTP17 or snoZ107-SnoR29b) is the orthologue in Tremellomycetes with fission yeast snR88 D’-guide.

>AE017348.1:681933-682016 Cryptococcus neoformans var. neoformans JEC21 chromosome 8 sequence
CACTCGGATGAAAAAACCTATGACATAACCTTCGTTCTGAAGACTCAAACATATGGTTACTCTTTTTTCT
TCACTTTCTGAAAA




snRcnh01600

  • snRcnh01600_intronic-boxCDsnoRNA-70nt-in-CNH01600

  • Predicted target in 25S rRNA: aagActaatcg

  • Requires experimental verification as D’ and C’ motifs are not obvious.

  • Nucleotide to be modified appears unique for Tremellomycetes

../../_images/snRcnh01600-align.png

>AE017348.1:682139-682208 Cryptococcus neoformans var. neoformans JEC21 chromosome 8 sequence
ACAGATGATTTATTACGATTAGTCTTTAAGACACCTACATGGTTCCAACTTGCTTTATTTTGCTGATACT







  • Image source snR88:

# STOCKHOLM 1.0
#=GF RW van Nues, July 2023
#=GF https://coalispr.codeberg.page/paper
Annot/1-49                   -------RTGATGA---------------------aCUGUA--UGGAAGCAACTGA-------------------RTGATGA----------AAAGAGGUGAARCTGA-----
#=GS snR88/1-84 DE intronic-boxCDsnoRNA-84nt_in-CNH01600 ncrna 8:681932:682016:1
snR88/1-84                   ---CACTCGGATGAAA------------AAACCTATGACAT-AACCTTCGTTCTGAAGACTCAAAC-------ATATGGTTACTCTT----TTTTCTTCACTTTCTGAAAA--
#=GS H99/1-83 DE CP003833.2:c501869-501787 Cryptococcus neoformans var. grubii H99 chromosome 14, complete sequence
H99/1-83                     ---TACTCGGATGAAA------------AAACCTATGACAT-AACCTTCGTTCTGAAGACCCAAAC-------ATATGGTTACTCTT----TTTTCTTCACTTTCTGAAA---
#=GS R265/1-83 DE CP025768.1:c394331-394249 Cryptococcus gattii VGII R265 chromosome 10, complete sequence
R265/1-83                    ---TACTCGGATGAAA------------CAACCTATGACAT-AACCTTCGTTCTGAAGACTCAAA-------CATATGGTTACTCTT----TTTTCTTCACTTTCTGAAA---
#=GS WM276/1-84 DE CP000297.1:c394321-394238 Cryptococcus gattii WM276 chromosome L, complete sequence
WM276/1-84                   ---TACTCGGATGAAA------------CAACCTATGACAT-AACCTTCGTTCTGAAGACTCAAA-------CATATGGTTACTCTT----TTTTCTTCACTTTCTGAAAA--
#=GS KwoSha/1-86 DE NQVO01000031.1:63608-63693 Kwoniella shandongensis strain CBS 12478 scaffold00031, whole genome shotgun sequence
KwoSha/1-86                  --TATCCCGGATGATA------------AAAAATATGACAT-AACCTTCGTTCTGAAGACATAAA-------CACATGGTTATCCTT-ATA-TTTCTTCACTTTCTGAAA---
#=GS NaeEnc/1-81 DE MCFC01000037.1:c161464-161384 Naematelia encephala strain 68-887.2 BCR39scaffold_37, whole genome shotgun sequence
NaeEnc/1-81                  --TCTCCCGGATGAAA------------CAAACTATGACATT-ACCTTCGTTCTGAAGACTA--T-------CCCATGGTTACACT-----TTTTCTTCACTTTCTGAAA---
#=GS NaeAur/1-81 DE JAKFAO010000004.1:1532558-1532638 Naematelia aurantialba strain NX-20 Contig4, whole genome shotgun sequence
NaeAur/1-81                  --TTTCCGGGATGAGA------------CAAC-TATGACATT-ACCTTCGTTCTGAAGACTCC---------TACATGGTTATCCT-----TTTTCTTCACTTTCTGAAAA--
#=GS CryFlo/1-86 DE RRZH01000015.1:c317652-317567 Cryptococcus floricola strain DSM 27421 chromosome 14, whole genome shotgun sequence
CryFlo/1-86                  --TACCCCTGATGAGA------------AAAAATATGACAT-AACCTTCGTTCTGAAGACTAATT-------CCCATGGTTACCAT--CTATTTTCTTCACTTTCTGAAA---
#=GS CryAmy/1-87 DE MEKH01000013.1:c322436-322350 Cryptococcus amylolentus CBS 6273 supercont2.13, whole genome shotgun sequence
CryAmy/1-87                  --TACCCCTGATGAGA------------AAAAATATGACAT-AACCTTCGTTCTGAAGACTAATT-------CCCATGGTTACCAT--CTATTTTCTTCACTTTCTGAAAT--
#=GS KwoMan/1-86 DE ASQF01000001.1:c790611-790526 Kwoniella mangroviensis CBS 8886 cont1.1, whole genome shotgun sequence
KwoMan/1-86                  ---TACTCGGATGAAA------------CAAAATATGACAT-AACCTTCGTTCTGAAGACATAAA-------ATCATGGTTATTATT-ATA-TTTCTTCACTTTCTGAACC--
#=GS KwoHev/1-89 DE ASQB01000033.1:49862-49950 Kwoniella heveanensis BCC8398 cont1.33, whole genome shotgun sequence
KwoHev/1-89                  -CCTTCCCTGATGAAA------------CAAATTATGACATTAACCTTCGTTCTGAAGACACA-A-------CACATGGTTATCACTCATA-TTTCTTCACTTTCTGAAAA--
#=GS BulAlb/1-84 DE CAMYTR010000041.1:c218016-217933 Bullera alba genome assembly, contig: jcf7180000012134, whole genome shotgun sequence
BulAlb/1-84                  --CATCTCGGATGATA------------CAAAATATGACAT-AACCTTCGTTCTTAAGACTAT---------TACATGGTTACATT--ATA-TTTCTTCACTTTCTGAAAC--
#=GS CrySki/1-88 DE BCHT01000004.1:298391-298478 Cryptococcus skinneri DNA, scaffold: scaffold_3, strain: JCM 9039, whole genome shotgun sequence
CrySki/1-88                  CTTATCTATGATGATA------------CAAA-TATGACAT-AACCTTCGTTCTGAAGACATA---------CCCATGGTTATTCTT-ATA-TTTCTTCACTTTCTGAAATAC
#=GS PapTer/1-83 DE JAHXHD010000043.1:c4188-4106 Papiliotrema terrestris strain LS28 scaffold-42, whole genome shotgun sequence
PapTer/1-83                  --CGTCTCTGATGAAA------------CAAACT-TGACAT-AACCTTCGTTCTTAAGACACC---------CACATGGTTACGATT--CA-TTTCTTCACTTTCTGAAAC--
#=GS PapLau/1-84 DE JAAZPX010000001.1:341195-341278 Papiliotrema laurentii strain IF7SW-F4 scaffold1_cov209, whole genome shotgun sequence
PapLau/1-84                  --TTTCTGGGATGAGA------------AAAAT--TGACATTAACCTTCGTTCTTAAGACACC---------TACATGGTTATCCTTT-CA-TTTCTTCACTTTCTGAAAA--
#=GS CryGC4/1-83 DE JALPCA010000504.1:9806-9888 Cryptococcus sp. GC_Crypt_4 iso00_46_537, whole genome shotgun sequence
CryGC4/1-83                  --CATCTCGGATGAAA------------CAAACT-TGACAT-AACCTTCGTTCTTAAGACAAAC--------CCCATGGTTACGATA--CA-TTTCTTCACTTTCTGAAA---
#=GS TreTag/1-89 DE CAJHEQ010000942.1:2058-2146 MAG: Tremellales sp. Tagirdzhanova-0007 genome assembly, contig: TREM_942, whole genome shotgun sequence
TreTag/1-89                  --TTTTTGGGATGAGA------------CAACA-ATGACATTAACCTTCGTTCTGAAGACTTTAAAA-----AACATGGTTACGCT---CATTTTCTTCACTTTCTGAAGCG-
#=GS TreYok/1-82 DE BRDC01000026.1:153136-153217 Tremella yokohamensis NBRC 100148 DNA, KCNB35TY.26, whole genome shotgun sequence
TreYok/1-82                  -----CCCTGATGAAA------------CAAACT-TGACATTAACCTTCGTTCTGAAGACATTC--------ACCCTGGTTACTCT---CATTTTCTTCACTTTCTGAAGC--
#=GS TreMes/1-89 DE SDIL01000126.1:8155-8243 Tremella mesenterica strain ATCC 28783 supercont1.126, whole genome shotgun sequence
TreMes/1-89                  CTCTCCTCTGATGATA------------CCAA-TATGACATTAACCTTCGTTCTGAAGACTAT---------CACATGGTTACGCTCG-TA-TTTCTTCACTTCCTGACTACT
#=GS CryFla/1-83 DE CAUG01000211.1:c64505-64423 Cryptococcus flavescens NRRL Y-50378 WGS project CAUG00000000 data, contig NODE_284_length_200747_cov_45_572124, whole genome shotgun sequence
CryFla/1-83                  ---TACTCTGATGAAA------------CAAACT-TGACAT-AACCTTCGTTCTTAAGACATC---------CACATGGTTACGATA--CA-TTTCTTCACTTTCTGAAACT-
#=GS TriOvo/1-100 DE JAMFRG010000016.1:c290339-290240 Trichosporon ovoides strain Y9002B ctg_16, whole genome shotgun sequence
TriOvo/1-100                 -----TCCTGATGAGAAACATGACACGACATTCTTTAATTTAAGACTCACAAATCGGGACT-TTGTC-----CCAATGGTTACTCAAA-CA-TTTCTTCACTTTCTGATCCGA
#=GS TriInk/1-104 DE JXYM01000003.1:2528582-2528685 Trichosporon inkin strain JCM 9195 scaffold_0003, whole genome shotgun sequence
TriInk/1-104                 TCTCTCCCTGATGAGAAACATGACACGACATTCTTTACCTAAAGACGCACAA-TCGGGACTCTCGTC-----CCAATGGTTACTCAAA-CA-TTTCTTCACTTTCTGATCCA-
#=GS SchPom-snR88/1-84 DE Schizosaccharomyces_pombe snR88 http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi?mode=sno_info&id=Schizosaccharomyces_pombe300057
SchPom-snR88/1-84            -----TATCGAGGAGG------------ATAAAAATGACATGTCAAGCTCAACAATATGAAAAATTATGATTTTTTT------------CTATTTCTTCACTTTCTGAGATGT
Annot-SacCer/1-46            -------RTGATGA---------------------------AUUGAAAGCAAGA-CTGA----------------RTGATGA----------------------CTGA-----
#=GS SacCer-snR54/1-86 DE 18S:A974 Saccharomyces_cerevisiae snR54 http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi?mode=sno_info&id=Saccharomyces_cerevisiae300071
SacCer-snR54/1-86            ---TAAGATGATGATCAA----------CTTTTTATATCAATAACTTTCGTTCTACTGACTGTGATCAAACGATCTTGTAGAG-----------AACTTTTACTCTGAAT---
#=GS HomSap-SNORD59A/1-75 DE 18S:A1031 http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi?mode=sno_info&id=Homo_sapiens300691
HomSap-SNORD59A/1-75         -CCTTCTATGATGAT----------------TTTATCAAAATGACTTTCGTTCTTCTGAGTT-----------TGCTGAAGCCA----------CATTTAGGTACTGAGAAGG
#=GS HomSap-SNORD59B/1-71 DE 18S:A1031 http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi?mode=sno_info&id=Homo_sapiens300690
HomSap-SNORD59B/1-71         --CCTCACTGATGAGT-------------------ACGTTCTGACTTTCGTTCTTCTGAGTT-----------TGCTGAAGCCA----------GATGCAATTTCTGAGAAGG
#=GS AraTha-SnoR59a/1-76 DE 18S:A975,25S:G1845  Arabidopsis_thaliana
AraTha-SnoR59a/1-76          --CTCTTATGATGTCAA-------------------------AACTTTCGTTCTCCTGAGATTTC----AATATGCTGAAAAAAA------TTGGAGACCTGAACTGAAAGAG
//

  • Image source snRcnh01600:

# STOCKHOLM 1.0
#=GF RW van Nues, July 2023
#=GF https://coalispr.codeberg.page/paper
Annot/1-33               ---RTGATGA----------GCUAAUCAGAA-CTGA---------------RTGATGA--------------------------CTGA--------
#=GS snRcnh01600/1-70 DE intronic-boxCDsnoRNA-70nt-in-CNH01600 ncrna 8:682138:682266:1
snRcnh01600/1-70         --ACAGATGATTTATTA---CGATTAGTCTTTAAGACACCTA--------CATGGTTCCAACT---------TGCTTTATTTTGCTGATACT----
#=GS H99/1-70 DE CP003833.2:c501664-501595 Cryptococcus neoformans var. grubii H99 chromosome 14, complete sequence
H99/1-70                 --ACAGATGATTTATTA---CGATTAGTCTTTAAGACACCTA--------CATGGTTCCAACT---------TGCTTTATTTTGCTGATACT----
#=GS R265/1-70 DE CP025768.1:c394125-394056 Cryptococcus gattii VGII R265 chromosome 10, complete sequence
R265/1-70                --ACAAATGATTTATTA---CGATTAGTCTTTAAGACACCTA--------CATGGTTCCAACT---------TGCTTTATTTTGCTGATATT----
#=GS WM276/1-70 DE CP000297.1:c394114-394045 Cryptococcus gattii WM276 chromosome L, complete sequence
WM276/1-70               --ACAGATGATTTATTA---CGATTAGTCTTTAAGACACCTA--------CATGGTTCCAACT---------TGCTTTATTTTGCTGATACT----
#=GS CryFlo/1-68 DE RRZH01000015.1:c317441-317374 Cryptococcus floricola strain DSM 27421 chromosome 14, whole genome shotgun sequence
CryFlo/1-68              --TATGATGTTTAA------CGATTAGTCTTTAAGACAACTA--------CATGGTTCCAACTT-------ACGCTTTACCT-GCTGAACCT----
#=GS CryAmy/1-72 DE MEKH01000013.1:c322224-322153 Cryptococcus amylolentus CBS 6273 supercont2.13, whole genome shotgun sequence
CryAmy/1-72              --TATGATGTTGAA------CGATTAGTCTTTAAGACAACTA--------CATGGTTCCTACTT-------ACGCTTTACCT-GCTGAACCTTCTT
#=GS NaeEnc/2-72 DE MCFC01000037.1:c161299-161228 Naematelia encephala strain 68-887.2 BCR39scaffold_37, whole genome shotgun sequence
NaeEnc/2-72              TTTATGATGAGTATA-----CGATTAGTCTTTAAGACTTCTA--------CATGGTTCCTAACA-------ATGCATGGCTTT-CTGATCCT----
#=GS NaeAur/1-72 DE JAKFAO010000004.1:1532730-1532801 Naematelia aurantialba strain NX-20 Contig4, whole genome shotgun sequence
NaeAur/1-72              TCTATGATGAGTATA-----CGATTAGTCTTTAAGACTTCTA--------CATGGTTCCTACCA-------ATGCATGGCTTT-CTGACACAC---
#=GS KwoMan/1-80 DE ASQF01000001.1:c790356-790277 Kwoniella mangroviensis CBS 8886 cont1.1, whole genome shotgun sequence
KwoMan/1-80              --AATGATGACTACT-----TGATTAGTCTTTAAGACTTCACAGTAAACTTATGGTTATAAACC-------ATGCATGGCTTT-CTGATACTCTT-
#=GS BulAlb/1-73 DE CAMYTR010000041.1:c217802-217730 Bullera alba genome assembly, contig: jcf7180000012134, whole genome shotgun sequence
BulAlb/1-73              -CAGTGATGAGTAAC-----CGATTAGTCTTTAAGACACATA--------CGTGGTTCCAAACTCCA----ATGCATGGCTTT-CTGATCAT----
#=GS CrySki/1-82 DE BCHT01000004.1:298637-298718 Cryptococcus skinneri DNA, scaffold: scaffold_3, strain: JCM 9039, whole genome shotgun sequence
CrySki/1-82              TCTATGATGAATTCAAAAATCGATTAGTCTTGAAGACACCTT--------CATGGTTACAAAAATTTAC-AATGCATGGCTTT-CTGATCTT----
#=GS PapTer/2-75 DE JAHXHD010000043.1:c3988-3914 Papiliotrema terrestris strain LS28 scaffold-42, whole genome shotgun sequence
PapTer/2-75              ACAGTGATGATCAAC-----CGATTAGTCTTGAAGACACCTA--------CATGGTTTCAAACTCCA----ATGCATGGCTTT-CTGACCTT----
#=GS PapLau/3-73 DE JAAZPX010000001.1:341412-341484 Papiliotrema laurentii strain IF7SW-F4 scaffold1_cov209, whole genome shotgun sequence
PapLau/3-73              TCAATGATGAGCAC------CGATTAGTCTTTAAGACATCTA--------CATGGTTCCAAACTC------ATGCATGGCTTA-CTGATCCT----
#=GS CryGC4/2-71 DE JALPCA010000504.1:10035-10105 Cryptococcus sp. GC_Crypt_4 iso00_46_537, whole genome shotgun sequence
CryGC4/2-71              TTCATGATGATCAA------CGATTAGTCTTTAAGACTTACA--------CATGGTTCCAAACA-------ATGCATGGCTTT-CTGATACT----
#=GS TreTag/2-82 DE CAJHEQ010000942.1:2280-2361 MAG: Tremellales sp. Tagirdzhanova-0007 genome assembly, contig: TREM_942, whole genome shotgun sequence
TreTag/2-82              TTCGTGATGATCGCAA----CGATTAGTCTTGAAGACATATACT------CATGGTTTCACATTCTGTCA-ATGCATGGCTTT-CTGATACCA---
#=GS TreYok/2-74 DE BRDC01000026.1:153357-153430 Tremella yokohamensis NBRC 100148 DNA, KCNB35TY.26, whole genome shotgun sequence
TreYok/2-74              TCTATGATGAGCACA-----CGATTAGTCTTTAAGACACCCA--------CATGGTTTCAAACAAC-----ATGCATGGCTTT-CTGACCCT----
#=GS TreMes/2-70 DE SDIL01000126.1:8434-8507 Tremella mesenterica strain ATCC 28783 supercont1.126, whole genome shotgun sequence
TreMes/2-70              TTTATGATGAGCAA------CGATTAGTCTTTAAGACTCACA--------CATGGTTCCAAAACTC-----ATGCATGGCTTA-CTGAA-------
#=GS KocImp/4-73 DE NBSH01000008.1:c624743-624671 Kockovaella imperatae strain NRRL Y-17943 BD324scaffold_8, whole genome shotgun sequence
KocImp/4-73              TTCATGATGAGCAA------CGATTAGTCTTTAAGACTTCTA--------CATGGTTCCAAATC-------ATGCATGGCTTA-CTGATTCA----
#=GS VanFra/2-80 DE BEDY01000002.1:2380378-2380457 Vanrija fragicola DNA, scaffold: scaffold_2, strain: JCM 1530, whole genome shotgun sequence
VanFra/2-80              ACAGTGATGATTGAGAT---CGATTAGTCTTGAAGACTCCAAA-------CATGGTTAAACAACCTCCA--ATGCATGGCTTT-CTGACCCT----
#=GS TriOvo/1-85 DE JAMFRG010000016.1:c290086-290006 Trichosporon ovoides strain Y9002B ctg_16, whole genome shotgun sequence
TriOvo/1-85              TTCATGATGAGCGAGAT---CGATTAGTCTTGAAGACCCTAAA-------CGTGGTTAAACAACCCCTCTTATGCATGGCTTT-CTGATTCCACCT
//