snR71-SNORD29

../../_images/snR71_h99_igb.png

  • snR71_intronic-boxCDsnoRNA-76nt-in-CNF00890

  • Within intron of CNF00890 (CNAG_05884) for importin beta-4 subunit

  • Predicted target in 25S rRNA: gtgAgctggg

  • Orthologue of yeast snR71, human SNORD29

../../_images/snR71-align.png

>AE017346.1:285916-285991 Cryptococcus neoformans var. neoformans JEC21 chromosome 6 sequence
ACGAATGAGGACAACTTTAACTCAGCTCACTCCGAGCCAATGTGCCATGAGGCTATCTATATAATTTATC
TGATCC



snR71b

../../_images/cnag13104_h99_igb.png

  • snR71b_intronic-boxCDsnoRNA-96nt-as-CNAG_13104

  • Within intron of a non-coding transcript (as CNAG_13104)

  • Predicted target for D’ guide in 25S rRNA: gtgAgctggg

  • Orthologous to yeast snR71, human SNORD29

  • Possible target for D guide in 25S rRNA: gggTtgaaga

  • Appears to be unique for Cryptococcus (no orthologs)

../../_images/snR71b-align.png

>AE017356.1:c40535-40440 Cryptococcus neoformans var. neoformans JEC21 chromosome 14 sequence
ATGCTGGATGAAAAATCTTAACTCAGCTCACTCCGAATGCGGCCCCTCAAAGGGGTTTTGCTCTGAGGCT
ACCTTTATCTTCAACCCCCTGATTCT







  • Image source snR71:

# STOCKHOLM 1.0
#=GF RW van Nues, July 2023
#=GF https://coalispr.codeberg.page/paper
Annot/1-32                ------RTGATGA----------------GGGUCGAGUG-CTGA-----------------RTGATGA------------------------------CTGA-------
#=GS snR71/1-76 DE intronic-boxCDsnoRNA-76nt-in-CNF00890 ncrna 6:285915:285991:1
snR71/1-76                --ACGAATGAGGACAAC-TTT------AACTCAGCTCACTCCGAGCCAA-----TGTGCC-ATGAGGCTATC--------------TATATAATTTATCTGATCC----
#=GS CNAG_05884/1-77 DE CP003826.1:c1112820-1112744 Cryptococcus neoformans var. grubii H99 chromosome 7, complete sequence
CNAG_05884/1-77           --ACGCATGAGGAAACATTTT------AACTCAGCTCACTCCGAGCCAA-----TGTGCC-ATGAGGCTATC--------------TATATAATTTGTCTGATAC----
#=GS WM276/1-76 DE CP000291.1:c1046507-1046432 Cryptococcus gattii WM276 chromosome F, complete sequence
WM276/1-76                --ACGCATGAGGAAAA-TTTT------AACTCAGCTCACTCCGAGCCAT-----TGTGCC-ATGAGGCTATC--------------AATATAATTCATCTGATCC----
#=GS R265/1-77 DE CP025763.1:c1050606-1050530 Cryptococcus gattii VGII R265 chromosome 5, complete sequence
R265/1-77                 --ACGCATGAGGAAAAATTTC------AACTCAGCTCACTCCGAGCCAT-----TGTGCC-ATGAGGCTATC--------------TATATAATTCATCTGATCC----
#=GS KwoMan/1-83 DE ASQE01000063.1:170219-170301 Kwoniella mangroviensis CBS 8507 cont2.62, whole genome shotgun sequence
KwoMan/1-83               --ACATATGATGATAAA-TTT------AACTCAGCTCACTCCGAAGCACTAAAAAGTGTCCTTGAGGCTAC-------------TATATACATTTTATCTGATAC----
#=GS KwoMan/1-84 DE ASQF01000004.1:1415947-1416030 Kwoniella mangroviensis CBS 8886 cont1.4, whole genome shotgun sequence
KwoMan/1-84               -CACATATGATGATAAA-TTT------AACTCAGCTCACTCCGAAGCACTAAAAAGTGTTCTTGAGGCTAC-------------TATATACATTTTATCTGATAC----
#=GS CryFlo/1-83 DE RRZH01000002.1:1747138-1747220 Cryptococcus floricola strain DSM 27421 chromosome 2, whole genome shotgun sequence
CryFlo/1-83               CTTTGCGTGATGAGAAAA-CT-------ACTCAGCTCACTCCGAGCACAA----TGTGCT-ATGAGGCTTCA---------TTTATTTTAATTAGACACTGATTC----
#=GS CryFlo/1-88 DE RRZH01000002.1:1747647-1747734 Cryptococcus floricola strain DSM 27421 chromosome 2, whole genome shotgun sequence
CryFlo/1-88               --ATGTATGATGAGAAAAACT-------ACTCAGCTCACTCCGAGCCCAAA--TTGTGGCTATGAGGCTTCCA-------TTTATTTTTAATTAGACCCTGATCCT---
#=GS CryWin/1-86 DE AWGH01000002.1:669008-669093 Cryptococcus wingfieldii CBS 7118 supercont1.2, whole genome shotgun sequence
CryWin/1-86               CCATGTATGATGAGAAAA-CT-------ACTCAGCTCACTCCGAGCCCGA---TTGTGGCTATGAGGCTTCA---------TTTAT-TTAATTAGACCCTGATCCTT--
#=GS CryWin/1-84 DE AWGH01000002.1:668475-668558 Cryptococcus wingfieldii CBS 7118 supercont1.2, whole genome shotgun sequence
CryWin/1-84               TTTTGCGTGATGAGAAAA-CT-------ACTCAGCTCACTCCGAGCATAA----TGTGCT-ATGAGGCTTCA---------TTTATTTTAATTAGACACTGATCCA---
#=GS CrySki/1-91 DE BCHT01000002.1:c974037-973947 Cryptococcus skinneri DNA, scaffold: scaffold_1, strain: JCM 9039, whole genome shotgun sequence
CrySki/1-91               -CCTATCGGATGAGTCTTTATTTCGTTAACTCAGCTCACTTCGACGCACAA---TGTGCA-ATGAGACGAACACG-----------ATACATCAACTTCTGATTCCC--
#=GS TriOvo/1-84 DE WEIQ01000034.1:c233108-233025 Trichosporon ovoides strain 2NF903A scaffold34-size509535, whole genome shotgun sequence
TriOvo/1-84               --CCAAATGATGATAAA-TTT------AACTCAGCTCACTTCGAGCCCAAA----GGGCC-TTGAGACTACT-----------TTTTTTTCATTTTATCTGACACACTC
#=GS TriCor/1-86 DE JXYL01000018.1:256757-256842 Trichosporon coremiiforme strain JCM 2938 scaffold_0018, whole genome shotgun sequence
TriCor/1-86               --CCAAATGATGATAAACTTT-------ACTCAGCTCACTTCGAGCCCAAA---TGGGCC-TTGAGACTACA--------TTTTTTTTCCAACCATATCTGACACAC--
#=GS TriAsa/1-83 DE JAMYHT010000031.1:170781-170863 Trichosporon asahii strain F6008 ctg_31, whole genome shotgun sequence
TriAsa/1-83               --CCAAATGATGATAAACTTT-------ACTCAGCTCACTTCGAGCCCACA---TGGGCC-TTGAGACT-ACA----------TTTTTTCCAACGTATCTGACACCT--
#=GS SacCer-snR71/1-90 DE  25S:A2946 Saccharomyces_cerevisiae snR71 http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi?mode=sno_info&id=Saccharomyces_cerevisiae300030
SacCer-snR71/1-90         -GTTATATGATGATAACCTT---------CTCAGCTCACTCAGATC---TTTTGATATG-ATTGATAAAAATTTCCTATCCAACATTCATCAATTTATCTGACC-----
#=GS SNORD29/1-65 DE Homo_sapiens SNORD29 http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi?mode=sno_info&id=Homo_sapiens300165
SNORD29/1-65              -TTTCTATGATGAATC----------AAACT-AGCTCACTATGAC------CGACA-----GTGAAAATAC-------------------ATGAACACCTGAGAAAC--
//

  • Image source snR71b:

# STOCKHOLM 1.0
#=GF RW van Nues, August 2023
#=GF https://coalispr.codeberg.page/paper
Annot/1-42                   -----RTGATGA----------GGGUCGAGUG-CTGA------------------------------RTGATGA----------AGAAGUUGGG-CTGA-----
#=GS snR71b/1-96 DE intronic-boxCDsnoRNA-94nt ncrna 14:40441:40535:-1
snR71b/1-96                  -ATGCTGGATGAAAAATCTTAACTCAGCTCACTCCGAATGCGGCCCCTC--AAA--GGGGTTTTGCTCTGAGGC-TACCTTT-ATCTTCAACCCCCTGATTCT-
#=GS WM276/1-96 DE CP000299.1:c36317-36222 Cryptococcus gattii WM276 chromosome N, complete sequence
WM276/1-96                   -ATGCTGGATGAAAAATCTTAACTCAGCTCACTCCGAATGCGGCCTC--AATAAGG--GGTTTTGCTCTGAGGC-TACTTTT-ATCTTCAACCCCCTGATTCT-
#=GS R265/1-96 DE CP025771.1:612219-612314 Cryptococcus gattii VGII R265 chromosome 13, complete sequence
R265/1-96                    -ATGCTGGATGAAAAATCTTAACTCAGCTCACTCCGAATGCGGCCCTC--ATATG--GGGTTTTGCTCTGAGGC-TACTTTT-ATCTTCAACCCCCTGATTCT-
#=GS in-CNAG_13104/1-93 DE 3832.1:c64017-63925 Cryptococcus neoformans var. grubii H99 chromosome 13, complete sequence
in-CNAG_13104/1-93           -ACGCTGGATGAAAAATCTTAACTCAGCTCACTCCGAATGCGACCCCTC--AA---GGGGTTTTGCTCTGAGGC-TAAATTT-ATCTTCAACCCCCTGATT---
#=GS CryFlo/1-102 DE RRZH01000003.1:c1720707-1720606 Cryptococcus floricola strain DSM 27421 chromosome 3, whole genome shotgun sequence
CryFlo/1-102                 -ACGCTGGATGAACCAAATTAACTCAGCTCACTCCGAAGGGCCCGTCCCACGGGATCGGTTACCCTACTGAGGCATACATTTAATCTTCAACCCCCTGATTCT-
#=GS CryAmy/1-99 DE MEKH01000011.1:19379-19477 Cryptococcus amylolentus CBS 6273 supercont2.11, whole genome shotgun sequence
CryAmy/1-99                  -ACGCTGGATGAACCAAATTAACTCAGCTCACTCCGAAGGGCC-GTCCCACGGGATCGGT-ACCCTACTGAGGCATACATT-AATCTTCAACCCCCTGATTCT-
#=GS CryWin/1-101 DE AWGH01000053.1:c31328-31228 Cryptococcus wingfieldii CBS 7118 supercont1.53, whole genome shotgun sequence
CryWin/1-101                 -ACGCTGGATGAACCAAATTAACTCAGCTCACTCCGAAGGGCC-GTCCCACGGGATCGGTTACCCTACTGAGGCATACATTTAATCTTCAACCCCCTGATTCT-
#=GS KwoMan/1-84 DE ASQF01000004.1:1415948-1416083 Kwoniella mangroviensis CBS 8886 cont1.4, whole genome shotgun sequence
KwoMan/1-84                  -ACATATGATGA-TAAATTTAACTCAGCTCACTCCGAAGCACT--------AAAA-----AGTGTTCTTGAGGC-TACT---ATATACATTTTATCTGATACC-
#=GS KwoBes/1-83 DE ASCK01000001.1:c244412-244307 Kwoniella bestiolae CBS 10118 cont1.1, whole genome shotgun sequence
KwoBes/1-83                  -ATACGTGATGAT-AATCTTAACTCAGCTCACTCCGAAACAC--------AAAAA------GTGTTCTTGAGGC-TACTTT-ATAT--ATTTTATCTGATCCC-
#=GS KwoSha/2-93 DE NQVO01000012.1:c433266-433130 Kwoniella shandongensis strain CBS 12478 scaffold00012, whole genome shotgun sequence
KwoSha/2-93                  -ATACAAGATGAGAAAACTTAACTCAGCTCACTCTGATGTGCATAT----AATAA---ATATACACCAAGCTGC-TACTTTTA-AT-CAATACCTCTGATTCT-
Annot-SacCer/1-32            -----RTGATGA----------GGGUCGAGUG-CTGA-----------------RTGA-TGA---------------------------------CTGA-----
#=GS SacCer-snR71/1-90 DE  Saccharomyces_cerevisiae snR71 25S:A2946  http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi?mode=sno_info&id=Saccharomyces_cerevisiae300030
SacCer-snR71/1-90            GTTATATGATGAT---AACCTTCTCAGCTCACTCAGATCTTT--------TGATATGATTGATAAAAATTTCCTATCCAACATTCATCAATTTATCTGACC---
#=GS SNORD29/1-65 DE Homo_sapiens SNORD29 http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi?mode=sno_info&id=Homo_sapiens300165
SNORD29/1-65                 TTTCTATGATGAATC----AAACT-AGCTCACTATGAC------CGACA-----GTGAAAA-----------------------TACATGAACACCTGAGAAAC
//