snR39b

../../_images/snr39b_h99_igb.png

  • snR39b_intronic-boxCDsnoRNA-87nt-in-CNA06360

  • Within CNA06360 (CNAG_00656) for large subunit ribosomal protein L7e

  • Predicted target in 25S rRNA: cccGaaagatggt

  • Orthologue of yeast snR39b (D guide), human SNORD2 (D' guide)

../../_images/snr39b-align.png

>AE017341.1:1727325-1727411 Cryptococcus neoformans var. neoformans JEC21 chromosome 1, complete sequence
CAGAATGATGCATAACACCGACGTCCGTCGGATCACGGCTAGCTTCGACAATGCTGCTCGTAATTAACCA
TCTTTCGGGGCTGAACC







  • Image source:

# STOCKHOLM 1.0
#=GF RW van Nues, June 2023
#=GF https://coalispr.codeberg.page/paper
Annot/1-35                 -------RTGATGA-----------------------------------------CTGA--------------RTGATGA----------------UGGUAGAAAGCCC-CTGA------------------------------------
#=GS snR39b/1-87 DE AE017341.1:1727325-1727411 Cryptococcus neoformans var. neoformans JEC21 chromosome 1, complete sequence
snR39b/1-87                ---CAGAATGATGCA-TAACA-CCGACG-TC--CGTCGG-----ATC----ACGGCTAGCT---TC---GACAATGCTGCTC---GTAATTA----ACCATCTTTCGGGGCTGAACC---------------------------------
#=GS H99/1-86 DE CP003820.1:1707859-1707945 Cryptococcus neoformans var. grubii H99 chromosome 1, complete sequence
H99/1-86                   ---CAGAATGATGCA-GAACA-CCGACG-TC--CGTCGG-----CTC----ACGGCTAGCT---TT---GACAATGCTGCTC---GTAATTA----ACCATCTTTCGGGGCTGAAC----------------------------------
#=GS R265/1-87 DE CP025761.1:c566518-566432 Cryptococcus gattii VGII R265 chromosome 3, complete sequence
R265/1-87                  ---CAGAATGATGCA-GAACA-CCGAC-ATCC--GTCGG-----ATC----ACGGCTAGCT---TA---GACAATGCTGCTC---GTAATTA----ACCATCTTTCGGGGCTGAACC---------------------------------
#=GS WM276/1-87 DE CP000286.1:1431360-1431446 Cryptococcus gattii WM276 chromosome A, complete sequence
WM276/1-87                 ---CAGAATGATGCA-GAACA-CCGAC-ATCC--GTCGG-----ATC----ACGGCTAGCT---TA---GACAATGCTGCTC---GTAATTA----ACCATCTTTCGGGGCTGAACC---------------------------------
#=GS CrySki/81-167 DE BCHT01000007.1:c577996-577830 Cryptococcus skinneri DNA, scaffold: scaffold_6, strain: JCM 9039, whole genome shotgun sequence
CrySki/81-167              ---CACAATGATGCA-AAATCGCCGAC-GAC---GTCGG-----ATC----ACGGCTAGCT---AC---GGCCATGCTGCCT---GTAATTA----ACCATCTTTCGGGGCTGAATA---------------------------------
#=GS CryWin/1-87 DE CP034261.1:716320-716406 Cryptococcus wingfieldii strain CBS7118 chromosome 1, complete sequence
CryWin/1-87                -----CAATGATGCA-AAACCACCGAC-AACTC-GTCGG-----CAT----ACAGCTAGCT---TT---GGCGATGCTGCTT---GTAATTA----ACCATCTTTCGGGGCTGAACC---------------------------------
#=GS CryFlo/59-148 DE RRZH01000001.1:c1614092-1613945 Cryptococcus floricola strain DSM 27421 chromosome 1, whole genome shotgun sequence
CryFlo/59-148              --CTACAATGATGCA-AAACCACCGAC-AACTC-GTCGG-----CAT----ACAGCTAGCT---TT---GGCGATGCTGCTT---GTAATTA----ACCATCTTTCGGGGCTGAACC---------------------------------
#=GS NaeAur/55-141 DE JAKFAO010000003.1:c1236291-1236150 Naematelia aurantialba strain NX-20 Contig3, whole genome shotgun sequence
NaeAur/55-141              ---CATCATGATGTA-CAACA-CCG-C-TGTC--G-CGG-----ATC----ACGGCTAGCC--AAAC--GGCGATGCTGCCT---GTAATTA----ACCATCTTTCGGGGCTGAATC---------------------------------
#=GS KwoPin/59-145 DE ASCL01000033.1:327000-327145 Kwoniella pini CBS 10737 cont1.33, whole genome shotgun sequence
KwoPin/59-145              ---CTTCATGATGCA-TAACA-CCGACG-TC--CGTCGG-----CAC----ACGGCTAGCT---TA---GACAATGCTGCTC---GTAATTA----ACCATCTTTCGGGGCTGAACA---------------------------------
#=GS KwoMan/70-153 DE ASQF01000003.1:c28749-28597 Kwoniella mangroviensis CBS 8886 cont1.3, whole genome shotgun sequence
KwoMan/70-153              ------CATGATGCA-CAACA-CCGAC-GTCT--GTCGG-----CAC----ACGGCTAGCT---TC---GGCAATGCTGCTC---GTAATTA----ACCATCTTTCGGGGCTGATCA---------------------------------
#=GS KwoBes/66-152 DE ASCK01000005.1:1648304-1648455 Kwoniella bestiolae CBS 10118 cont1.5, whole genome shotgun sequence
KwoBes/66-152              --CATCGATGATGCA-CAACA-CCGAC-GTCT--GTCGG-----CAC----ACGGCTAGCT---TA---GGCGATGCTGCTC---GTAATTA----ACCATCTTTCGGGGCTGAAC----------------------------------
#=GS VanFra/59-145 DE BEDY01000002.1:1541790-1541935 Vanrija fragicola DNA, scaffold: scaffold_2, strain: JCM 1530, whole genome shotgun sequence
VanFra/59-145              --CCACAATGATGCA--AAGA-CCGAC-ACTC--GTCGG-----ACC----ACGGCTAGCT---AC---AACGATGCTGCCT---GTAATTA----ACCATCTTTCGGGGCTGAACA---------------------------------
#=GS VanHum/71-156 DE BFAH01000027.1:c1031289-1031133 Vanrija humicola UJ1 DNA, scaffold28, whole genome shotgun sequence
VanHum/71-156              ---CACAATGATGCA--AAGA-CCAAC-ACTC--GTTGG-----ACC----ACGGCTAGCT---AC---GACAATGCTGCCT---GTAATTA----ACCATCTTTCGGGGCTGAATC---------------------------------
#=GS ApiAki/71-160 DE PQXP01000012.1:48403-48562 Apiotrichum akiyoshidainum strain HP2023 Contig329, whole genome shotgun sequence
ApiAki/71-160              --CTTCAGTGATGAG--AA---CCGAC-TCT---GTCGG----ATCCT---TCGGCTAGCTC-TAAC-GAGCGATGCTGTCT---GTAATTA----ACCATCTTTCGGGACTGAAAA---------------------------------
#=GS ApiSia/51-141 DE JALJEG010000006.1:124241-124396 Apiotrichum siamense strain L8in5 NODE_6_length_670236_cov_10.895171, whole genome shotgun sequence
ApiSia/51-141              ----CGGATGATGAA--AGG--CCGAC-TCTC--GTCGG-----ATTC---TCGGCTAGCTCTCTCGGGGGCGATGCTGTCT---GTAATTA----ACCATCTTTCGGGGCTTACGG---------------------------------
#=GS ApiSia/46-141 DE JALJEG010000006.1:c35494-35329 Apiotrichum siamense strain L8in5 NODE_6_length_670236_cov_10.895171, whole genome shotgun sequence
ApiSia/46-141              ----CGGATGATGAA--AGG--CCGACT-CG--AGTCGG--GATATCTTC-TAGGCTAGCCTCTCTGCGGGCGATGCTGTCT---TTAATTA----ACCATCTTTCGGGGCTTACGG---------------------------------
#=GS PapLau/66-151 DE JDSR01000278.1:c4542-4390 Papiliotrema laurentii RY1 contig_287, whole genome shotgun sequence
PapLau/66-151              --CATCTATGATGCA-AAACT-TCGAC-ACCA--GTCGA------T-----ACGGCTAGCT---AC---GGCGATGCTGCTT---GTAATTA----ACCATCTTTCGGGGCTGAACT---------------------------------
#=GS PapTer/61-147 DE JAHXHD010000837.1:c35123-34977 Papiliotrema terrestris strain LS28 scaffold-836, whole genome shotgun sequence
PapTer/61-147              ---CACAATGATGCACAACTT-CCGAC-ATCCC-GTCGG-------C----TAGGCTAGC---TACTT--GCGATGCTGTC----TTAATCA----ACCATCTTTCGGGGCTGAACC---------------------------------
#=GS TakTep/59-149 DE BCKS01000014.1:176163-176311 Takashimella tepidaria DNA, scaffold: scaffold_13, strain: JCM 11965, whole genome shotgun sequence
TakTep/59-149              ---CTCAATGATGCA--AAGA-CCGACA-TT--TGTCGG----AAAC----ACGGCTAGCCT--ACA-AGGCAATGCTGCCC---GTAATTAT---ACCATCTTTCGGGGCTGAACC---------------------------------
#=GS CutMuc/58-145 DE BCJT01000057.1:c8635-8490 Cutaneotrichosporon mucoides DNA, scaffold: scaffold_56, strain: JCM 9939, whole genome shotgun sequence
CutMuc/58-145              --CTTCAATGATGTA--AAGA-CCGAC-TTC---GTCGG-----ACC----ACGGCTAGC---TTTT---GCGATGCTGTC----GTAATTGTTA-ACCATCTTTCGGGGCTGAAAC---------------------------------
#=GS TriGue/78-163 DE BCJX01000001.1:c1240599-1240437 Trichosporon guehoae DNA, scaffold: scaffold_0, strain: JCM 10690, whole genome shotgun sequence
TriGue/78-163              -----CAATGATGTA--AAGA-CCGAC-ACTC--GTCGG-----ACC----ACGGCTAGCA---AAT--TGCAATGCTGTCT---GTAAATTA---ACCATCTTTCGGGGCTGAATG---------------------------------
#=GS SacCer-snR39b/1-96 DE http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi?mode=sno_info&id=Saccharomyces_cerevisiae300029
SacCer-snR39b/1-96         --ATTTAGTGATGATAC-----TGCCG-ATTC--TGGCA-TTCCAAAAA--GTGACTAGCAA--AA--TTGCGATGTTGTCAAC-TTAAATTAC--ACCATCTTTCGGGGCTGATA----------------------------------
#=GS HomSap-SNORD2/1-70 DE http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi?mode=sno_info&id=Homo_sapiens300757
HomSap-SNORD2/1-70         ------------------------------------------------------------------AAGTGAAATGATGGCA--------------ATCATCTTTCGGGACTGACCTGAAATGAAGAGAATACTCATTGCTGATCACTTG
#=GC SS_cons               ----------------------((((((.....))))))---------------------------------------------------------------------------------------------------------------
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