snR38

../../_images/snr38_h99_igb.png

  • snR38_intronic-boxCDsnoRNA-91nt-in-CNA04050

  • Within intron of CNA04050 (CNAG_00417) for Elongation factor 1-gamma EF1G

  • Predicted target in 25S rRNA: (tacc)acagGgataagctg, with possibly extended base-pairing via (gt)ggta.

  • Orthologue of yeast snR38, human SNORD1A

../../_images/snr38-align.png

>AE017341.1:c1087388-1087298 Cryptococcus neoformans var. neoformans JEC21 chromosome 1, complete sequence
TTGAAGGATGAGACTTCTATCTCAGTTATCCCTGTCTTAATGACTTGTGTCGAGAATTTTCCGGCGGGTG
GTACCGTCATACCTCTGACCA







  • Image source:

# STOCKHOLM 1.0
#=GF RW van Nues, June 2023
#=GF https://coalispr.codeberg.page/paper
Annot/1-41                  ---------RTGATGA-----------------GUCAAUAGGGACACTGA  --------------------------RTGATGA   ------------cACCAU-----------CTGA------
#=GS snR38/1-91 DE AE017341.1:c1087388-1087298 Cryptococcus neoformans var. neoformans JEC21 chromosome 1, complete sequence
snR38/1-91                  -----TTGAAGGATGAGACTTCTATC------TCAGTTATCCCTGTCTTAA----------TGAC-----------TTGTGTCGAGAATTTT-CCGGCGGGTGGTACCGTCATACCTCTGACCA---
#=GS H99/1-91 DE CP003820.1:c1095849-1095759 Cryptococcus neoformans var. grubii H99 chromosome 1, complete sequence
H99/1-91                    -----TTGAAGGATGAGACTTCTATC------TCAGTTATCCCTGTCTTAA----------TGAC-----------TTGTGTCGAGAATTTT-CCGGCGGGTGGTACCGTCATACCTCTGACCA---
#=GS WM276/1-91 DE >P000286.1:c825434-825344 Cryptococcus gattii WM276 chromosome A, complete sequence
WM276/1-91                  -----TTGAAGGATGAGACTTCTATC------TCAGTTATCCCTGTCTTAA----------TGAC-----------TTGTGTCGAGAATTTT-CCGGCGGGTGGTACCGTCATACCTCTGACCA---
#=GS NaeAur/2-91 DE JAKFAO010000012.1:381596-381686 Naematelia aurantialba strain NX-20 Contig12, whole genome shotgun sequence
NaeAur/2-91                 -----TCGAAGGATGAGACTTCTTT-------TCAGTTATCCCTGTCTTAA----------TGAC-----------TTGTGTCGAGATAATT-CCGGCGAGTGGTATCGTCATTTCTCTGAATC---
#=GS SaiPod/1-90 DE RSCD01000013.1:335021-335110 Saitozyma podzolica strain DSM 27192 scaffold_13, whole genome shotgun sequence
SaiPod/1-90                 -----TTTTCGGATGAGACTTATC--------TCAGTTATCCCTGTCTTAA----------TGAC-----------TTGTGTCGAGAATTTAACCGACGAGTGGTATCGTCATATCTCTGATCA---
#=GS CutMuc/1-88 DE BCJT01000007.1:1348178-1348266 Cutaneotrichosporon mucoides DNA, scaffold: scaffold_6, strain: JCM 9939, whole genome shotgun sequence
CutMuc/1-88                 -----TTGCAGGACGAGACTCTTTTAT-----TCAGTTATCCCTGTCTTAA----------TGAC-----------TTGTGTCGATAATTT--CCG-CGGGTGGTACCGC-AT-TCTCTGATAC---
#=GS VanPse/2-89 DE CP086719.1:914068-914156 Vanrija pseudolonga isolate DUCC4014 chromosome 6
VanPse/2-89                 -----TTCTATGATGAGACTTATCT-------TCAGTTATCCCTGTCTTAA----------TGAC-----------TTGTGTCGACAAACT--TTTGCGGGTGGTACCGC-GTATCTCTGAGCC---
#=GS CutDep/1-89 DE WGK01000010.1:456163-456268 Cryptococcus depauperatus CBS 7841 supercont1.10, whole genome shotgun sequence
CutDep/1-89                 ------TTTAGGATGAAACCTTTTC-------TCAGGTATCCCTGTCTTAA----------TGAT-----------ATGTGTCGAGAGTTTT-CAAGCGGGTGGTACCATCGCTTTTCTGAATC---
#=GS BulALb/1-93 DE CAMYTR010000156.1:c495530-495438 Bullera alba genome assembly, contig: jcf7180000012257, whole genome shotgun sequence
BulALb/1-93                 -----TTTCATGATGAGACTTACTTT------TCAGTTATCCCTGTCTTAA----------TGACT----------ATATGTCGAGATTTACTCCGGCGAGTGGTATCGCTATATCTCTGATCA---
#=GS TakTep/2-94 DE BCKS01000019.1:c314497-314404 Takashimella tepidaria DNA, scaffold: scaffold_18, strain: JCM 11965, whole genome shotgun sequence
TakTep/2-94                 -----TTTTCGGATGAGACTTTTCTAT-----TCAGTTATCCCTGTCTTAA----------TGACC----------TTGTGTCGAGACTTTT-CCGGCGGGTGGTACCGTCATTTCTCTGATTT---
#=GS DioHun/2-92 DE JAMRJJ010000001.1:c1113979-1113888 Dioszegia hungarica strain Y1 Contig1, whole genome shotgun sequence
DioHun/2-92                 -----TTCTATGATGAGACTTCTTT-------TCAGTTATCCCTGTCTTAA---------TTGAC-----------CTGTGTCGAGAATT-AACCGGCGGGTGGTACCGTCATACCTCTGATCT---
#=GS KwoSha/2-92 DE NQVO01000009.1:436861-436952 Kwoniella shandongensis strain CBS 12478 scaffold00009, whole genome shotgun sequence
KwoSha/2-92                 -----TCGAAGGATGAGACCTATAC-------TCAGTTATCCCTGTCTTAA---------TTGAC-----------CTGTGTCGAGAATTTT-CCGGCGGGTGGTACCGTCATATCTCTGATAA---
#=GS PapTer/1-92 DE JAHXHD010000491.1:c17403-17312 Papiliotrema terrestris strain LS28 scaffold-490, whole genome shotgun sequence
PapTer/1-92                 -----TTTTATGATGAGACCTATAC-------TCAGTTATCCCTGTCTTAA---------TTGAC-----------CTGTGTCGATAATTCTTCCGGCGAGTGGTATCGCTATTTCTCTGATTC---
#=GS KwoMan/1-92 DE ASQE01000006.1:311456-311547 Kwoniella mangroviensis CBS 8507 cont2.6, whole genome shotgun sequence
KwoMan/1-92                 -----TTCAATGATGAGACTTACTTC------TCAGTTATCCCTGTCTTAAT----------GAC----------ACTGTGTCGAGAATTTT-CCGGCGGGTGGTACCGTCATACCTCTGAATT---
#=GS KwoPin/1-92 DE ASCL01000001.1:431207-431298 Kwoniella pini CBS 10737 cont1.1, whole genome shotgun sequence
KwoPin/1-92                 -----TTTTAGGATGAGACTTACTTC------TCAGTTATCCCTGTCTTAAT----------GAC----------ATTGTGTCGAGAATTTT-CCGGCGGGTGGTACCGTCATACCTCTGAATC---
#=GS TriVee/1-89 DE BCKJ01000010.1:c1200228-1200140 Trichosporon veenhuisii DNA, scaffold: scaffold_9, strain: JCM 10691, whole genome shotgun sequence
TriVee/1-89                 -----TTACATGACGAGACTTCTTT-------TCAGTTATCCCTGTCTTAAT---------CACA----------AATGTGTCGACAGTTTT---CGCGGGTGGTACCGC-ATATCTCTGATAC---
#=GS CryWin/2-98 DE CP034272.1:c417783-417686 Cryptococcus wingfieldii strain CBS7118 chromosome 12, complete sequence
CryWin/2-98                 -----TTTAAGGATGAGACTTACAT-------TCAGTTATCCCTGTCTTAATGGC------TTCG--------GCCTTATGTCGAGGATTTT-CCGGCGGGTGGTACCGTCATACCTCTGAAAC---
#=GS CryAmy/1-97 DE MEKH01000011.1:685186-685282 Cryptococcus amylolentus CBS 6273 supercont2.11, whole genome shotgun sequence
CryAmy/1-97                 -----TTCAAGGATGAGACTTACAT-------TCAGTTATCCCTGTCTTAATGGC------TTCG--------GTCTTATGTCGAGGATTTT-CCGGCGGGTGGTACCGTCATACCTCTGAAAC---
#=GS GofGil/2-93 DE >JANGFI010000887.1:1552-1645 Goffeauzyma gilvescens strain DBVPG 4707 DBVPG_4707;Ctg0887, whole genome shotgun sequence
GofGil/2-93                 -----TCTAAAGATGAGCTTTACATA------TTAGTTATCCCTGTCCAAA----------TGAT-----------TTGTGTCGACGAATTTTCCGACGGATGGTACCGTCATACCTCTGAAAC---
#=GS SacCer-snR38/1-95 DE http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi?mode=sno_info&id=Saccharomyces_cerevisiae300069
SacCer-snR38/1-95           -----CATAATGATGAAAAAAAATTTTATCAAACAGTTATCCCTGTCTGAATGGGTAATAATAGGTAACCTCTCATATGTTGA-----------------------TATTTGTATTTCTGATA----
#=GS HomSap-SNORD1A/1-72 DE http://snoopy.med.miyazaki-u.ac.jp/snorna_db.cgi?mode=sno_info&id=Homo_sapiens300042
HomSap-SNORD1A/1-72         CACAAGCCTATGATGG----------------TTAGTTATCCCTGTCTGAA---------AATCTG----------GACTGAGGGAAATAAT--------------------CTATTCTGAGGCTTA
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