Summary
Clan
This family is a member of clan (CL00021), which contains the following 6 members:
snopsi28S-3327 SNORA16 SNORA2 snR189 snR46 S_pombe_snR46Wikipedia annotation Edit Wikipedia article
The Rfam group coordinates the annotation of Rfam families in Wikipedia. This family is described by a Wikipedia entry Small nucleolar RNA. More...
This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.
Sequences
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Table view (25 sequence regions)
Original order | Download FASTA | Accession | Bit score | Type | Start | End | Description | Species | View context |
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0 | X62452.1 | N/A | seed | 873 | 682 | S. cerevisiae DNA for long ORF (YCR 601) | Saccharomyces cerevisiae (baker's yeast) |
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1 | AABZ01000039.1 | N/A | seed | 16,243 | 16,432 | Saccharomyces mikatae IFO 1815 contig_216, whole genome shotgun sequence. | Saccharomyces mikatae IFO 1815 |
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2 | AACA01000006.1 | N/A | seed | 89,474 | 89,283 | Saccharomyces bayanus MCYC 623 contig_94, whole genome shotgun sequence. | Saccharomyces bayanus MCYC 623 |
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3 | AACI02000034.1 | N/A | seed | 9,484 | 9,289 | Saccharomyces kudriavzevii IFO 1802 YM6553-Contig02.2075, whole genome shotgun sequence. | Saccharomyces kudriavzevii IFO 1802 |
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0 | BK006937.2 | 237.70 | full | 178,798 | 178,607 | TPA: Saccharomyces cerevisiae S288C chromosome III, complete sequence. | Saccharomyces cerevisiae S288c |
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1 | JH796485.1 | 218.20 | full | 7,924 | 7,729 | Saccharomyces kudriavzevii IFO 1802 unplaced genomic scaffold c2035, whole genome shotgun sequence. | Saccharomyces kudriavzevii IFO 1802 |
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2 | CM001565.1 | 210.30 | full | 169,001 | 168,811 | Saccharomyces arboricola H-6 chromosome III, whole genome shotgun sequence. | Saccharomyces arboricola H-6 |
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3 | HE616747.1 | 86.20 | full | 544,805 | 544,586 | Torulaspora delbrueckii CBS 1146 chromosome 6, complete genome | Torulaspora delbrueckii CBS 1146 |
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4 | CP058605.1 | 79.10 | full | 1,138,446 | 1,138,246 | CP058605.1 Zygotorulaspora mrakii strain NRRL Y-6702 chromosome 2 | Zygosaccharomyces mrakii |
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5 | DS480383.1 | 74.20 | full | 126,736 | 126,915 | Vanderwaltozyma polyspora DSM 70294 KpolScaffold2002 genomic scaffold, whole genome shotgun sequence. | Vanderwaltozyma polyspora DSM 70294 |
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6 | LT598469.1 | 69.10 | full | 669,103 | 669,236 | Lachancea mirantina genome assembly, chromosome: G | Lachancea mirantina |
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7 | LT598486.1 | 67.90 | full | 348,663 | 348,825 | Lachancea fermentati genome assembly, chromosome: G | Lachancea fermentati |
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8 | HE612860.1 | 67.50 | full | 740,259 | 739,986 | Tetrapisispora phaffii CBS 4417 chromosome 5, complete genome | Tetrapisispora phaffii CBS 4417 |
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9 | CR382122.1 | 66.90 | full | 666,607 | 666,503 | Kluyveromyces lactis strain NRRL Y-1140 chromosome B complete sequence. | Kluyveromyces lactis |
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10 | CU928170.1 | 66.30 | full | 344,383 | 344,555 | Lachancea thermotolerans CBS 6340 chromosome F complete sequence. | Lachancea thermotolerans CBS 6340 |
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11 | CP059270.1 | 64.60 | full | 420,444 | 420,665 | CP059270.1 Torulaspora sp. CBS 2947 strain CBS2947 chromosome 4 | Torulaspora sp. CBS 2947 |
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12 | HE576760.1 | 62.80 | full | 564,497 | 564,286 | Naumovozyma castellii CBS 4309 chromosome 9, complete genome | Naumovozyma castellii CBS 4309 |
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13 | AE016818.2 | 61.60 | full | 344,509 | 344,687 | Ashbya gossypii ATCC 10895 chromosome V, complete sequence. | Ashbya gossypii ATCC 10895 |
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14 | LT598461.1 | 61.30 | full | 332,599 | 332,710 | Lachancea dasiensis CBS 10888 genome assembly, chromosome: H | Lachancea dasiensis CBS 10888 |
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15 | CU928175.1 | 60.90 | full | 951,861 | 951,664 | Zygosaccharomyces rouxii strain CBS732 chromosome C complete sequence. | Zygosaccharomyces rouxii CBS 732 |
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16 | LN736370.1 | 60.20 | full | 327,537 | 327,679 | Lachancea lanzarotensis strain CBS 12615 genome assembly, scaffold: LALA0S11 | Lachancea lanzarotensis |
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17 | JAEUBF010000325.1 | 55.10 | full | 30,272 | 30,143 | JAEUBF010000325.1 Wickerhamomyces mucosus strain CBS6341 scaffold51, whole genome shotgun sequence | Wickerhamomyces mucosus |
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18 | CP002504.1 | 53.60 | full | 275,962 | 275,775 | Eremothecium cymbalariae DBVPG#7215 chromosome 8, complete sequence. | Eremothecium cymbalariae DBVPG#7215 |
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19 | MPUK01000003.1 | 52.90 | full | 621,184 | 620,998 | Cyberlindnera fabianii strain 65 BON22_Sc03, whole genome shotgun sequence. | Cyberlindnera fabianii |
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20 | FXLY01000003.1 | 51.70 | full | 1,277,959 | 1,278,150 | Kazachstania saulgeensis genome assembly, contig: scaffold_02 | Kazachstania saulgeensis |
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Alignment
There are various ways to view or download the seed alignments that we store. You can use a sequence viewer to look at them, or you can look at a plain text version of the sequence in a variety of different formats. More...
View options
You can view Rfam seed alignments in your browser in various ways. Choose the viewer that you want to use and click the "View" button to show the alignment in a pop-up window.
Formatting options
You can view or download Rfam seed alignments in several formats. Check either the "download" button, to save the formatted alignment, or "view", to see it in your browser window, and click "Generate".
Download
Download a gzip-compressed, Stockholm-format file containing the seed alignment for this family. You may find RALEE useful when viewing sequence alignments.
Submit a new alignment
We're happy receive updated seed alignments for new or existing families. Submit your new alignment and we'll take a look.
Secondary structure
Species distribution
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Colour assignments
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Selections
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...
Tree controls
HideThe tree shows the occurrence of this RNA across different species. More...
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Trees
This page displays the predicted phylogenetic tree for the alignment. More...
Note: You can also download the data file for the seed tree.
References
This section shows the database cross-references that we have for this Rfam family.
Literature references
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Thompson JR, Zagorski J, Woolford JL, Fournier MJ Nucleic Acids Res. 1988;16:5587-5601. Sequence and genetic analysis of a dispensible 189 nucleotide snRNA from Saccharomyces cerevisiae. PUBMED:3290853
External database links
Gene Ontology: | GO:0006396 (RNA processing); GO:0005730 (nucleolus); |
Sequence Ontology: | SO:0000594 (H_ACA_box_snoRNA); |
Curation and family details
This section shows the detailed information about the Rfam family. We're happy to receive updated or improved alignments for new or existing families. Submit your new alignment and we'll take a look.
Curation
Seed source | Predicted; WAR; Wilkinson A | ||||||
Structure source | Predicted; WAR; Wilkinson A | ||||||
Type | Gene; snRNA; snoRNA; HACA-box; | ||||||
Author |
Wilkinson A |
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Alignment details |
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Model information
Build commands |
cmbuild -F CM SEED
cmcalibrate --mpi CM
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Search command |
cmsearch --cpu 4 --verbose --nohmmonly -T 29.00 -Z 2958934 CM SEQDB
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Gathering cutoff | 50.0 |
Trusted cutoff | 51.7 |
Noise cutoff | 49.8 |
Covariance model | Download |