0  structures 21  species 21  sequences

Family: snoR29 (RF01603)

Description: small nucleolar RNA snoR29

Summary

Wikipedia 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 (21 sequence regions)

Original order Download FASTA Accession Bit score Type Start End Description Species View context
0
ABHA01003077.1 N/A seed 169 252 Plasmodium falciparum Santa Lucia cont1.3077, whole genome shotgun sequence. Plasmodium falciparum Santa Lucia ENA graphic
1
ABGY01002358.1 N/A seed 1,180 1,264 Plasmodium falciparum D6 cont1.2358, whole genome shotgun sequence. Plasmodium falciparum D6 ENA graphic
2
AABL01002376.1 N/A seed 9,610 9,528 Plasmodium yoelii yoelii 17XNL contig MALPY02383, whole genome shotgun sequence. Plasmodium yoelii yoelii ENA graphic
0
KE123882.1 110.30 full 141,372 141,456 Plasmodium falciparum NF54 unplaced genomic scaffold supercont1.338, whole genome shotgun sequence. Plasmodium falciparum NF54 ENA graphic
1
KE124730.1 110.30 full 20,422 20,506 Plasmodium falciparum UGT5.1 unplaced genomic scaffold supercont1.496, whole genome shotgun sequence. Plasmodium falciparum UGT5.1 ENA graphic
2
KI925618.1 110.30 full 126,557 126,641 Plasmodium falciparum MaliPS096_E11 unplaced genomic scaffold supercont1.150, whole genome shotgun sequence. Plasmodium falciparum MaliPS096_E11 ENA graphic
3
KI926537.1 110.30 full 57,229 57,313 Plasmodium falciparum Tanzania (2000708) unplaced genomic scaffold supercont1.288, whole genome shotgun sequence. Plasmodium falciparum Tanzania (2000708) ENA graphic
4
KI927384.1 110.30 full 1,027,804 1,027,888 Plasmodium falciparum Palo Alto/Uganda unplaced genomic scaffold supercont1.147, whole genome shotgun sequence. Plasmodium falciparum Palo Alto/Uganda ENA graphic
5
KI927559.1 110.30 full 14,355 14,439 KI927559.1 Plasmodium falciparum CAMP/Malaysia unplaced genomic scaffold supercont1.104, whole genome shotgun sequence Plasmodium falciparum (isolate Camp / Malaysia) ENA graphic
6
LN999946.1 110.30 full 981,588 981,672 LN999946.1 Plasmodium falciparum 3D7 genome assembly, chromosome: 14 Plasmodium falciparum 3D7 ENA graphic
7
CH671967.1 110.30 full 93,341 93,425 CH671967.1 Plasmodium falciparum HB3 supercont1.50 genomic scaffold, whole genome shotgun sequence Plasmodium falciparum HB3 ENA graphic
8
LK023125.2 92.60 full 805,128 805,046 LK023125.2 Plasmodium berghei ANKA genome assembly, chromosome: 10 Plasmodium berghei str. ANKA ENA graphic
9
GG665194.1 82.70 full 17,443 17,530 Plasmodium falciparum IGH-CR14 genomic scaffold supercont1.236, whole genome shotgun sequence. Plasmodium falciparum IGH-CR14 ENA graphic
10
LN835308.1 71.60 full 1,063,467 1,063,390 LN835308.1 Plasmodium relictum strain SGS1 genome assembly, chromosome: 13 Plasmodium relictum ENA graphic
11
LT594634.1 60.20 full 1,313,364 1,313,281 LT594634.1 Plasmodium malariae genome assembly, chromosome: 13 Plasmodium malariae ENA graphic
12
CM000454.1 57.60 full 1,056,445 1,056,358 Plasmodium vivax chromosome 13, whole genome shotgun sequence. Plasmodium vivax Sal-1 ENA graphic
13
FLQU01000572.1 55.00 full 650 730 Plasmodium ovale curtisi genome assembly, contig: contig572 Plasmodium ovale curtisi ENA graphic
14
LT594594.1 55.00 full 1,135,342 1,135,262 LT594594.1 Plasmodium ovale genome assembly, chromosome: 13 Plasmodium ovale (malaria parasite P. ovale) ENA graphic
15
AM910995.2 53.90 full 1,526,121 1,526,034 AM910995.2 Plasmodium knowlesi strain H genome assembly, chromosome: 13 Plasmodium knowlesi strain H ENA graphic
16
DF157105.1 53.90 full 1,095,172 1,095,085 Plasmodium cynomolgi strain B DNA, chromosome 13. Plasmodium cynomolgi strain B ENA graphic
17
FLRD01000136.1 51.70 full 196,653 196,575 FLRD01000136.1 Plasmodium ovale wallikeri genome assembly, contig: contig136, whole genome shotgun sequence Plasmodium ovale wallikeri ENA graphic

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.

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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".

Alignment format:
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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

This section shows a variety of different secondary structure representations for this family. More...

You can view the secondary structure of the family using the VARNA applet. You can see more information about VARNA iself here.

Current Rfam structure

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R-scape optimised structure

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  • Colours
  •  Statistically significant basepair with covariation
  •  97% conserved nucleotide
  •  90% conserved nucleotide
  •  75% conserved nucleotide
  •  50% conserved nucleotide
  • Nucleotides
  • R: A or G
  • Y: C or U

Tip: The diagrams are interactive:
you can pan and zoom to see more details
or hover over nucleotides and basepairs.

R-scape is a method for testing whether covariation analysis supports the presence of a conserved RNA secondary structure. This page shows R-scape analysis of the secondary structure from the Rfam seed alignment and a new structure with covariation support that is compatible with the same alignment.

To find out more about the method, see the R-scape paper by Rivas et al., 2016. The structures are visualised using R2R.

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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

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The 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...

This tree was built using the fasttree method.

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Note: You can also download the data file for the seed tree.

Motif matches

There are 1 motifs which match this family.

This section shows the Rfam motifs that match sequences within the seed alignment of this family. Users should be aware that the motifs are structural constructs and do not necessarily conform to taxonomic boundaries in the way that Rfam families do. More...

Original order Motif Accession Motif Description Number of Hits Fraction of Hits Sum of Bits Image
7 RM00004 CRC binding motif 4 1.333 30.4 Match Image

References

This section shows the database cross-references that we have for this Rfam family.

Literature references

  1. Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP, Ares M Jr; RNA. 2007;13:1923-1939. Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis. PUBMED:17901154

External database links

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 INFERNAL
Structure source Predicted; Osuch I
Type Gene; snRNA; snoRNA; CD-box;
Author Osuch I
Alignment details
Alignment Number of
sequences
full 18
seed 3

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 35.65 -Z 2958934 CM SEQDB
Gathering cutoff 50.0
Trusted cutoff 51.7
Noise cutoff 44.1
Covariance model Download
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