0  structures 16  species 41  sequences

Family: TB10Cs1H3 (RF01524)

Description: Trypanosomatid snoRNA TB10cs1H3

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 Trypanosome H/ACA box snoRNAs. 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 (41 sequence regions)

Original order Download FASTA Accession Bit score Type Start End Description Species View context
0
AAHK01011372.1 N/A seed 538 464 Trypanosoma cruzi strain CL Brener tcruzi_1047053427975, whole genome shotgun sequence. Trypanosoma cruzi ENA graphic
1
AAHA01000001.1 N/A seed 1,729,154 1,729,225 Trypanosoma brucei brucei strain 927/4 GUTat10.1 chromosome 10 tba1_340_1, whole genome shotgun sequence. Trypanosoma brucei brucei strain 927/4 GUTat10.1 ENA graphic
2
FR799010.1 N/A seed 955,856 955,929 Leishmania braziliensis MHOM/BR/75/M2904 complete genome, chromosome 36 Leishmania braziliensis MHOM/BR/75/M2904 ENA graphic
3
FR796468.1 N/A seed 1,551,018 1,551,091 Leishmania infantum JPCM5 genome chromosome 36 Leishmania infantum JPCM5 ENA graphic
4
FN554973.1 N/A seed 1,694,600 1,694,671 Trypanosoma brucei gambiense DAL972 chromosome 10, complete sequence Trypanosoma brucei gambiense DAL972 ENA graphic
0
CM000208.1 91.50 full 1,729,154 1,729,225 Trypanosoma brucei brucei strain 927/4 GUTat10.1 chromosome 10, whole genome shotgun sequence. Trypanosoma brucei TREU927 ENA graphic
1
CM000208.1 89.40 full 1,730,617 1,730,688 Trypanosoma brucei brucei strain 927/4 GUTat10.1 chromosome 10, whole genome shotgun sequence. Trypanosoma brucei TREU927 ENA graphic
2
CM000208.1 89.40 full 1,738,889 1,738,960 Trypanosoma brucei brucei strain 927/4 GUTat10.1 chromosome 10, whole genome shotgun sequence. Trypanosoma brucei TREU927 ENA graphic
3
FR796468.1 88.20 full 1,552,239 1,552,312 Leishmania infantum JPCM5 genome chromosome 36 Leishmania infantum JPCM5 ENA graphic
4
FR796468.1 88.20 full 934,654 934,727 Leishmania infantum JPCM5 genome chromosome 36 Leishmania infantum JPCM5 ENA graphic
5
AAHK01005119.1 87.10 full 129 203 Trypanosoma cruzi strain CL Brener tcruzi_1047053431855, whole genome shotgun sequence. Trypanosoma cruzi strain CL Brener ENA graphic
6
AAHK01005119.1 87.10 full 1,547 1,621 Trypanosoma cruzi strain CL Brener tcruzi_1047053431855, whole genome shotgun sequence. Trypanosoma cruzi strain CL Brener ENA graphic
7
CH473379.1 87.10 full 65,475 65,401 Trypanosoma cruzi strain CL Brener 1047053516661 genomic scaffold, whole genome shotgun sequence. Trypanosoma cruzi strain CL Brener ENA graphic
8
FR796432.1 86.80 full 942,463 942,536 Leishmania major strain Friedlin complete genome, chromosome 36 Leishmania major strain Friedlin ENA graphic
9
AYLP01000112.1 85.70 full 42,507 42,433 Trypanosoma cruzi Dm28c contig00112, whole genome shotgun sequence. Trypanosoma cruzi Dm28c ENA graphic
10
AAHK01027807.1 85.70 full 528 454 Trypanosoma cruzi strain CL Brener tcruzi_1047053452225, whole genome shotgun sequence. Trypanosoma cruzi strain CL Brener ENA graphic
11
FR799010.1 85.60 full 956,972 957,045 Leishmania braziliensis MHOM/BR/75/M2904 complete genome, chromosome 36 Leishmania braziliensis MHOM/BR/75/M2904 ENA graphic
12
AHKC01009854.1 83.50 full 2,959 3,033 Trypanosoma cruzi marinkellei strain B7 TcMARK_CONTIG_9855, whole genome shotgun sequence. Trypanosoma cruzi marinkellei ENA graphic
13
NBCO01000002.1 80.30 full 428,637 428,565 Trypanosoma theileri isolate Edinburgh TM35_Tth_2_V1, whole genome shotgun sequence. Trypanosoma theileri ENA graphic
14
MKGL01000353.1 77.40 full 19,211 19,285 MKGL01000353.1 Trypanosoma rangeli strain AM80 Tra_15.4_contig_00352, whole genome shotgun sequence Trypanosoma rangeli ENA graphic
15
MKGL01000914.1 77.40 full 1,006 1,080 MKGL01000914.1 Trypanosoma rangeli strain AM80 Tra_15.4_contig_00961, whole genome shotgun sequence Trypanosoma rangeli ENA graphic
16
MKGL01000914.1 77.40 full 187 261 MKGL01000914.1 Trypanosoma rangeli strain AM80 Tra_15.4_contig_00961, whole genome shotgun sequence Trypanosoma rangeli ENA graphic
17
MKGL01000914.1 77.40 full 2,464 2,538 MKGL01000914.1 Trypanosoma rangeli strain AM80 Tra_15.4_contig_00961, whole genome shotgun sequence Trypanosoma rangeli ENA graphic
18
MKGL01000135.1 76.80 full 765 691 MKGL01000135.1 Trypanosoma rangeli strain AM80 Tra_15.4_contig_00137, whole genome shotgun sequence Trypanosoma rangeli ENA graphic
19
MKKU01000730.1 75.70 full 499 424 MKKU01000730.1 Trypanosoma conorhini strain 025E Tco_14.4_contig_00735, whole genome shotgun sequence Trypanosoma conorhini ENA graphic
20
CAEX01000471.1 75.60 full 387 459 Trypanosoma vivax Y486, WGS project CAEX01000000 data, contig: 1423 Trypanosoma vivax Y486 ENA graphic
21
AAHK01007050.1 69.90 full 1,265 1,191 Trypanosoma cruzi strain CL Brener tcruzi_1047053426515, whole genome shotgun sequence. Trypanosoma cruzi strain CL Brener ENA graphic
22
AAHK01009958.1 69.90 full 496 570 Trypanosoma cruzi strain CL Brener tcruzi_1047053423485, whole genome shotgun sequence. Trypanosoma cruzi strain CL Brener ENA graphic
23
CH473379.1 69.90 full 77,034 76,960 Trypanosoma cruzi strain CL Brener 1047053516661 genomic scaffold, whole genome shotgun sequence. Trypanosoma cruzi strain CL Brener ENA graphic
24
CH473379.1 69.90 full 78,460 78,386 Trypanosoma cruzi strain CL Brener 1047053516661 genomic scaffold, whole genome shotgun sequence. Trypanosoma cruzi strain CL Brener ENA graphic
25
LGTL01000009.1 62.20 full 810,322 810,394 Leptomonas pyrrhocoris LpyrH10_09, whole genome shotgun sequence. Leptomonas pyrrhocoris ENA graphic
26
LGTL01000009.1 62.20 full 817,909 817,981 Leptomonas pyrrhocoris LpyrH10_09, whole genome shotgun sequence. Leptomonas pyrrhocoris ENA graphic
27
LGTL01000009.1 62.20 full 816,632 816,704 Leptomonas pyrrhocoris LpyrH10_09, whole genome shotgun sequence. Leptomonas pyrrhocoris ENA graphic
28
LGTL01000009.1 62.20 full 815,380 815,452 Leptomonas pyrrhocoris LpyrH10_09, whole genome shotgun sequence. Leptomonas pyrrhocoris ENA graphic
29
LGTL01000009.1 62.20 full 814,103 814,175 Leptomonas pyrrhocoris LpyrH10_09, whole genome shotgun sequence. Leptomonas pyrrhocoris ENA graphic
30
LGTL01000009.1 62.20 full 812,826 812,898 Leptomonas pyrrhocoris LpyrH10_09, whole genome shotgun sequence. Leptomonas pyrrhocoris ENA graphic
31
LGTL01000009.1 62.20 full 811,574 811,646 Leptomonas pyrrhocoris LpyrH10_09, whole genome shotgun sequence. Leptomonas pyrrhocoris ENA graphic
32
LGTL01000009.1 62.20 full 809,045 809,117 Leptomonas pyrrhocoris LpyrH10_09, whole genome shotgun sequence. Leptomonas pyrrhocoris ENA graphic
33
LGTL01000009.1 62.20 full 807,775 807,847 Leptomonas pyrrhocoris LpyrH10_09, whole genome shotgun sequence. Leptomonas pyrrhocoris ENA graphic
34
LR877147.1 52.50 full 696,484 696,557 LR877147.1 Angomonas deanei strain Crithidia deanei Carvalho (ATCC PRA-265) genome assembly, chromosome: 03 Angomonas deanei ENA graphic
35
LR877147.1 50.10 full 876,696 876,626 LR877147.1 Angomonas deanei strain Crithidia deanei Carvalho (ATCC PRA-265) genome assembly, chromosome: 03 Angomonas deanei 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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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.

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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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Lineage

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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...

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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.

References

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

Literature references

  1. Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S RNA. 2005;11:619-645. A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA modification. PUBMED:15840815

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 Predicted; WAR;
Structure source Predicted; WAR;
Type Gene; snRNA; snoRNA; HACA-box;
Author Doniger TORCID logo, Michaeli S, Unger R, Osuch I
Alignment details
Alignment Number of
sequences
full 36
seed 5

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 26.72 -Z 2958934 CM SEQDB
Gathering cutoff 50.0
Trusted cutoff 50.1
Noise cutoff 47.1
Covariance model Download
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