0  structures 57  species 71  sequences

Family: mir-275 (RF00757)

Description: microRNA mir-275

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 Mir-275 microRNA precursor family. More...

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

Sequences

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.

Viewer:

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:
Download/view:

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.

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

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

Selections

Click on a node to select that node and its sub-tree.

Clear selection

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

Hide

The tree shows the occurrence of this RNA across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Trees

This page displays the predicted phylogenetic tree for the alignment. More...

This tree was built using the fasttree method.

Label the trees using or

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. Winter F, Edaye S, Huttenhofer A, Brunel C Nucleic Acids Res. 2007;35:6953-6962. Anopheles gambiae miRNAs as actors of defence reaction against Plasmodium invasion. PUBMED:17933784

  2. Skalsky RL, Vanlandingham DL, Scholle F, Higgs S, Cullen BR BMC Genomics. 2010;11:119. Identification of microRNAs expressed in two mosquito vectors, Aedes albopictus and Culex quinquefasciatus. PUBMED:20167119

  3. Lai EC, Tomancak P, Williams RW, Rubin GM Genome Biol 2003;4:R42. Computational identification of Drosophila microRNA genes. PUBMED:12844358

  4. Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, Snyder B, Gaasterland T, Meyer J, Tuschl T Dev Cell 2003;5:337-350. The small RNA profile during Drosophila melanogaster development. PUBMED:12919683

  5. Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC Genome Res. 2007;17:1850-1864. Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs PUBMED:17989254

  6. Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M Genome Res. 2007;17:1865-1879. Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes PUBMED:17989255

  7. Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Beukeboom LW, Desplan C, Elsik CG, Grimmelikhuijzen CJ, Kitts P, Lynch JA, Murphy T, Oliveira DC, Smith CD, van de Zande L, Worley KC, Zdobnov EM, Aerts M, Albert S, Anaya VH, Anzola JM, Barchuk AR, Behura SK, Bera AN, Berenbaum MR, Bertossa RC, Bitondi MM, Bordenstein SR, Bork P, Bornberg-Bauer E, Brunain M, Cazzamali G, Chaboub L, Chacko J, Chavez D, Childers CP, Choi JH, Clark ME, Claudianos C, Clinton RA, Cree AG, Cristino AS, Dang PM, Darby AC, de Graaf DC, Devreese B, Dinh HH, Edwards R, Elango N, Elhaik E, Ermolaeva O, Evans JD, Foret S, Fowler GR, Gerlach D, Gibson JD, Gilbert DG, Graur D, Grunder S, Hagen DE, Han Y, Hauser F, Hultmark D, Hunter HC 4th, Hurst GD, Jhangian SN, Jiang H, Johnson RM, Jones AK, Junier T, Kadowaki T, Kamping A, Kapustin Y, Kechavarzi B, Kim J, Kim J, Kiryutin B, Koevoets T, Kovar CL, Kriventseva EV, Kucharski R, Lee H, Lee SL, Lees K, Lewis LR, Loehlin DW, Logsdon JM Jr, Lopez JA, Lozado RJ, Maglott D, Maleszka R, Mayampurath A, Mazur DJ, McClure MA, Moore AD, Morgan MB, Muller J, Munoz-Torres MC, Muzny DM, Nazareth LV, Neupert S, Nguyen NB, Nunes FM, Oakeshott JG, Okwuonu GO, Pannebakker BA, Pejaver VR, Peng Z, Pratt SC, Predel R, Pu LL, Ranson H, Raychoudhury R, Rechtsteiner A, Reese JT, Reid JG, Riddle M, Robertson HM, Romero-Severson J, Rosenberg M, Sackton TB, Sattelle DB, Schluns H, Schmitt T, Schneider M, Schuler A, Schurko AM, Shuker DM, Simoes ZL, Sinha S, Smith Z, Solovyev V, Souvorov A, Springauf A, Stafflinger E, Stage DE, Stanke M, Tanaka Y, Telschow A, Trent C, Vattathil S, Verhulst EC, Viljakainen L, Wanner KW, Waterhouse RM, Whitfield JB, Wilkes TE, Williamson M, Willis JH, Wolschin F, Wyder S, Yamada T, Yi SV, Zecher CN, Zhang L, Gibbs RA Science. 2010;327:343-348. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. PUBMED:20075255

  8. Yu X, Zhou Q, Li SC, Luo Q, Cai Y, Lin WC, Chen H, Yang Y, Hu S, Yu J PLoS One. 2008;3:e2997. The silkworm (Bombyx mori) microRNAs and their expressions in multiple developmental stages. PUBMED:18714353

  9. Cao J, Tong C, Wu X, Lv J, Yang Z, Jin Y Insect Biochem Mol Biol. 2008;38:1066-1071. Identification of conserved microRNAs in Bombyx mori (silkworm) and regulation of fibroin L chain production by microRNAs in heterologous system. PUBMED:18977439

  10. Liu S, Li D, Li Q, Zhao P, Xiang Z, Xia Q BMC Genomics. 2010;11:148. MicroRNAs of Bombyx mori identified by Solexa sequencing. PUBMED:20199675

  11. Yu X, Zhou Q, Cai Y, Luo Q, Lin H, Hu S, Yu J Genomics. 2009;94:438-444. A discovery of novel microRNAs in the silkworm (Bombyx mori) genome. PUBMED:19699294

  12. Cai Y, Yu X, Zhou Q, Yu C, Hu H, Liu J, Lin H, Yang J, Zhang B, Cui P, Hu S, Yu J Funct Integr Genomics. 2010;10:405-415. Novel microRNAs in silkworm (Bombyx mori). PUBMED:20229201

  13. Li S, Mead EA, Liang S, Tu Z BMC Genomics. 2009;10:581. Direct sequencing and expression analysis of a large number of miRNAs in Aedes aegypti and a multi-species survey of novel mosquito miRNAs. PUBMED:19961592

  14. Marco A, Hui JH, Ronshaugen M, Griffiths-Jones S Genome Biol Evol. 2010;2:686-696. Functional shifts in insect microRNA evolution. PUBMED:20817720

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 miRBase; Wilkinson A
Structure source Predicted; WAR; Wilkinson A
Type Gene; miRNA;
Author Wilkinson AORCID logo
Alignment details
Alignment Number of
sequences
full 56
seed 15

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
Gathering cutoff 60.0
Trusted cutoff 63.0
Noise cutoff 59.6
Covariance model Download