0  structures 36  species 183  sequences

Family: mir-500 (RF01903)

Description: microRNA mir-500

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-500 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. Linsen SE, de Wit E, de Bruijn E, Cuppen E; BMC Genomics. 2010;11:249. Small RNA expression and strain specificity in the rat. PUBMED:20403161

  2. Zhou M, Wang Q, Sun J, Li X, Xu L, Yang H, Shi H, Ning S, Chen L, Li Y, He T, Zheng Y Genomics. 2009;94:125-131. In silico detection and characteristics of novel microRNA genes in the Equus caballus genome using an integrated ab initio and comparative genomic approach PUBMED:19406225

  3. Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A, Einat P, Einav U, Meiri E, Sharon E, Spector Y, Bentwich Z Nat Genet. 2005;37:766-770. Identification of hundreds of conserved and nonconserved human microRNAs PUBMED:15965474

  4. Wheeler G, Ntounia-Fousara S, Granda B, Rathjen T, Dalmay T FEBS Lett. 2006;580:2195-2200. Identification of new central nervous system specific mouse microRNAs PUBMED:16566924

  5. Strozzi F, Mazza R, Malinverni R, Williams JL Anim Genet. 2009;40:125. Annotation of 390 bovine miRNA genes by sequence similarity with other species PUBMED:18945293

  6. Brameier M BMC Res Notes. 2010;3:64. Genome-wide comparative analysis of microRNAs in three non-human primates PUBMED:20214803

  7. Friedlander MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S, Rajewsky N Nat Biotechnol. 2008;26:407-415. Discovering microRNAs from deep sequencing data using miRDeep PUBMED:18392026

  8. Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A, Marra MA, Rajkovic A Mol Hum Reprod. 2010;16:463-471. MicroRNA transcriptome in the newborn mouse ovaries determined by massive parallel sequencing PUBMED:20215419

  9. Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V, Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B, Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G, Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN, Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo JJ, Sander C, Zavolan M, Tuschl T; Cell. 2007;129:1401-1414. A mammalian microRNA expression atlas based on small RNA library sequencing. PUBMED:17604727

  10. Baev V, Daskalova E, Minkov I Comput Biol Chem. 2009;33:62-70. Computational identification of novel microRNA homologs in the chimpanzee genome PUBMED:18760970

  11. Goff LA, Davila J, Swerdel MR, Moore JC, Cohen RI, Wu H, Sun YE, Hart RP PLoS One. 2009;4:e7192. Ago2 immunoprecipitation identifies predicted microRNAs in human embryonic stem cells and neural precursors PUBMED:19784364

  12. Sharbati S, Friedlander MR, Sharbati J, Hoeke L, Chen W, Keller A, Stahler PF, Rajewsky N, Einspanier R BMC Genomics. 2010;11:275. Deciphering the porcine intestinal microRNA transcriptome PUBMED:20433717

  13. Long JE, Chen HX Biochem Genet. 2009;47:329-343. Identification and characteristics of cattle microRNAs by homology searching and small RNA cloning PUBMED:19267191

  14. Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel DP Genes Dev. 2010;24:992-1009. Mammalian microRNAs: experimental evaluation of novel and previously annotated genes PUBMED:20413612

  15. Yue J, Sheng Y, Orwig KE BMC Genomics. 2008;9:8. Identification of novel homologous microRNA genes in the rhesus macaque genome PUBMED:18186931

  16. Mineno J, Okamoto S, Ando T, Sato M, Chono H, Izu H, Takayama M, Asada K, Mirochnitchenko O, Inouye M, Kato I Nucleic Acids Res. 2006;34:1765-1771. The expression profile of microRNAs in mouse embryos PUBMED:16582102

  17. Jin W, Grant JR, Stothard P, Moore SS, Guan LL BMC Mol Biol. 2009;10:90. Characterization of bovine miRNAs by sequencing and bioinformatics analysis PUBMED:19758457

  18. Artzi S, Kiezun A, Shomron N BMC Bioinformatics. 2008;9:39. miRNAminer: a tool for homologous microRNA gene search PUBMED:18215311

  19. Sewer A, Paul N, Landgraf P, Aravin A, Pfeffer S, Brownstein MJ, Tuschl T, van Nimwegen E, Zavolan M BMC Bioinformatics. 2005;6:267. Identification of clustered microRNAs using an ab initio prediction method PUBMED:16274478

  20. Zhu JY, Strehle M, Frohn A, Kremmer E, Hofig KP, Meister G, Adler H J Virol. 2010;1:1. Identification and analysis of expression of novel microRNAs of murine gammaherpesvirus 68 PUBMED:20668074

  21. Witten D, Tibshirani R, Gu SG, Fire A, Lui WO BMC Biol. 2010;8:58. Ultra-high throughput sequencing-based small RNA discovery and discrete statistical biomarker analysis in a collection of cervical tumours and matched controls PUBMED:20459774

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; ClustalW2
Structure source Predicted; RNAalifold
Type Gene; miRNA;
Author Boursnell CORCID logo
Alignment details
Alignment Number of
sequences
full 157
seed 26

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 62.0
Trusted cutoff 63.1
Noise cutoff 60.8
Covariance model Download