0  structures 103  species 122  sequences

Family: mir-363 (RF01898)

Description: microRNA mir-363

Summary

Clan

This family is a member of clan (CL00110), which contains the following 2 members:

mir-19 mir-363

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-363 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.

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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.

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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.

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...

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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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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. 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

  3. Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Kunstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J, Southey B, Gunaratne P, Watson M, Nam K, Backstrom N, Smeds L, Nabholz B, Itoh Y, Whitney O, Pfenning AR, Howard J, Volker M, Skinner BM, Griffin DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J, Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H, Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T, Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK Nature. 2010;464:757-762. The genome of a songbird. PUBMED:20360741

  4. Nielsen M, Hansen JH, Hedegaard J, Nielsen RO, Panitz F, Bendixen C, Thomsen B Anim Genet. 2010;41:159-168. MicroRNA identity and abundance in porcine skeletal muscles determined by deep sequencing. PUBMED:19917043

  5. 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

  6. Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z, Kellis M, Grutzner F, Stark A, Hannon GJ Genome Res. 2008;18:995-1004. Conservation of small RNA pathways in platypus. PUBMED:18463306

  7. 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

  8. Coutinho LL, Matukumalli LK, Sonstegard TS, Van Tassell CP, Gasbarre LC, Capuco AV, Smith TP Physiol Genomics. 2007;29:35-43. Discovery and profiling of bovine microRNAs from immune-related and embryonic tissues. PUBMED:17105755

  9. 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

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

  11. 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

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

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

  14. 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

  15. 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

  16. Kozomara A, Birgaoanu M, Griffiths-Jones S Nucleic Acids Res. 2019;47:D155. miRBase: from microRNA sequences to function. PUBMED:30423142

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 Griffiths-Jones SR
Structure source Predicted; RNAalifold
Type Gene; miRNA;
Author Griffiths-Jones SRORCID logo
Alignment details
Alignment Number of
sequences
full 100
seed 22

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 25.00 -Z 742849.287494 CM SEQDB
Gathering cutoff 58.0
Trusted cutoff 58.1
Noise cutoff 48.7
Covariance model Download