0  structures 110  species 187  sequences

Family: mir-193 (RF01895)

Description: microRNA mir-193

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-193 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

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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. Lui WO, Pourmand N, Patterson BK, Fire A Cancer Res. 2007;67:6031-6043. Patterns of known and novel small RNAs in human cervical cancer. PUBMED:17616659

  3. Shao P, Zhou H, Xiao ZD, He JH, Huang MB, Chen YQ, Qu LH Gene. 2008;418:34-40. Identification of novel chicken microRNAs and analysis of their genomic organization. PUBMED:18511220

  4. Glazov EA, Cottee PA, Barris WC, Moore RJ, Dalrymple BP, Tizard ML Genome Res. 2008;18:957-964. A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. PUBMED:18469162

  5. Cho IS, Kim J, Seo HY, Lim do H, Hong JS, Park YH, Park DC, Hong KC, Whang KY, Lee YS Mol Biol Rep. 2010;37:3567-3574. Cloning and characterization of microRNAs from porcine skeletal muscle and adipose tissue. PUBMED:20180025

  6. 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

  7. 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

  8. 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

  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. 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

  11. 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

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

  13. 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

  14. Houbaviy HB, Murray MF, Sharp PA; Dev Cell. 2003;5:351-358. Embryonic stem cell-specific MicroRNAs. PUBMED:12919684

  15. 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

  16. 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

  17. 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

  18. Lagos-Quintana M, Rauhut R, Meyer J, Borkhardt A, Tuschl T RNA 2003;9:175-179. New microRNAs from mouse and human. PUBMED:12554859

  19. 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

  20. Devor EJ, Samollow PB J Hered. 2008;99:66-72. In vitro and in silico annotation of conserved and nonconserved microRNAs in the genome of the marsupial Monodelphis domestica. PUBMED:17965199

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

  22. 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

  23. 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

  24. Kuchenbauer F, Morin RD, Argiropoulos B, Petriv OI, Griffith M, Heuser M, Yung E, Piper J, Delaney A, Prabhu AL, Zhao Y, McDonald H, Zeng T, Hirst M, Hansen CL, Marra MA, Humphries RK Genome Res. 2008;18:1787-1797. In-depth characterization of the microRNA transcriptome in a leukemia progression model. PUBMED:18849523

  25. Watanabe T, Takeda A, Tsukiyama T, Mise K, Okuno T, Sasaki H, Minami N, Imai H Genes Dev. 2006;20:1732-1743. Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes. PUBMED:16766679

  26. Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T; Genes Dev. 2005;19:1288-1293. The developmental miRNA profiles of zebrafish as determined by small RNA cloning. PUBMED:15937218

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 170
seed 17

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 21.61 -Z 549862.597050 CM SEQDB
Gathering cutoff 60.0
Trusted cutoff 62.1
Noise cutoff 59.7
Covariance model Download