0  structures 103  species 135  sequences

Family: mir-142 (RF01896)

Description: microRNA mir-142

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 MicroRNA. 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 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. Michael MZ, O' Connor SM, van Holst Pellekaan NG, Young GP, James RJ Mol Cancer Res 2003;1:882-891. Reduced accumulation of specific microRNAs in colorectal neoplasia. PUBMED:14573789

  3. 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

  4. 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

  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. Kasashima K, Nakamura Y, Kozu T Biochem Biophys Res Commun. 2004;322:403-410. Altered expression profiles of microRNAs during TPA-induced differentiation of HL-60 cells. PUBMED:15325244

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

  9. 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

  10. Gu Z, Eleswarapu S, Jiang H FEBS Lett. 2007;581:981-988. Identification and characterization of microRNAs from the bovine adipose tissue and mammary gland. PUBMED:17306260

  11. 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

  12. Miska EA, Alvarez-Saavedra E, Townsend M, Yoshii A, Sestan N, Rakic P, Constantine-Paton M, Horvitz HR Genome Biol. 2004;5:R68. Microarray analysis of microRNA expression in the developing mammalian brain. PUBMED:15345052

  13. 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

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

  15. Xu H, Wang X, Du Z, Li N FEBS Lett. 2006;580:3610-3616. Identification of microRNAs from different tissues of chicken embryo and adult chicken. PUBMED:16750530

  16. 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

  17. Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T Curr Biol 2002;12:735-739. Identification of tissue-specific microRNAs from mouse. PUBMED:12007417

  18. Yao Y, Zhao Y, Xu H, Smith LP, Lawrie CH, Watson M, Nair V; J Virol. 2008;82:4007-4015. MicroRNA profile of Marek's disease virus-transformed T-cell line MSB-1: predominance of virus-encoded microRNAs. PUBMED:18256158

  19. Tang GQ, Maxwell ES Genome Res. 2008;18:104-112. Xenopus microRNA genes are predominantly located within introns and are differentially expressed in adult frog tissues via post-transcriptional regulation PUBMED:18032731

  20. 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

  21. 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

  22. 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

  23. Wienholds E, Kloosterman WP, Miska E, Alvarez-Saavedra E, Berezikov E, de Bruijn E, Horvitz HR, Kauppinen S, Plasterk RH Science. 2005;309:310-311. MicroRNA expression in zebrafish embryonic development PUBMED:15919954

  24. International Chicken Genome Sequencing Consortium Nature. 2004;432:695-716. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution PUBMED:15592404

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

  26. 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

  27. 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 122
seed 13

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 73.0
Trusted cutoff 81.4
Noise cutoff 65.7
Covariance model Download