0  structures 496  species 1972  sequences

Family: mascRNA-menRNA (RF01684)

Description: MALAT1-associated small cytoplasmic RNA/MEN beta RNA

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 MALAT1-associated small cytoplasmic RNA. 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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Note: You can also download the data file for the seed tree.

Motif matches

There are 2 motifs which match this family.

This section shows the Rfam motifs that match sequences within the seed alignment of this family. Users should be aware that the motifs are structural constructs and do not necessarily conform to taxonomic boundaries in the way that Rfam families do. More...

Original order Motif Accession Motif Description Number of Hits Fraction of Hits Sum of Bits Image
7 RM00005 CsrA/RsmA binding motif 7 0.132 63.2 Match Image
7 RM00024 T-loop 36 0.679 397.3 Match Image

References

This section shows the database cross-references that we have for this Rfam family.

Literature references

  1. Wilusz JE, Freier SM, Spector DL Cell. 2008;135:919-932. 3' end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. PUBMED:19041754

  2. Sunwoo H, Dinger ME, Wilusz JE, Amaral PP, Mattick JS, Spector DL Genome Res. 2009;19:347-359. MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. PUBMED:19106332

  3. Ji P, Diederichs S, Wang W, Böing S, Metzger R, Schneider PM, Tidow N, Brandt B, Buerger H, Bulk E, Thomas M, Berdel WE, Serve H, Müller-Tidow C Oncogene. 2003;22:8031-8041. MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer. PUBMED:12970751

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 Marz M, Stadler PF
Structure source Published; PMID:19041754;
Type Gene;
Author Marz MORCID logo, Stadler PFORCID logo, Gardner PPORCID logo
Alignment details
Alignment Number of
sequences
full 1,919
seed 53

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi CM
Search command
cmsearch --cpu 4 --verbose --nohmmonly -T 27.80 -Z 2958934 CM SEQDB
Gathering cutoff 42.0
Trusted cutoff 42.0
Noise cutoff 41.9
Covariance model Download