Wikipedia annotation Edit Wikipedia article
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...
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.
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".
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.
Weight segments by...
Change the size of the sunburst
Click on a node to select that node and its sub-tree.
This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
The tree shows the occurrence of this RNA across different species. More...
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.
This page displays the predicted phylogenetic tree for the alignment. More...
Note: You can also download the data file for the seed tree.
There are 3 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...
|Number of Hits
|Fraction of Hits
|Sum of Bits
This section shows the database cross-references that we have for this Rfam family.
Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS Nucleic Acids Res 2002;30:3141-3151. Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation. PUBMED:12136096
Gelfand MS, Mironov AA, Jomantas J, Kozlov YI, Perumov DA Trends Genet 1999;15:439-442. A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes. PUBMED:10529804
Winkler WC, Cohen-Chalamish S, Breaker RR Proc Natl Acad Sci U S A 2002;99:15908-15913. An mRNA structure that controls gene expression by binding FMN. PUBMED:12456892
Serganov A, Huang L, Patel DJ Nature. 2009;458:233-237. Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch. PUBMED:19169240
Wilt HM, Yu P, Tan K, Wang YX, Stagno JR J Struct Biol X. 2020;4:100035. FMN riboswitch aptamer symmetry facilitates conformational switching through mutually exclusive coaxial stacking configurations. PUBMED:33103111
External database links
|GO:0010181 (FMN binding);
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.
|Vitreshchak A, Gelfand M, Bateman A, Ontiveros-Palacios N
cmbuild -F CM SEED
cmcalibrate --mpi CM
cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 742849.287494 CM SEQDB