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-399 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.
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".
Download
Download a gzip-compressed, Stockholm-format file containing the seed alignment for this family. You may find RALEE useful when viewing sequence alignments.
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.
Secondary structure
Species distribution
Sunburst controls
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Change the size of the sunburst
Colour assignments
Archea | Eukaryota |
Bacteria | Other sequences |
Viruses | Unclassified |
Viroids | Unclassified sequence |
Selections
Click on a node to select that node and its sub-tree.
Clear selection
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...
Tree controls
HideThe tree shows the occurrence of this RNA across different species. More...
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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.
Trees
This page displays the predicted phylogenetic tree for the alignment. More...
Note: You can also download the data file for the seed tree.
References
This section shows the database cross-references that we have for this Rfam family.
Literature references
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Jones-Rhoades MW, Bartel DP; Mol Cell 2004;14:787-799. Computational Identification of Plant MicroRNAs and Their Targets, Including a Stress-Induced miRNA. PUBMED:15200956
External database links
Gene Ontology: | GO:0035195 (miRNA-mediated post-transcriptional gene silencing); GO:0016442 (RISC complex); |
Sequence Ontology: | SO:0001244 (pre_miRNA); |
MicroRNA: | MI0001020 MI0001021 MI0001022 MI0001023 MI0001024 MI0001025 MI0001053 MI0001054 MI0001055 MI0001056 MI0001057 MI0001058 MI0001059 MI0001060 MI0001061 MI0001062 MI0001063 MI0001064 MI0001065 |
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 | Moxon SJ | ||||||
Structure source | Predicted; PFOLD | ||||||
Type | Gene; miRNA; | ||||||
Author | Moxon SJ | ||||||
Alignment details |
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Model information
Build commands |
cmbuild -F CM SEED
cmcalibrate --mpi CM
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Search command |
cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 2958934 CM SEQDB
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Gathering cutoff | 57.0 |
Trusted cutoff | 57.0 |
Noise cutoff | 56.9 |
Covariance model | Download |