Summary
Wikipedia annotation Edit Wikipedia article
The Rfam group coordinates the annotation of Rfam data in Wikipedia. This motif is described by a Wikipedia entry entitled Shine-Dalgarno sequence. More...
This page is based on a wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.
Alignments
You can either download the motif alignment or view it directly in your browser window. More...
Formatting options
You can view or download motif 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".
Family matches
There are 13 Rfam families which match this motif.
This section shows the families which have been annotated with this motif. 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 | Family Accession | Family Description | Number of Hits | Fraction of Hits | Sum of Bits | Image |
---|---|---|---|---|---|---|
3 | RF00265 | Small nucleolar RNA SNORA69 | 7 | 0.438 | 141.9 | |
3 | RF00503 | RNAIII | 3 | 0.300 | 43.3 | |
3 | RF01471 | Listeria sRNA rliB | 2 | 0.500 | 33.2 | |
3 | RF01473 | Listeria sRNA rli41 | 6 | 1.000 | 111.4 | |
3 | RF01492 | Listeria sRNA rli28 | 2 | 0.095 | 32.7 | |
3 | RF01570 | Dictyostelium signal recognition particle | 2 | 0.667 | 39.4 | |
3 | RF01766 | cspA thermoregulator | 3 | 0.200 | 51.6 | |
3 | RF01824 | RNA of unknown function 20 | 2 | 0.333 | 28.6 | |
3 | RF01888 | Embryonic ventral forebrain RNA 1 conserved region 2 | 10 | 0.526 | 146.7 | |
3 | RF02052 | Enterobacterial sRNA STnc630 | 8 | 0.800 | 123.8 | |
3 | RF02574 | Rickettsia sRNA 10 | 2 | 0.667 | 32.7 | |
3 | RF02644 | S. pyogenes small RNA Spy490380c | 4 | 1.000 | 65.6 | |
3 | RF04310 | nqrA-II ncRNA motif | 2 | 0.133 | 30.2 |
References
This section shows the database cross-references that we have for this Rfam motif.
Literature references
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Shine J, Dalgarno L Nature. 1975;254:34-38. Determinant of cistron specificity in bacterial ribosomes. PUBMED:803646
External database links
Curation and motif details
This section shows the detailed information about the Rfam motif. 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; Gardner PP | ||||||||
Structure source | N/A | ||||||||
Type | Specific Recognition Motif | ||||||||
Author | Gardner PP | ||||||||
Alignment details |
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Model information
Build commands |
cmbuild -F CM SEED
cmcalibrate --mpi --seed 1 CM
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Gathering cutoff | 14.0 |
Covariance model | Download the Infernal CM for the motif here |