RNA STRAND v2.0 - The RNA secondary STRucture and statistical ANalysis Database

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General features for molecule RFA_00638
(click to expand/contract all tables)

Format:
Molecule ID [?]:RFA_00638
Molecule name [?]:Hepatitis delta virus ribozyme, RF00094, U81988.1/679-767
Source [?]:Rfam Database
Source ID [?]:RF00094 U81988.1/767-679
Reference [?]:Sam Griffiths-Jones, Simon Moxon, Mhairi Marshall, Ajay Khanna, Sean R. Eddy and Alex Bateman, Rfam: annotating non-coding RNAs in complete genomes, Nucleic Acids Res. 2005 33:D121-D124.
Type [?]:Hepatitis Delta Virus Ribozyme

[?]     PS figure     PDF figure
Figure from original source
Organism [?]:Hepatitis delta virus
Validated by NMR or X-Ray [?]:No
Method for secondary structure determination [?]:Comparative sequence analysis
Number of molecules [?]:1
Length [?]:89
Fragments used [?]:N/A
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:1
Number of unpaired bases [?]:33
Number of paired bases [?]:56

Click on any header below for additional features.

Stem features

Number of stems [?]:3
Number of base pairs in stems [?]:16
Maximum length of a stem [?]:9
Average length of a stem [?]:5.33
Minimum length of a stem [?]:3
Maximum estimated free energy [?]:-4.1
Average estimated free energy [?]:-10.3
Minimum estimated free energy [?]:-20.1

Hairpin loop features

Number of hairpin loops [?]:2
Maximum number of free bases in hairpin loops [?]:8
Average number of free bases in hairpin loops [?]:5.5
Minimum number of free bases in hairpin loop [?]:3

Bulge loop features
Number of bulge loops [?]:1
Maximum number of free bases in bulge loops [?]:1
Average number of free bases in bulge loops [?]:0.5
Minimum number of free bases in bulge loop [?]:0

Internal loop features

Multi-loop features

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 1
Total number of AC non-canonical base pairs:1

Pseudoknot features
Number of pseudoknots [?]:1
Number of bands:2
Number of base pairs in bands:12
Maximum band length:6
Average band length:6
Minimum band length:6
Maximum number of bands per pseudoknot:2
Average number of bands per pseudoknot:2
Minimum number of bands per pseudoknot:2
Maximum number of un-bands:2
Average number of un-bands:2
Minimum number of un-bands:2
Maximum number of in-bands:0
Average number of in-bands:0
Minimum number of in-bands:0
Maximum number of unpaired bases:15
Average number of unpaired bases:15
Minimum number of unpaired bases:15
Several ways to remove minimum number of base pairs, per molecule:Yes
Minimum number of base pairs to remove, per molecule:6
Maximum number of base pairs to remove, per pseudoknot:6
Average number of base pairs to remove, per pseudoknot:6
Minimum number of base pairs to remove, per pseudoknot:6
Minimum number of bands to remove, per molecule:1
Maximum number of bands to remove, per pseudoknot:1
Average number of bands to remove, per pseudoknot:1
Minimum number of bands to remove, per pseudoknot:1



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