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

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General features for molecule RFA_00446
(click to expand/contract all tables)

Format:
Molecule ID [?]:RFA_00446
Molecule name [?]:Hammerhead ribozyme (type III), RF00008, M63666.1/246-192
Source [?]:Rfam Database
Source ID [?]:RF00008 M63666.1/192-246
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 [?]:Hammerhead Ribozyme

[?]     PS figure     PDF figure
Figure from original source
Organism [?]:N/A
Validated by NMR or X-Ray [?]:No
Method for secondary structure determination [?]:Comparative sequence analysis
Number of molecules [?]:1
Length [?]:55
Fragments used [?]:N/A
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:1
Number of unpaired bases [?]:25
Number of paired bases [?]:30

Click on any header below for additional features.

Stem features

Number of stems [?]:3
Number of base pairs in stems [?]:15
Maximum length of a stem [?]:6
Average length of a stem [?]:5
Minimum length of a stem [?]:4
Maximum estimated free energy [?]:-7.5
Average estimated free energy [?]:-8.4
Minimum estimated free energy [?]:-9.8

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 [?]:6
Minimum number of free bases in hairpin loop [?]:4

Bulge loop features
Number of bulge loops [?]:0
Maximum number of free bases in bulge loops [?]:N/A
Average number of free bases in bulge loops [?]:N/A
Minimum number of free bases in bulge loop [?]:N/A

Internal loop features

Multi-loop features
Number of multi-loops [?]:1
Maximum number of free bases in multi-loops:7
Average number of free bases in multi-loops:3.67
Minimum number of free bases in multi-loop:1
Maximum multi-loop absolute asymmetry:6
Average multi-loop absolute asymmetry:4
Minimum multi-loop absolute asymmetry:2
Maximum multi-loop relative asymmetry:7
Average multi-loop relative asymmetry:2.21
Minimum multi-loop relative asymmetry:0.14
Maximum number of branches in multi-loops:3
Average number of branches in multi-loops:3
Minimum number of branches in multi-loops:3

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

Pseudoknot features



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