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

    [ Home | Search | Analyse | Submit structures | News | Help ]



General features for molecule RFA_00660
(click to expand/contract all tables)

Format:
Molecule ID [?]:RFA_00660
Molecule name [?]:Hammerhead ribozyme (type I), RF00163, AF036391.1/121-168
Source [?]:Rfam Database
Source ID [?]:RF00163 AF036391.1/168-121
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 [?]:48
Fragments used [?]:N/A
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:1
Number of unpaired bases [?]:20
Number of paired bases [?]:28

Click on any header below for additional features.

Stem features

Number of stems [?]:3
Number of base pairs in stems [?]:14
Maximum length of a stem [?]:6
Average length of a stem [?]:4.67
Minimum length of a stem [?]:4
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-3.73
Minimum estimated free energy [?]:-8

Hairpin loop features

Number of hairpin loops [?]:2
Maximum number of free bases in hairpin loops [?]:6
Average number of free bases in hairpin loops [?]:3
Minimum number of free bases in hairpin loop [?]:6

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:4.67
Minimum number of free bases in multi-loop:3
Maximum multi-loop absolute asymmetry:4
Average multi-loop absolute asymmetry:2.67
Minimum multi-loop absolute asymmetry:1
Maximum multi-loop relative asymmetry:2.33
Average multi-loop relative asymmetry:1.19
Minimum multi-loop relative asymmetry:0.43
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 [?]: 4
Total number of AC non-canonical base pairs:1
Total number of CC non-canonical base pairs:1
Total number of GG non-canonical base pairs:2

Pseudoknot features



    [ Home | Search | Analyse | Submit structures | News | Help ]

For questions, comments, suggestions and bug reports, please contact:

Copyright © 2004-2008 BETA LAB - University of British Columbia