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

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General features for molecule RFA_00654
(click to expand/contract all tables)

Format:
Molecule ID [?]:RFA_00654
Molecule name [?]:Vimentin 3 prime UTR protein-binding region, RF00109, V00447.1/86-155
Source [?]:Rfam Database
Source ID [?]:RF00109 V00447.1/155-86
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 [?]:Cis-regulatory element

[?]     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 [?]:70
Fragments used [?]:N/A
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:1
Number of unpaired bases [?]:34
Number of paired bases [?]:36

Click on any header below for additional features.

Stem features

Number of stems [?]:5
Number of base pairs in stems [?]:18
Maximum length of a stem [?]:6
Average length of a stem [?]:3.6
Minimum length of a stem [?]:2
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-3.44
Minimum estimated free energy [?]:-7.3

Hairpin loop features

Number of hairpin loops [?]:2
Maximum number of free bases in hairpin loops [?]:12
Average number of free bases in hairpin loops [?]:10.5
Minimum number of free bases in hairpin loop [?]:9

Bulge loop features
Number of bulge loops [?]:2
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
Number of multi-loops [?]:1
Maximum number of free bases in multi-loops:3
Average number of free bases in multi-loops:1
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:3
Average multi-loop absolute asymmetry:2
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:0
Average multi-loop relative asymmetry:0
Minimum multi-loop relative asymmetry:0
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 [?]: 3
Total number of CC non-canonical base pairs:1
Total number of UU non-canonical base pairs:2

Pseudoknot features



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