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

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General features for molecule RFA_00793
(click to expand/contract all tables)

Format:
Molecule ID [?]:RFA_00793
Molecule name [?]:Gammaretrovirus core encapsidation signal, RF00374, M64095.1/673-772
Source [?]:Rfam Database
Source ID [?]:RF00374 M64095.1/772-673
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 [?]:100
Fragments used [?]:N/A
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:3
Number of unpaired bases [?]:36
Number of paired bases [?]:64

Click on any header below for additional features.

Stem features

Number of stems [?]:9
Number of base pairs in stems [?]:32
Maximum length of a stem [?]:6
Average length of a stem [?]:3.56
Minimum length of a stem [?]:1
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-5.08
Minimum estimated free energy [?]:-10.2

Hairpin loop features

Number of hairpin loops [?]:3
Maximum number of free bases in hairpin loops [?]:4
Average number of free bases in hairpin loops [?]:4
Minimum number of free bases in hairpin loop [?]:4

Bulge loop features
Number of bulge loops [?]:4
Maximum number of free bases in bulge loops [?]:3
Average number of free bases in bulge loops [?]:0.88
Minimum number of free bases in bulge loop [?]:0

Internal loop features
Number of internal loops [?]:2
Maximum number of free bases in internal loops:2
Average number of free bases in internal loops:1.5
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:0
Average internal loop absolute asymmetry:0
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:1
Average internal loop relative asymmetry:1
Minimum internal loop relative asymmetry:1

Multi-loop features

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 2
Total number of AC non-canonical base pairs:1
Total number of UU non-canonical base pairs:1

Pseudoknot features



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