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

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General features for molecule RFA_00628
(click to expand/contract all tables)

Format:
Molecule ID [?]:RFA_00628
Molecule name [?]:RNase E 5 prime UTR element, RF00040, AF259269.1/38-376
Source [?]:Rfam Database
Source ID [?]:RF00040 AF259269.1/376-38
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 [?]:RNase E 5 UTR

[?]     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 [?]:339
Fragments used [?]:N/A
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:3
Number of unpaired bases [?]:167
Number of paired bases [?]:172

Click on any header below for additional features.

Stem features

Number of stems [?]:15
Number of base pairs in stems [?]:86
Maximum length of a stem [?]:11
Average length of a stem [?]:5.73
Minimum length of a stem [?]:2
Maximum estimated free energy [?]:-3.4
Average estimated free energy [?]:-10.01
Minimum estimated free energy [?]:-25.1

Hairpin loop features

Number of hairpin loops [?]:5
Maximum number of free bases in hairpin loops [?]:11
Average number of free bases in hairpin loops [?]:6.4
Minimum number of free bases in hairpin loop [?]:4

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
Number of internal loops [?]:8
Maximum number of free bases in internal loops:17
Average number of free bases in internal loops:5.62
Minimum number of free bases in internal loop:2
Maximum internal loop absolute asymmetry:9
Average internal loop absolute asymmetry:3.25
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:4
Average internal loop relative asymmetry:1.75
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:1
Maximum number of free bases in multi-loops:9
Average number of free bases in multi-loops:5.25
Minimum number of free bases in multi-loop:1
Maximum multi-loop absolute asymmetry:8
Average multi-loop absolute asymmetry:4.17
Minimum multi-loop absolute asymmetry:1
Maximum multi-loop relative asymmetry:9
Average multi-loop relative asymmetry:2.25
Minimum multi-loop relative asymmetry:0.11
Maximum number of branches in multi-loops:4
Average number of branches in multi-loops:4
Minimum number of branches in multi-loops:4

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 4
Total number of AA non-canonical base pairs:1
Total number of AC non-canonical base pairs:2
Total number of UU non-canonical base pairs:1

Pseudoknot features



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