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

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General features for molecule TMR_00035
(click to expand/contract all tables)

Format:
Molecule ID [?]:TMR_00035
Molecule name [?]:Arth.spec._CP000454_1-369
Source [?]:tmRNA Database
Source ID [?]:Arth.spec._CP000454_1-369
Reference [?]:Zwieb, C., Gorodkin, J., Knudsen B., Burks, J., and Wower, J. (2003) tmRDB (tmRNA database) Nucleic Acids Res, 31, 446-447.
Type [?]:Transfer Messenger RNA

[?]     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 [?]:369
Fragments used [?]:No
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:1
Number of unpaired bases [?]:173
Number of paired bases [?]:196

Click on any header below for additional features.

Stem features

Number of stems [?]:9
Number of base pairs in stems [?]:41
Maximum length of a stem [?]:7
Average length of a stem [?]:4.56
Minimum length of a stem [?]:1
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-8.71
Minimum estimated free energy [?]:-13.2

Hairpin loop features

Number of hairpin loops [?]:2
Maximum number of free bases in hairpin loops [?]:7
Average number of free bases in hairpin loops [?]:5.5
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
Number of internal loops [?]:5
Maximum number of free bases in internal loops:7
Average number of free bases in internal loops:3.2
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:3
Average internal loop absolute asymmetry:1.2
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:4
Average internal loop relative asymmetry:1.6
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:2
Maximum number of free bases in multi-loops:29
Average number of free bases in multi-loops:5.67
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:29
Average multi-loop absolute asymmetry:9.1
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:9.67
Average multi-loop relative asymmetry:1.09
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:6
Average number of branches in multi-loops:4.5
Minimum number of branches in multi-loops:3

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 0

Pseudoknot features
Number of pseudoknots [?]:4
Number of bands:8
Number of base pairs in bands:57
Maximum band length:13
Average band length:7.12
Minimum band length:4
Maximum number of bands per pseudoknot:2
Average number of bands per pseudoknot:2
Minimum number of bands per pseudoknot:2
Maximum number of un-bands:0
Average number of un-bands:0
Minimum number of un-bands:0
Maximum number of in-bands:0
Average number of in-bands:0
Minimum number of in-bands:0
Maximum number of unpaired bases:38
Average number of unpaired bases:18.75
Minimum number of unpaired bases:11
Several ways to remove minimum number of base pairs, per molecule:No
Minimum number of base pairs to remove, per molecule:22
Maximum number of base pairs to remove, per pseudoknot:7
Average number of base pairs to remove, per pseudoknot:5.5
Minimum number of base pairs to remove, per pseudoknot:4
Minimum number of bands to remove, per molecule:4
Maximum number of bands to remove, per pseudoknot:1
Average number of bands to remove, per pseudoknot:1
Minimum number of bands to remove, per pseudoknot:1



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