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

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General features for molecule TMR_00074
(click to expand/contract all tables)

Format:
Molecule ID [?]:TMR_00074
Molecule name [?]:Brad.japo._BA000040_1-315
Source [?]:tmRNA Database
Source ID [?]:Brad.japo._BA000040_1-315
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 [?]:315
Fragments used [?]:No
Duplicated sequence [?]:Molecules in the database with the same sequence: TMR_00075
Number of domains [?]:1
Number of unpaired bases [?]:159
Number of paired bases [?]:156

Click on any header below for additional features.

Stem features

Number of stems [?]:15
Number of base pairs in stems [?]:59
Maximum length of a stem [?]:10
Average length of a stem [?]:3.93
Minimum length of a stem [?]:1
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-6.91
Minimum estimated free energy [?]:-18.1

Hairpin loop features

Number of hairpin loops [?]:4
Maximum number of free bases in hairpin loops [?]:7
Average number of free bases in hairpin loops [?]:3.75
Minimum number of free bases in hairpin loop [?]:2

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:5
Average number of free bases in internal loops:1.75
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:4
Average internal loop absolute asymmetry:1
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:5
Average internal loop relative asymmetry:1.88
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:2
Maximum number of free bases in multi-loops:31
Average number of free bases in multi-loops:10
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:31
Average multi-loop absolute asymmetry:12.03
Minimum multi-loop absolute asymmetry:1
Maximum multi-loop relative asymmetry:15.5
Average multi-loop relative asymmetry:1.92
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 [?]:2
Number of bands:4
Number of base pairs in bands:19
Maximum band length:6
Average band length:4.75
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:12
Average number of unpaired bases:10.5
Minimum number of unpaired bases:9
Several ways to remove minimum number of base pairs, per molecule:No
Minimum number of base pairs to remove, per molecule:8
Maximum number of base pairs to remove, per pseudoknot:4
Average number of base pairs to remove, per pseudoknot:4
Minimum number of base pairs to remove, per pseudoknot:4
Minimum number of bands to remove, per molecule:2
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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