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

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General features for molecule TMR_00162
(click to expand/contract all tables)

Format:
Molecule ID [?]:TMR_00162
Molecule name [?]:Desu.desu._U68081_1-378
Source [?]:tmRNA Database
Source ID [?]:Desu.desu._U68081_1-378
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 [?]:378
Fragments used [?]:No
Duplicated sequence [?]:Molecules in the database with the same sequence: TMR_00161
Number of domains [?]:1
Number of unpaired bases [?]:186
Number of paired bases [?]:192

Click on any header below for additional features.

Stem features

Number of stems [?]:7
Number of base pairs in stems [?]:35
Maximum length of a stem [?]:8
Average length of a stem [?]:5
Minimum length of a stem [?]:2
Maximum estimated free energy [?]:-2.5
Average estimated free energy [?]:-8.64
Minimum estimated free energy [?]:-13.9

Hairpin loop features

Number of hairpin loops [?]:2
Maximum number of free bases in hairpin loops [?]:8
Average number of free bases in hairpin loops [?]:5.5
Minimum number of free bases in hairpin loop [?]:3

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 [?]:3
Maximum number of free bases in internal loops:4
Average number of free bases in internal loops:3.17
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:3
Average internal loop absolute asymmetry:1.67
Minimum internal loop absolute asymmetry:1
Maximum internal loop relative asymmetry:4
Average internal loop relative asymmetry:2
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:1
Maximum number of free bases in multi-loops:33
Average number of free bases in multi-loops:5.86
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:33
Average multi-loop absolute asymmetry:10.29
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:16.5
Average multi-loop relative asymmetry:1.88
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:7
Average number of branches in multi-loops:7
Minimum number of branches in multi-loops:7

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:61
Maximum band length:12
Average band length:7.62
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:24
Average number of unpaired bases:15.5
Minimum number of unpaired bases:8
Several ways to remove minimum number of base pairs, per molecule:No
Minimum number of base pairs to remove, per molecule:24
Maximum number of base pairs to remove, per pseudoknot:8
Average number of base pairs to remove, per pseudoknot:6
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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