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

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General features for molecule TMR_00069
(click to expand/contract all tables)

Format:
Molecule ID [?]:TMR_00069
Molecule name [?]:Bord.para._TRW-257311_1-387
Source [?]:tmRNA Database
Source ID [?]:Bord.para._TRW-257311_1-387
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 [?]:387
Fragments used [?]:No
Duplicated sequence [?]:Molecules in the database with the same sequence: TMR_00068, TMR_00070
Number of domains [?]:1
Number of unpaired bases [?]:157
Number of paired bases [?]:230

Click on any header below for additional features.

Stem features

Number of stems [?]:11
Number of base pairs in stems [?]:55
Maximum length of a stem [?]:8
Average length of a stem [?]:5
Minimum length of a stem [?]:1
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-9.64
Minimum estimated free energy [?]:-17.5

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 [?]:4.75
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 [?]:3
Maximum number of free bases in internal loops:5
Average number of free bases in internal loops:2.67
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:3
Average internal loop absolute asymmetry:1.33
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:2
Average internal loop relative asymmetry:1.33
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:3
Maximum number of free bases in multi-loops:33
Average number of free bases in multi-loops:5.17
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:33
Average multi-loop absolute asymmetry:7.22
Minimum multi-loop absolute asymmetry:1
Maximum multi-loop relative asymmetry:33
Average multi-loop relative asymmetry:1.78
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:6
Average number of branches in multi-loops:4
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:60
Maximum band length:12
Average band length:7.5
Minimum band length:5
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:1
Average number of in-bands:0.25
Minimum number of in-bands:0
Maximum number of unpaired bases:19
Average number of unpaired bases:13.75
Minimum number of unpaired bases:10
Several ways to remove minimum number of base pairs, per molecule:Yes
Minimum number of base pairs to remove, per molecule:23
Maximum number of base pairs to remove, per pseudoknot:7
Average number of base pairs to remove, per pseudoknot:5.75
Minimum number of base pairs to remove, per pseudoknot:5
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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