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

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General features for molecule TMR_00012
(click to expand/contract all tables)

Format:
Molecule ID [?]:TMR_00012
Molecule name [?]:Acin.spec._CR543861_1-360
Source [?]:tmRNA Database
Source ID [?]:Acin.spec._CR543861_1-360
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 [?]:360
Fragments used [?]:No
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:1
Number of unpaired bases [?]:198
Number of paired bases [?]:162

Click on any header below for additional features.

Stem features

Number of stems [?]:14
Number of base pairs in stems [?]:55
Maximum length of a stem [?]:8
Average length of a stem [?]:3.93
Minimum length of a stem [?]:1
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-6.01
Minimum estimated free energy [?]:-16.1

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 [?]:5
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 [?]:3
Average number of free bases in bulge loops [?]:1.5
Minimum number of free bases in bulge loop [?]:0

Internal loop features
Number of internal loops [?]:7
Maximum number of free bases in internal loops:6
Average number of free bases in internal loops:2.29
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:1
Average internal loop absolute asymmetry:0.29
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:1
Average internal loop relative asymmetry:1
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:2
Maximum number of free bases in multi-loops:47
Average number of free bases in multi-loops:11.67
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:47
Average multi-loop absolute asymmetry:15.1
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:15.67
Average multi-loop relative asymmetry:2.19
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:26
Maximum band length:10
Average band length:6.5
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:0
Average number of in-bands:0
Minimum number of in-bands:0
Maximum number of unpaired bases:24
Average number of unpaired bases:17
Minimum number of unpaired bases:10
Several ways to remove minimum number of base pairs, per molecule:No
Minimum number of base pairs to remove, per molecule:10
Maximum number of base pairs to remove, per pseudoknot:5
Average number of base pairs to remove, per pseudoknot:5
Minimum number of base pairs to remove, per pseudoknot:5
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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