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

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General features for molecule TMR_00173
(click to expand/contract all tables)

Format:
Molecule ID [?]:TMR_00173
Molecule name [?]:Emil.huxl._AY741371_1-291
Source [?]:tmRNA Database
Source ID [?]:Emil.huxl._AY741371_1-291
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 [?]:291
Fragments used [?]:No
Duplicated sequence [?]:Molecules in the database with the same sequence: TMR_00174
Number of domains [?]:1
Number of unpaired bases [?]:207
Number of paired bases [?]:84

Click on any header below for additional features.

Stem features

Number of stems [?]:9
Number of base pairs in stems [?]:34
Maximum length of a stem [?]:7
Average length of a stem [?]:3.78
Minimum length of a stem [?]:1
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-4.73
Minimum estimated free energy [?]:-14.5

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 [?]:6
Minimum number of free bases in hairpin loop [?]:5

Bulge loop features
Number of bulge loops [?]:1
Maximum number of free bases in bulge loops [?]:147
Average number of free bases in bulge loops [?]:73.5
Minimum number of free bases in bulge loop [?]:0

Internal loop features
Number of internal loops [?]:4
Maximum number of free bases in internal loops:4
Average number of free bases in internal loops:2.25
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:1
Average internal loop absolute asymmetry:0.5
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:2
Average internal loop relative asymmetry:1.25
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:2
Maximum number of free bases in multi-loops:12
Average number of free bases in multi-loops:3
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:12
Average multi-loop absolute asymmetry:4.67
Minimum multi-loop absolute asymmetry:1
Maximum multi-loop relative asymmetry:4
Average multi-loop relative asymmetry:0.84
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:3
Average number of branches in multi-loops:3
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 [?]:1
Number of bands:2
Number of base pairs in bands:8
Maximum band length:5
Average band length:4
Minimum band length:3
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:8
Average number of unpaired bases:8
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:3
Maximum number of base pairs to remove, per pseudoknot:3
Average number of base pairs to remove, per pseudoknot:3
Minimum number of base pairs to remove, per pseudoknot:3
Minimum number of bands to remove, per molecule:1
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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