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

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General features for molecule TMR_00047
(click to expand/contract all tables)

Format:
Molecule ID [?]:TMR_00047
Molecule name [?]:Baci.G._TRW-12333_1-312
Source [?]:tmRNA Database
Source ID [?]:Baci.G._TRW-12333_1-312
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 [?]:312
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 [?]:114

Click on any header below for additional features.

Stem features

Number of stems [?]:6
Number of base pairs in stems [?]:32
Maximum length of a stem [?]:7
Average length of a stem [?]:5.33
Minimum length of a stem [?]:4
Maximum estimated free energy [?]:-3.4
Average estimated free energy [?]:-8.22
Minimum estimated free energy [?]:-12.4

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 [?]:0
Maximum number of free bases in bulge loops [?]:N/A
Average number of free bases in bulge loops [?]:N/A
Minimum number of free bases in bulge loop [?]:N/A

Internal loop features
Number of internal loops [?]:2
Maximum number of free bases in internal loops:7
Average number of free bases in internal loops:5
Minimum number of free bases in internal loop:3
Maximum internal loop absolute asymmetry:4
Average internal loop absolute asymmetry:3
Minimum internal loop absolute asymmetry:2
Maximum internal loop relative asymmetry:2
Average internal loop relative asymmetry:1.5
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:2
Maximum number of free bases in multi-loops:65
Average number of free bases in multi-loops:12.43
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:65
Average multi-loop absolute asymmetry:20.33
Minimum multi-loop absolute asymmetry:1
Maximum multi-loop relative asymmetry:21.67
Average multi-loop relative asymmetry:2.76
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:4
Average number of branches in multi-loops:3.5
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:25
Maximum band length:8
Average band length:6.25
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:43
Average number of unpaired bases:37.5
Minimum number of unpaired bases:32
Several ways to remove minimum number of base pairs, per molecule:No
Minimum number of base pairs to remove, per molecule:11
Maximum number of base pairs to remove, per pseudoknot:7
Average number of base pairs to remove, per pseudoknot:5.5
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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