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

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General features for molecule TMR_00246
(click to expand/contract all tables)

Format:
Molecule ID [?]:TMR_00246
Molecule name [?]:Grac.tenu._AY673996_1-396
Source [?]:tmRNA Database
Source ID [?]:Grac.tenu._AY673996_1-396
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 [?]:396
Fragments used [?]:No
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:1
Number of unpaired bases [?]:328
Number of paired bases [?]:68

Click on any header below for additional features.

Stem features

Number of stems [?]:7
Number of base pairs in stems [?]:27
Maximum length of a stem [?]:7
Average length of a stem [?]:3.86
Minimum length of a stem [?]:1
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-5.56
Minimum estimated free energy [?]:-12.5

Hairpin loop features

Number of hairpin loops [?]:1
Maximum number of free bases in hairpin loops [?]:7
Average number of free bases in hairpin loops [?]:7
Minimum number of free bases in hairpin loop [?]:7

Bulge loop features
Number of bulge loops [?]:1
Maximum number of free bases in bulge loops [?]:274
Average number of free bases in bulge loops [?]:137
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:7
Average number of free bases in internal loops:2.88
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:1
Average internal loop absolute asymmetry:0.25
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 [?]:1
Maximum number of free bases in multi-loops:9
Average number of free bases in multi-loops:3.33
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:9
Average multi-loop absolute asymmetry:6
Minimum multi-loop absolute asymmetry:1
Maximum multi-loop relative asymmetry:9
Average multi-loop relative asymmetry:2.28
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:7
Maximum band length:4
Average band length:3.5
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:10
Average number of unpaired bases:10
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: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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