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

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General features for molecule TMR_00297
(click to expand/contract all tables)

Format:
Molecule ID [?]:TMR_00297
Molecule name [?]:Lact.raff._AF375578_1-353
Source [?]:tmRNA Database
Source ID [?]:Lact.raff._AF375578_1-353
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 [?]:353
Fragments used [?]:No
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:1
Number of unpaired bases [?]:203
Number of paired bases [?]:150

Click on any header below for additional features.

Stem features

Number of stems [?]:6
Number of base pairs in stems [?]:22
Maximum length of a stem [?]:5
Average length of a stem [?]:3.67
Minimum length of a stem [?]:2
Maximum estimated free energy [?]:-2.5
Average estimated free energy [?]:-4.93
Minimum estimated free energy [?]:-7.6

Hairpin loop features

Number of hairpin loops [?]:1
Maximum number of free bases in hairpin loops [?]:9
Average number of free bases in hairpin loops [?]:9
Minimum number of free bases in hairpin loop [?]:9

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 [?]:4
Maximum number of free bases in internal loops:5
Average number of free bases in internal loops:3.38
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:3
Average internal loop absolute asymmetry:0.75
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 [?]:1
Maximum number of free bases in multi-loops:36
Average number of free bases in multi-loops:8
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:36
Average multi-loop absolute asymmetry:13.33
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:18
Average multi-loop relative asymmetry:2.07
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:6
Average number of branches in multi-loops:6
Minimum number of branches in multi-loops:6

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:53
Maximum band length:11
Average band length:6.62
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:20
Average number of unpaired bases:15.25
Minimum number of unpaired bases:7
Several ways to remove minimum number of base pairs, per molecule:No
Minimum number of base pairs to remove, per molecule:21
Maximum number of base pairs to remove, per pseudoknot:7
Average number of base pairs to remove, per pseudoknot:5.25
Minimum number of base pairs to remove, per pseudoknot:4
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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