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

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General features for molecule TMR_00120
(click to expand/contract all tables)

Format:
Molecule ID [?]:TMR_00120
Molecule name [?]:Chro.spec._AY082650_1-383
Source [?]:tmRNA Database
Source ID [?]:Chro.spec._AY082650_1-383
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 [?]:383
Fragments used [?]:No
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:1
Number of unpaired bases [?]:211
Number of paired bases [?]:172

Click on any header below for additional features.

Stem features

Number of stems [?]:13
Number of base pairs in stems [?]:27
Maximum length of a stem [?]:7
Average length of a stem [?]:2.08
Minimum length of a stem [?]:1
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-2.09
Minimum estimated free energy [?]:-9.7

Hairpin loop features

Number of hairpin loops [?]:1
Maximum number of free bases in hairpin loops [?]:5
Average number of free bases in hairpin loops [?]:5
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 [?]:11
Maximum number of free bases in internal loops:4
Average number of free bases in internal loops:2.5
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:2
Average internal loop absolute asymmetry:0.27
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:3
Average internal loop relative asymmetry:1.18
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:1
Maximum number of free bases in multi-loops:29
Average number of free bases in multi-loops:5.57
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:29
Average multi-loop absolute asymmetry:9.43
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:29
Average multi-loop relative asymmetry:3.17
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:7
Average number of branches in multi-loops:7
Minimum number of branches in multi-loops:7

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 0

Pseudoknot features
Number of pseudoknots [?]:5
Number of bands:10
Number of base pairs in bands:59
Maximum band length:8
Average band length:5.9
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:18
Average number of unpaired bases:12
Minimum number of unpaired bases:5
Several ways to remove minimum number of base pairs, per molecule:Yes
Minimum number of base pairs to remove, per molecule:27
Maximum number of base pairs to remove, per pseudoknot:7
Average number of base pairs to remove, per pseudoknot:5.4
Minimum number of base pairs to remove, per pseudoknot:4
Minimum number of bands to remove, per molecule:5
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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