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

    [ Home | Search | Analyse | Submit structures | News | Help ]



General features for molecule TMR_00128
(click to expand/contract all tables)

Format:
Molecule ID [?]:TMR_00128
Molecule name [?]:Clos.diff._AM180355_1-350
Source [?]:tmRNA Database
Source ID [?]:Clos.diff._AM180355_1-350
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 [?]:350
Fragments used [?]:No
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:1
Number of unpaired bases [?]:158
Number of paired bases [?]:192

Click on any header below for additional features.

Stem features

Number of stems [?]:7
Number of base pairs in stems [?]:38
Maximum length of a stem [?]:9
Average length of a stem [?]:5.43
Minimum length of a stem [?]:2
Maximum estimated free energy [?]:-3.4
Average estimated free energy [?]:-9.09
Minimum estimated free energy [?]:-13.3

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 [?]:6.5
Minimum number of free bases in hairpin loop [?]:6

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 [?]:3
Maximum number of free bases in internal loops:5
Average number of free bases in internal loops:3.17
Minimum number of free bases in internal loop:2
Maximum internal loop absolute asymmetry:3
Average internal loop absolute asymmetry:1
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:2
Average internal loop relative asymmetry:1.33
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:2
Maximum number of free bases in multi-loops:35
Average number of free bases in multi-loops:6.44
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:35
Average multi-loop absolute asymmetry:10.16
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:17.5
Average multi-loop relative asymmetry:1.71
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:6
Average number of branches in multi-loops:4.5
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 [?]:4
Number of bands:8
Number of base pairs in bands:58
Maximum band length:13
Average band length:7.25
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:33
Average number of unpaired bases:16
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:22
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: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



    [ Home | Search | Analyse | Submit structures | News | Help ]

For questions, comments, suggestions and bug reports, please contact:

Copyright © 2004-2008 BETA LAB - University of British Columbia