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

General features for molecule TMR_00258 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: TMR_00258 Molecule name [?]: Heli.ganm._DQ250622_1-370 Source [?]: tmRNA Database Source ID [?]: Heli.ganm._DQ250622_1-370 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 [?]: 370 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 204 Number of paired bases [?]: 166

Click on any header below for additional features.

Stem features Number of stems [?]: 6 Number of base pairs in stems [?]: 30 Maximum length of a stem [?]: 9 Average length of a stem [?]: 5 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: -2.5 Average estimated free energy [?]: -7.22 Minimum estimated free energy [?]: -11.4

Hairpin loop features Number of hairpin loops [?]: 1 Maximum number of free bases in hairpin loops [?]: 18 Average number of free bases in hairpin loops [?]: 18 Minimum number of free bases in hairpin loop [?]: 18

Bulge loop features Number of bulge loops [?]: 1 Maximum number of free bases in bulge loops [?]: 5 Average number of free bases in bulge loops [?]: 2.5 Minimum number of free bases in bulge loop [?]: 0

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: 2.33 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 3 Average internal loop absolute asymmetry: 1.33 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 2 Average internal loop relative asymmetry: 1.67 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 1 Maximum number of free bases in multi-loops: 38 Average number of free bases in multi-loops: 8 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 38 Average multi-loop absolute asymmetry: 13.47 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 12.67 Average multi-loop relative asymmetry: 2.06 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: 22 Average number of unpaired bases: 15.5 Minimum number of unpaired bases: 11 Several ways to remove minimum number of base pairs, per molecule: Yes 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

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

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