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

General features for molecule CRW_00526 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: CRW_00526 Molecule name [?]: d.233.e.O.sativa Source [?]: Gutell Lab CRW Site Source ID [?]: d.233.e.O.sativa Reference [?]: http://www.rna.ccbb.utexas.edu; Cannone J.J., Subramanian S., Schnare M.N., Collett J.R., D Souza L.M., Du Y., Feng B., Lin N., Madabusi L.V., Muller K.M., Pande N., Shang Z., Yu N., and Gutell R.R. (2002). The Comparative RNA Web (CRW) Site: An Online Database of Comparative Sequence and Structure Information for Ribosomal, Intron, and other RNAs. BioMed Central Bioinformatics, 3:2. [Correction: BioMed Central Bioinformatics. 3:15.] Type [?]: 23S Ribosomal RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: Oryza sativa Validated by NMR or X-Ray [?]: No Method for secondary structure determination [?]: Comparative sequence analysis Number of molecules [?]: 1 Length [?]: 3541 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 12 Number of unpaired bases [?]: 1517 Number of paired bases [?]: 2024

Click on any header below for additional features.

Stem features Number of stems [?]: 221 Number of base pairs in stems [?]: 1012 Maximum length of a stem [?]: 28 Average length of a stem [?]: 4.58 Minimum length of a stem [?]: 1 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -7.64 Minimum estimated free energy [?]: -48.2

Hairpin loop features Number of hairpin loops [?]: 80 Maximum number of free bases in hairpin loops [?]: 22 Average number of free bases in hairpin loops [?]: 5.7 Minimum number of free bases in hairpin loop [?]: 0 Total number of UUCG hairpin motifs per molecule [?]: 2

Bulge loop features Number of bulge loops [?]: 54 Maximum number of free bases in bulge loops [?]: 9 Average number of free bases in bulge loops [?]: 0.75 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 51 Maximum number of free bases in internal loops: 19 Average number of free bases in internal loops: 3.54 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 10 Average internal loop absolute asymmetry: 1.71 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 6 Average internal loop relative asymmetry: 1.94 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 36 Maximum number of free bases in multi-loops: 26 Average number of free bases in multi-loops: 4.04 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 15 Average multi-loop absolute asymmetry: 3.58 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 15 Average multi-loop relative asymmetry: 1.35 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 9 Average number of branches in multi-loops: 3.89 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 71 Total number of AA non-canonical base pairs: 2 Total number of AC non-canonical base pairs: 17 Total number of AG non-canonical base pairs: 25 Total number of CC non-canonical base pairs: 4 Total number of CU non-canonical base pairs: 10 Total number of GG non-canonical base pairs: 1 Total number of UU non-canonical base pairs: 12

Pseudoknot features

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

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