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

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



General features for molecule CRW_00294
(click to expand/contract all tables)

Format:
Molecule ID [?]:CRW_00294
Molecule name [?]:d.16.e.A.castellanii
Source [?]:Gutell Lab CRW Site
Source ID [?]:d.16.e.A.castellanii
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 [?]:16S Ribosomal 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 [?]:2290
Fragments used [?]:No
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:4
Number of unpaired bases [?]:1118
Number of paired bases [?]:1172

Click on any header below for additional features.

Stem features

Number of stems [?]:121
Number of base pairs in stems [?]:558
Maximum length of a stem [?]:16
Average length of a stem [?]:4.63
Minimum length of a stem [?]:1
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-6.44
Minimum estimated free energy [?]:-32.6

Hairpin loop features

Number of hairpin loops [?]:30
Maximum number of free bases in hairpin loops [?]:10
Average number of free bases in hairpin loops [?]:5.6
Minimum number of free bases in hairpin loop [?]:3

Bulge loop features
Number of bulge loops [?]:36
Maximum number of free bases in bulge loops [?]:5
Average number of free bases in bulge loops [?]:0.78
Minimum number of free bases in bulge loop [?]:0

Internal loop features
Number of internal loops [?]:38
Maximum number of free bases in internal loops:16
Average number of free bases in internal loops:3.62
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:7
Average internal loop absolute asymmetry:1.66
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:7
Average internal loop relative asymmetry:1.84
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:15
Maximum number of free bases in multi-loops:176
Average number of free bases in multi-loops:10.09
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:173
Average multi-loop absolute asymmetry:10.72
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:58.67
Average multi-loop relative asymmetry:2.37
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:5
Average number of branches in multi-loops:3.53
Minimum number of branches in multi-loops:3

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 48
Total number of AA non-canonical base pairs:1
Total number of AC non-canonical base pairs:13
Total number of AG non-canonical base pairs:11
Total number of CC non-canonical base pairs:3
Total number of CU non-canonical base pairs:9
Total number of GG non-canonical base pairs:2
Total number of UU non-canonical base pairs:9

Pseudoknot features
Number of pseudoknots [?]:3
Number of bands:6
Number of base pairs in bands:28
Maximum band length:9
Average band length:4.67
Minimum band length:2
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:3
Average number of un-bands:1
Minimum number of un-bands:0
Maximum number of in-bands:3
Average number of in-bands:1
Minimum number of in-bands:0
Maximum number of unpaired bases:32
Average number of unpaired bases:22.67
Minimum number of unpaired bases:17
Several ways to remove minimum number of base pairs, per molecule:No
Minimum number of base pairs to remove, per molecule:8
Maximum number of base pairs to remove, per pseudoknot:3
Average number of base pairs to remove, per pseudoknot:2.67
Minimum number of base pairs to remove, per pseudoknot:2
Minimum number of bands to remove, per molecule:3
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