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

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General features for molecule CRW_00541
(click to expand/contract all tables)

Format:
Molecule ID [?]:CRW_00541
Molecule name [?]:d.233.m.M.edulis
Source [?]:Gutell Lab CRW Site
Source ID [?]:d.233.m.M.edulis
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 [?]:N/A
Validated by NMR or X-Ray [?]:No
Method for secondary structure determination [?]:Comparative sequence analysis
Number of molecules [?]:1
Length [?]:1244
Fragments used [?]:No
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:6
Number of unpaired bases [?]:616
Number of paired bases [?]:628

Click on any header below for additional features.

Stem features

Number of stems [?]:69
Number of base pairs in stems [?]:272
Maximum length of a stem [?]:11
Average length of a stem [?]:3.94
Minimum length of a stem [?]:1
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-4.56
Minimum estimated free energy [?]:-13.2

Hairpin loop features

Number of hairpin loops [?]:34
Maximum number of free bases in hairpin loops [?]:15
Average number of free bases in hairpin loops [?]:5.97
Minimum number of free bases in hairpin loop [?]:3

Bulge loop features
Number of bulge loops [?]:16
Maximum number of free bases in bulge loops [?]:9
Average number of free bases in bulge loops [?]:0.94
Minimum number of free bases in bulge loop [?]:0

Internal loop features
Number of internal loops [?]:10
Maximum number of free bases in internal loops:33
Average number of free bases in internal loops:4.05
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:30
Average internal loop absolute asymmetry:4.3
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:11
Average internal loop relative asymmetry:2.7
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:9
Maximum number of free bases in multi-loops:9
Average number of free bases in multi-loops:2.84
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:9
Average multi-loop absolute asymmetry:2.42
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:9
Average multi-loop relative asymmetry:1.38
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:6
Average number of branches in multi-loops:4.11
Minimum number of branches in multi-loops:3

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 20
Total number of AA non-canonical base pairs:1
Total number of AC non-canonical base pairs:1
Total number of AG non-canonical base pairs:5
Total number of CU non-canonical base pairs:3
Total number of GG non-canonical base pairs:1
Total number of UU non-canonical base pairs:9

Pseudoknot features
Number of pseudoknots [?]:1
Number of bands:3
Number of base pairs in bands:42
Maximum band length:31
Average band length:14
Minimum band length:1
Maximum number of bands per pseudoknot:3
Average number of bands per pseudoknot:3
Minimum number of bands per pseudoknot:3
Maximum number of un-bands:5
Average number of un-bands:5
Minimum number of un-bands:5
Maximum number of in-bands:5
Average number of in-bands:5
Minimum number of in-bands:5
Maximum number of unpaired bases:152
Average number of unpaired bases:152
Minimum number of unpaired bases:152
Several ways to remove minimum number of base pairs, per molecule:No
Minimum number of base pairs to remove, per molecule:1
Maximum number of base pairs to remove, per pseudoknot:1
Average number of base pairs to remove, per pseudoknot:1
Minimum number of base pairs to remove, per pseudoknot:1
Minimum number of bands to remove, per molecule:1
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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