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

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



General features for molecule CRW_00642
(click to expand/contract all tables)

Format:
Molecule ID [?]:CRW_00642
Molecule name [?]:a.I1.e.C.grayi.UNK.SSU.1516
Source [?]:Gutell Lab CRW Site
Source ID [?]:a.I1.e.C.grayi.UNK.SSU.1516
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 [?]:Group I Intron

[?]     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 [?]:308
Fragments used [?]:No
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:4
Number of unpaired bases [?]:178
Number of paired bases [?]:130

Click on any header below for additional features.

Stem features

Number of stems [?]:12
Number of base pairs in stems [?]:53
Maximum length of a stem [?]:8
Average length of a stem [?]:4.42
Minimum length of a stem [?]:2
Maximum estimated free energy [?]:-0.9
Average estimated free energy [?]:-7.96
Minimum estimated free energy [?]:-14.5

Hairpin loop features

Number of hairpin loops [?]:6
Maximum number of free bases in hairpin loops [?]:23
Average number of free bases in hairpin loops [?]:8.83
Minimum number of free bases in hairpin loop [?]:4
Total number of UUCG hairpin motifs per molecule [?]:1

Bulge loop features
Number of bulge loops [?]:3
Maximum number of free bases in bulge loops [?]:6
Average number of free bases in bulge loops [?]:1.33
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:2
Average number of free bases in internal loops:1.5
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:1
Average internal loop absolute asymmetry:0.33
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

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 0

Pseudoknot features
Number of pseudoknots [?]:1
Number of bands:2
Number of base pairs in bands:12
Maximum band length:6
Average band length:6
Minimum band length:6
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:3
Minimum number of un-bands:3
Maximum number of in-bands:0
Average number of in-bands:0
Minimum number of in-bands:0
Maximum number of unpaired bases:19
Average number of unpaired bases:19
Minimum number of unpaired bases:19
Several ways to remove minimum number of base pairs, per molecule:Yes
Minimum number of base pairs to remove, per molecule:6
Maximum number of base pairs to remove, per pseudoknot:6
Average number of base pairs to remove, per pseudoknot:6
Minimum number of base pairs to remove, per pseudoknot:6
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



    [ 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