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

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General features for molecule CRW_00612
(click to expand/contract all tables)

Format:
Molecule ID [?]:CRW_00612
Molecule name [?]:a.I1.b.S.negevensis.B4.LSU.1931
Source [?]:Gutell Lab CRW Site
Source ID [?]:a.I1.b.S.negevensis.B4.LSU.1931
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 [?]:736
Fragments used [?]:No
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:3
Number of unpaired bases [?]:550
Number of paired bases [?]:186

Click on any header below for additional features.

Stem features

Number of stems [?]:14
Number of base pairs in stems [?]:81
Maximum length of a stem [?]:9
Average length of a stem [?]:5.79
Minimum length of a stem [?]:2
Maximum estimated free energy [?]:-2.4
Average estimated free energy [?]:-7.96
Minimum estimated free energy [?]:-14.1

Hairpin loop features

Number of hairpin loops [?]:5
Maximum number of free bases in hairpin loops [?]:385
Average number of free bases in hairpin loops [?]:80.2
Minimum number of free bases in hairpin loop [?]:3

Bulge loop features
Number of bulge loops [?]:4
Maximum number of free bases in bulge loops [?]:5
Average number of free bases in bulge loops [?]:1.62
Minimum number of free bases in bulge loop [?]:0

Internal loop features
Number of internal loops [?]:5
Maximum number of free bases in internal loops:7
Average number of free bases in internal loops:4.2
Minimum number of free bases in internal loop:2
Maximum internal loop absolute asymmetry:3
Average internal loop absolute asymmetry:1.6
Minimum internal loop absolute asymmetry:1
Maximum internal loop relative asymmetry:2
Average internal loop relative asymmetry:1.2
Minimum internal loop relative asymmetry:1

Multi-loop features

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 1
Total number of UU non-canonical base pairs:1

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:17
Average number of unpaired bases:17
Minimum number of unpaired bases:17
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



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