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

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General features for molecule CRW_00529
(click to expand/contract all tables)

Format:
Molecule ID [?]:CRW_00529
Molecule name [?]:d.233.e.S.cerevisiae
Source [?]:Gutell Lab CRW Site
Source ID [?]:d.233.e.S.cerevisiae
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 [?]:Saccharomyces cerevisiae
Validated by NMR or X-Ray [?]:No
Method for secondary structure determination [?]:Comparative sequence analysis
Number of molecules [?]:1
Length [?]:3554
Fragments used [?]:No
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:4
Number of unpaired bases [?]:1422
Number of paired bases [?]:2132

Click on any header below for additional features.

Stem features

Number of stems [?]:186
Number of base pairs in stems [?]:909
Maximum length of a stem [?]:27
Average length of a stem [?]:4.89
Minimum length of a stem [?]:1
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-7.31
Minimum estimated free energy [?]:-37.5

Hairpin loop features

Number of hairpin loops [?]:74
Maximum number of free bases in hairpin loops [?]:22
Average number of free bases in hairpin loops [?]:5.8
Minimum number of free bases in hairpin loop [?]:3
Total number of UUCG hairpin motifs per molecule [?]:2

Bulge loop features
Number of bulge loops [?]:44
Maximum number of free bases in bulge loops [?]:4
Average number of free bases in bulge loops [?]:0.69
Minimum number of free bases in bulge loop [?]:0

Internal loop features
Number of internal loops [?]:42
Maximum number of free bases in internal loops:9
Average number of free bases in internal loops:3.06
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:6
Average internal loop absolute asymmetry:1.4
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:6
Average internal loop relative asymmetry:1.71
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:25
Maximum number of free bases in multi-loops:16
Average number of free bases in multi-loops:3.64
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:15
Average multi-loop absolute asymmetry:3.2
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:15
Average multi-loop relative asymmetry:1.34
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:7
Average number of branches in multi-loops:3.52
Minimum number of branches in multi-loops:3

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 51
Total number of AA non-canonical base pairs:3
Total number of AC non-canonical base pairs:8
Total number of AG non-canonical base pairs:13
Total number of CU non-canonical base pairs:7
Total number of GG non-canonical base pairs:1
Total number of UU non-canonical base pairs:19

Pseudoknot features
Number of pseudoknots [?]:5
Number of bands:24
Number of base pairs in bands:157
Maximum band length:32
Average band length:6.54
Minimum band length:1
Maximum number of bands per pseudoknot:14
Average number of bands per pseudoknot:4.8
Minimum number of bands per pseudoknot:2
Maximum number of un-bands:8
Average number of un-bands:2.8
Minimum number of un-bands:1
Maximum number of in-bands:23
Average number of in-bands:4.6
Minimum number of in-bands:0
Maximum number of unpaired bases:273
Average number of unpaired bases:67.8
Minimum number of unpaired bases:5
Several ways to remove minimum number of base pairs, per molecule:No
Minimum number of base pairs to remove, per molecule:22
Maximum number of base pairs to remove, per pseudoknot:13
Average number of base pairs to remove, per pseudoknot:4.4
Minimum number of base pairs to remove, per pseudoknot:2
Minimum number of bands to remove, per molecule:11
Maximum number of bands to remove, per pseudoknot:5
Average number of bands to remove, per pseudoknot:2.2
Minimum number of bands to remove, per pseudoknot:1



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