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

General features for molecule CRW_00705 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: CRW_00705 Molecule name [?]: a.I1.m.M.senile.B2.ND5 Source [?]: Gutell Lab CRW Site Source ID [?]: a.I1.m.M.senile.B2.ND5 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 [?]: 1710 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 4 Number of unpaired bases [?]: 1538 Number of paired bases [?]: 172

Click on any header below for additional features.

Stem features Number of stems [?]: 14 Number of base pairs in stems [?]: 74 Maximum length of a stem [?]: 8 Average length of a stem [?]: 5.29 Minimum length of a stem [?]: 2 Maximum estimated free energy [?]: -1.3 Average estimated free energy [?]: -7.92 Minimum estimated free energy [?]: -13.9

Hairpin loop features Number of hairpin loops [?]: 7 Maximum number of free bases in hairpin loops [?]: 1388 Average number of free bases in hairpin loops [?]: 202 Minimum number of free bases in hairpin loop [?]: 3

Bulge loop features Number of bulge loops [?]: 1 Maximum number of free bases in bulge loops [?]: 1 Average number of free bases in bulge loops [?]: 0.5 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: 16 Average number of free bases in internal loops: 5.6 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 8 Average internal loop absolute asymmetry: 3.2 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 2 Average internal loop relative asymmetry: 1.4 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 1 Maximum number of free bases in multi-loops: 16 Average number of free bases in multi-loops: 6.33 Minimum number of free bases in multi-loop: 1 Maximum multi-loop absolute asymmetry: 15 Average multi-loop absolute asymmetry: 10 Minimum multi-loop absolute asymmetry: 1 Maximum multi-loop relative asymmetry: 16 Average multi-loop relative asymmetry: 4.45 Minimum multi-loop relative asymmetry: 0.06 Maximum number of branches in multi-loops: 3 Average number of branches in multi-loops: 3 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 3 Total number of AG non-canonical base pairs: 1 Total number of CU non-canonical base pairs: 2

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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