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

General features for molecule CRW_00523 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: CRW_00523 Molecule name [?]: d.233.c.Z.mays Source [?]: Gutell Lab CRW Site Source ID [?]: d.233.c.Z.mays 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 [?]: 2985 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 2227 Number of paired bases [?]: 758

Click on any header below for additional features.

Stem features Number of stems [?]: 64 Number of base pairs in stems [?]: 266 Maximum length of a stem [?]: 12 Average length of a stem [?]: 4.16 Minimum length of a stem [?]: 1 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -6.51 Minimum estimated free energy [?]: -22

Hairpin loop features Number of hairpin loops [?]: 24 Maximum number of free bases in hairpin loops [?]: 15 Average number of free bases in hairpin loops [?]: 5.96 Minimum number of free bases in hairpin loop [?]: 3 Total number of UUCG hairpin motifs per molecule [?]: 1

Bulge loop features Number of bulge loops [?]: 19 Maximum number of free bases in bulge loops [?]: 9 Average number of free bases in bulge loops [?]: 0.97 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 15 Maximum number of free bases in internal loops: 6 Average number of free bases in internal loops: 2.7 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 4 Average internal loop absolute asymmetry: 1 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 3 Average internal loop relative asymmetry: 1.6 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 6 Maximum number of free bases in multi-loops: 418 Average number of free bases in multi-loops: 21.23 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 418 Average multi-loop absolute asymmetry: 37.13 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 209 Average multi-loop relative asymmetry: 7.47 Minimum multi-loop relative asymmetry: 0 Maximum number of branches in multi-loops: 5 Average number of branches in multi-loops: 3.67 Minimum number of branches in multi-loops: 3

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 17 Total number of AA non-canonical base pairs: 1 Total number of AC non-canonical base pairs: 3 Total number of AG non-canonical base pairs: 9 Total number of CU non-canonical base pairs: 1 Total number of GG non-canonical base pairs: 1 Total number of UU non-canonical base pairs: 2

Pseudoknot features Number of pseudoknots [?]: 3 Number of bands: 19 Number of base pairs in bands: 113 Maximum band length: 32 Average band length: 5.95 Minimum band length: 1 Maximum number of bands per pseudoknot: 13 Average number of bands per pseudoknot: 6.33 Minimum number of bands per pseudoknot: 2 Maximum number of un-bands: 8 Average number of un-bands: 3.33 Minimum number of un-bands: 1 Maximum number of in-bands: 6 Average number of in-bands: 2 Minimum number of in-bands: 0 Maximum number of unpaired bases: 1469 Average number of unpaired bases: 498.33 Minimum number of unpaired bases: 10 Several ways to remove minimum number of base pairs, per molecule: No Minimum number of base pairs to remove, per molecule: 15 Maximum number of base pairs to remove, per pseudoknot: 11 Average number of base pairs to remove, per pseudoknot: 5 Minimum number of base pairs to remove, per pseudoknot: 1 Minimum number of bands to remove, per molecule: 9 Maximum number of bands to remove, per pseudoknot: 5 Average number of bands to remove, per pseudoknot: 3 Minimum number of bands to remove, per pseudoknot: 1