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

General features for molecule RFA_00828 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: RFA_00828 Molecule name [?]: Bicoid 3 prime-UTR regulatory element, RF00551, M32123.1/262-812 Source [?]: Rfam Database Source ID [?]: RF00551 M32123.1/812-262 Reference [?]: Sam Griffiths-Jones, Simon Moxon, Mhairi Marshall, Ajay Khanna, Sean R. Eddy and Alex Bateman, Rfam: annotating non-coding RNAs in complete genomes, Nucleic Acids Res. 2005 33:D121-D124. Type [?]: Other 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 [?]: 551 Fragments used [?]: N/A Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 231 Number of paired bases [?]: 320

Click on any header below for additional features.

Stem features Number of stems [?]: 33 Number of base pairs in stems [?]: 160 Maximum length of a stem [?]: 12 Average length of a stem [?]: 4.85 Minimum length of a stem [?]: 1 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -6.77 Minimum estimated free energy [?]: -21.9

Hairpin loop features Number of hairpin loops [?]: 3 Maximum number of free bases in hairpin loops [?]: 11 Average number of free bases in hairpin loops [?]: 9.67 Minimum number of free bases in hairpin loop [?]: 7

Bulge loop features Number of bulge loops [?]: 9 Maximum number of free bases in bulge loops [?]: 2 Average number of free bases in bulge loops [?]: 0.61 Minimum number of free bases in bulge loop [?]: 0

Internal loop features Number of internal loops [?]: 19 Maximum number of free bases in internal loops: 15 Average number of free bases in internal loops: 3.21 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 8 Average internal loop absolute asymmetry: 1.68 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 4 Average internal loop relative asymmetry: 1.42 Minimum internal loop relative asymmetry: 1

Multi-loop features Number of multi-loops [?]: 2 Maximum number of free bases in multi-loops: 26 Average number of free bases in multi-loops: 11.5 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 9 Average multi-loop absolute asymmetry: 3.67 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 1.53 Average multi-loop relative asymmetry: 0.52 Minimum multi-loop relative asymmetry: 0 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 [?]: 5 Total number of AA non-canonical base pairs: 2 Total number of AG non-canonical base pairs: 1 Total number of CU non-canonical base pairs: 1 Total number of UU non-canonical base pairs: 1

Pseudoknot features