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

General features for molecule RFA_00831 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: RFA_00831 Molecule name [?]: Bicoid 3 prime-UTR regulatory element, RF00551, M32126.1/307-857 Source [?]: Rfam Database Source ID [?]: RF00551 M32126.1/857-307 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 [?]: 247 Number of paired bases [?]: 304

Click on any header below for additional features.

Stem features Number of stems [?]: 40 Number of base pairs in stems [?]: 152 Maximum length of a stem [?]: 10 Average length of a stem [?]: 3.8 Minimum length of a stem [?]: 1 Maximum estimated free energy [?]: 0 Average estimated free energy [?]: -2.36 Minimum estimated free energy [?]: -9.7

Hairpin loop features Number of hairpin loops [?]: 3 Maximum number of free bases in hairpin loops [?]: 29 Average number of free bases in hairpin loops [?]: 15.33 Minimum number of free bases in hairpin loop [?]: 7

Bulge loop features Number of bulge loops [?]: 20 Maximum number of free bases in bulge loops [?]: 14 Average number of free bases in bulge loops [?]: 1.2 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: 18 Average number of free bases in internal loops: 2.9 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 14 Average internal loop absolute asymmetry: 1.93 Minimum internal loop absolute asymmetry: 0 Maximum internal loop relative asymmetry: 4 Average internal loop relative asymmetry: 1.53 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 Minimum number of free bases in multi-loop: 0 Maximum multi-loop absolute asymmetry: 10 Average multi-loop absolute asymmetry: 3.34 Minimum multi-loop absolute asymmetry: 0 Maximum multi-loop relative asymmetry: 1.62 Average multi-loop relative asymmetry: 0.54 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 [?]: 47 Total number of AA non-canonical base pairs: 5 Total number of AC non-canonical base pairs: 12 Total number of AG non-canonical base pairs: 8 Total number of CC non-canonical base pairs: 3 Total number of CU non-canonical base pairs: 12 Total number of GG non-canonical base pairs: 1 Total number of UU non-canonical base pairs: 6

Pseudoknot features