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

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General features for molecule TMR_00225
(click to expand/contract all tables)

Format:
Molecule ID [?]:TMR_00225
Molecule name [?]:Frag.pinn._AF550351_1-335
Source [?]:tmRNA Database
Source ID [?]:Frag.pinn._AF550351_1-335
Reference [?]:Zwieb, C., Gorodkin, J., Knudsen B., Burks, J., and Wower, J. (2003) tmRDB (tmRNA database) Nucleic Acids Res, 31, 446-447.
Type [?]:Transfer Messenger 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 [?]:335
Fragments used [?]:No
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:1
Number of unpaired bases [?]:279
Number of paired bases [?]:56

Click on any header below for additional features.

Stem features

Number of stems [?]:3
Number of base pairs in stems [?]:20
Maximum length of a stem [?]:8
Average length of a stem [?]:6.67
Minimum length of a stem [?]:5
Maximum estimated free energy [?]:-6.2
Average estimated free energy [?]:-8.67
Minimum estimated free energy [?]:-10

Hairpin loop features

Number of hairpin loops [?]:0
Maximum number of free bases in hairpin loops [?]:N/A
Average number of free bases in hairpin loops [?]:N/A
Minimum number of free bases in hairpin loop [?]:N/A

Bulge loop features
Number of bulge loops [?]:1
Maximum number of free bases in bulge loops [?]:192
Average number of free bases in bulge loops [?]:96
Minimum number of free bases in bulge loop [?]:0

Internal loop features
Number of internal loops [?]:2
Maximum number of free bases in internal loops:7
Average number of free bases in internal loops:5.75
Minimum number of free bases in internal loop:4
Maximum internal loop absolute asymmetry:3
Average internal loop absolute asymmetry:1.5
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:1
Average internal loop relative asymmetry:1
Minimum internal loop relative asymmetry:1

Multi-loop features

Non-canonical base pairs features
Total number of non-canonical base pairs [?]: 0

Pseudoknot features
Number of pseudoknots [?]:1
Number of bands:2
Number of base pairs in bands:8
Maximum band length:5
Average band length:4
Minimum band length:3
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:0
Average number of un-bands:0
Minimum number of un-bands:0
Maximum number of in-bands:0
Average number of in-bands:0
Minimum number of in-bands:0
Maximum number of unpaired bases:12
Average number of unpaired bases:12
Minimum number of unpaired bases:12
Several ways to remove minimum number of base pairs, per molecule:No
Minimum number of base pairs to remove, per molecule:3
Maximum number of base pairs to remove, per pseudoknot:3
Average number of base pairs to remove, per pseudoknot:3
Minimum number of base pairs to remove, per pseudoknot:3
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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