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

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General features for molecule TMR_00144
(click to expand/contract all tables)

Format:
Molecule ID [?]:TMR_00144
Molecule name [?]:Croc.wats._TRW-165597_1-386
Source [?]:tmRNA Database
Source ID [?]:Croc.wats._TRW-165597_1-386
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 [?]:386
Fragments used [?]:No
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:1
Number of unpaired bases [?]:180
Number of paired bases [?]:206

Click on any header below for additional features.

Stem features

Number of stems [?]:15
Number of base pairs in stems [?]:43
Maximum length of a stem [?]:8
Average length of a stem [?]:2.87
Minimum length of a stem [?]:1
Maximum estimated free energy [?]:0
Average estimated free energy [?]:-4.43
Minimum estimated free energy [?]:-16

Hairpin loop features

Number of hairpin loops [?]:2
Maximum number of free bases in hairpin loops [?]:7
Average number of free bases in hairpin loops [?]:5
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 [?]:2
Average number of free bases in bulge loops [?]:1
Minimum number of free bases in bulge loop [?]:0

Internal loop features
Number of internal loops [?]:10
Maximum number of free bases in internal loops:6
Average number of free bases in internal loops:2.25
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:1
Average internal loop absolute asymmetry:0.1
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
Number of multi-loops [?]:2
Maximum number of free bases in multi-loops:27
Average number of free bases in multi-loops:5.9
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:27
Average multi-loop absolute asymmetry:8.72
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:13.5
Average multi-loop relative asymmetry:1.36
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:7
Average number of branches in multi-loops:5
Minimum number of branches in multi-loops:3

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

Pseudoknot features
Number of pseudoknots [?]:5
Number of bands:10
Number of base pairs in bands:60
Maximum band length:11
Average band length:6
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:19
Average number of unpaired bases:12
Minimum number of unpaired bases:6
Several ways to remove minimum number of base pairs, per molecule:No
Minimum number of base pairs to remove, per molecule:25
Maximum number of base pairs to remove, per pseudoknot:7
Average number of base pairs to remove, per pseudoknot:5
Minimum number of base pairs to remove, per pseudoknot:3
Minimum number of bands to remove, per molecule:5
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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