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

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General features for molecule TMR_00108
(click to expand/contract all tables)

Format:
Molecule ID [?]:TMR_00108
Molecule name [?]:Chla.muri._AE002296_1-418
Source [?]:tmRNA Database
Source ID [?]:Chla.muri._AE002296_1-418
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 [?]:418
Fragments used [?]:No
Duplicated sequence [?]:No other molecule in the database has the same sequence
Number of domains [?]:1
Number of unpaired bases [?]:174
Number of paired bases [?]:244

Click on any header below for additional features.

Stem features

Number of stems [?]:15
Number of base pairs in stems [?]:49
Maximum length of a stem [?]:8
Average length of a stem [?]:3.27
Minimum length of a stem [?]:1
Maximum estimated free energy [?]:0.3
Average estimated free energy [?]:-4.11
Minimum estimated free energy [?]:-14.5

Hairpin loop features

Number of hairpin loops [?]:2
Maximum number of free bases in hairpin loops [?]:8
Average number of free bases in hairpin loops [?]:7.5
Minimum number of free bases in hairpin loop [?]:7

Bulge loop features
Number of bulge loops [?]:1
Maximum number of free bases in bulge loops [?]:1
Average number of free bases in bulge loops [?]:0.5
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:4
Average number of free bases in internal loops:1.55
Minimum number of free bases in internal loop:1
Maximum internal loop absolute asymmetry:3
Average internal loop absolute asymmetry:0.3
Minimum internal loop absolute asymmetry:0
Maximum internal loop relative asymmetry:4
Average internal loop relative asymmetry:1.3
Minimum internal loop relative asymmetry:1

Multi-loop features
Number of multi-loops [?]:2
Maximum number of free bases in multi-loops:55
Average number of free bases in multi-loops:8.33
Minimum number of free bases in multi-loop:0
Maximum multi-loop absolute asymmetry:55
Average multi-loop absolute asymmetry:13.53
Minimum multi-loop absolute asymmetry:0
Maximum multi-loop relative asymmetry:27.5
Average multi-loop relative asymmetry:2.13
Minimum multi-loop relative asymmetry:0
Maximum number of branches in multi-loops:6
Average number of branches in multi-loops:4.5
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 [?]:4
Number of bands:8
Number of base pairs in bands:73
Maximum band length:14
Average band length:9.12
Minimum band length:5
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:16
Average number of unpaired bases:12.75
Minimum number of unpaired bases:9
Several ways to remove minimum number of base pairs, per molecule:No
Minimum number of base pairs to remove, per molecule:26
Maximum number of base pairs to remove, per pseudoknot:8
Average number of base pairs to remove, per pseudoknot:6.5
Minimum number of base pairs to remove, per pseudoknot:5
Minimum number of bands to remove, per molecule:4
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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