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

General features for molecule PDB_01071 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01071 Molecule name [?]: SOLUTION STRUCTURE OF A PORTION OF THE 5'UTR OF HSPA MRNA OF BRADYRHIZOBIUM JAPONICUM Source [?]: RCSB Protein Data Bank Source ID [?]: 2GIO Reference [?]: S.CHOWDHURY,C.MARIS,F.H.ALLAIN,F.NARBERHAUS. MOLECULAR BASIS FOR TEMPERATURE SENSING BY AN RNA THERMOMETER.. EMBO J. V. 25 2487 2006 ASTM EMJODG UK ISSN 0261-4189 Type [?]: Synthetic RNA [?]     PS figure     PDF figure Figure from original source Organism [?]: SYNTHETIC Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: NMR; ran through RNAview Number of molecules [?]: 1 Length [?]: 29 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 3 Number of paired bases [?]: 26

Click on any header below for additional features.

Stem features Number of stems [?]: 2 Number of base pairs in stems [?]: 13 Maximum length of a stem [?]: 7 Average length of a stem [?]: 6.5 Minimum length of a stem [?]: 6 Maximum estimated free energy [?]: -6.6 Average estimated free energy [?]: -9.35 Minimum estimated free energy [?]: -12.1

Hairpin loop features Number of hairpin loops [?]: 1 Maximum number of free bases in hairpin loops [?]: 2 Average number of free bases in hairpin loops [?]: 2 Minimum number of free bases in hairpin loop [?]: 2

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

Multi-loop features

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 3 Total number of CU non-canonical base pairs: 1 Total number of GG non-canonical base pairs: 1 Total number of UU non-canonical base pairs: 1

Pseudoknot features