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

General features for molecule PDB_00112 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00112 Molecule name [?]: DIMER INITIATION SEQUENCE OF HIV-1LAI GENOMIC RNA: NMR SOLUTION STRUCTURE OF THE EXTENDED DUPLEX Source [?]: RCSB Protein Data Bank Source ID [?]: 1JU1 Reference [?]: F.GIRARD,F.BARBAULT,C.GOUYETTE,T.HUYNH-DINH, J.PAOLETTI,G.LANCELOT. DIMER INITIATION SEQUENCE OF HIV-1LAI GENOMIC RNA: NMR SOLUTION STRUCTURE OF THE EXTENDED DUPLEX.. J.BIOMOL.STRUCT.DYN. V. 16 1145 1999 ASTM JBSDD6 US ISSN 0739-1102 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 [?]: 2 Length [?]: 46 Fragments used [?]: No Duplicated sequence [?]: Molecules in the database with the same sequence: PDB_00817, PDB_00950, PDB_01186, PDB_01188, PDB_01189 Number of domains [?]: 1 Number of unpaired bases [?]: 4 Number of paired bases [?]: 42

Click on any header below for additional features.

Stem features Number of stems [?]: 3 Number of base pairs in stems [?]: 21 Maximum length of a stem [?]: 8 Average length of a stem [?]: 7 Minimum length of a stem [?]: 6 Maximum estimated free energy [?]: -12 Average estimated free energy [?]: -13 Minimum estimated free energy [?]: -15

Hairpin loop features Number of hairpin loops [?]: 1 Maximum number of free bases in hairpin loops [?]: 0 Average number of free bases in hairpin loops [?]: 0 Minimum number of free bases in hairpin loop [?]: 0

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 [?]: 1 Maximum number of free bases in internal loops: 2 Average number of free bases in internal loops: 1.5 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 1 Average internal loop absolute asymmetry: 1 Minimum internal loop absolute asymmetry: 1 Maximum internal loop relative asymmetry: 2 Average internal loop relative asymmetry: 2 Minimum internal loop relative asymmetry: 2

Multi-loop features

Non-canonical base pairs features Total number of non-canonical base pairs [?]: 1 Total number of AA non-canonical base pairs: 1

Pseudoknot features

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