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

General features for molecule PDB_00012 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_00012 Molecule name [?]: CIS-ACTING RNA REGULATORY ELEMENT (HIV-1 TAR), NMR, 20 STRUCTURES Source [?]: RCSB Protein Data Bank Source ID [?]: 1ANR Reference [?]: F.ABOUL-ELA,J.KARN,G.VARANI. STRUCTURE OF HIV-1 TAR RNA IN THE ABSENCE OF LIGANDS REVEALS A NOVEL CONFORMATION OF THE TRINUCLEOTIDE BULGE.. NUCLEIC ACIDS RES. V. 24 3974 1996 ASTM NARHAD UK ISSN 0305-1048 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 [?]: Molecules in the database with the same sequence: PDB_00306, PDB_00755, PDB_00756, PDB_00757 Number of domains [?]: 1 Number of unpaired bases [?]: 15 Number of paired bases [?]: 14

Click on any header below for additional features.

Stem features Number of stems [?]: 2 Number of base pairs in stems [?]: 7 Maximum length of a stem [?]: 4 Average length of a stem [?]: 3.5 Minimum length of a stem [?]: 3 Maximum estimated free energy [?]: -4.2 Average estimated free energy [?]: -6.05 Minimum estimated free energy [?]: -7.9

Hairpin loop features Number of hairpin loops [?]: 1 Maximum number of free bases in hairpin loops [?]: 6 Average number of free bases in hairpin loops [?]: 6 Minimum number of free bases in hairpin loop [?]: 6

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

Internal loop features Number of internal loops [?]: 1 Maximum number of free bases in internal loops: 4 Average number of free bases in internal loops: 2.5 Minimum number of free bases in internal loop: 1 Maximum internal loop absolute asymmetry: 3 Average internal loop absolute asymmetry: 3 Minimum internal loop absolute asymmetry: 3 Maximum internal loop relative asymmetry: 4 Average internal loop relative asymmetry: 4 Minimum internal loop relative asymmetry: 4

Multi-loop features

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

Pseudoknot features

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