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

General features for molecule PDB_01219 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: PDB_01219 Molecule name [?]: CRYSTAL STRUCTURE ANALYSIS OF THE RNA DODECAMER CGC-NF2- AAUUGGCG, WITH AN INCORPORATED 2,4-DIFLUORO Source [?]: RCSB Protein Data Bank Source ID [?]: 2Q1O Reference [?]: F.LI,P.S.PALLAN,M.A.MAIER,K.G.RAJEEV,S.L.MATHIEU, C.KREUTZ,Y.FAN,J.SANGHVI,R.MICURA,E.ROZNERS, M.MANOHARAN,M.EGLI. CRYSTAL STRUCTURE, STABILITY AND IN VITRO RNAI ACTIVITY OF OLIGORIBONUCLEOTIDES CONTAINING THE RIBO-DIFLUOROTOLUYL NUCLEOTIDE: INSIGHTS INTO SUBSTRATE REQUIREMENTS BY THE HUMAN RISC AGO2 ENZYME.. NUCLEIC ACIDS RES. V. 35 6424 2007 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 [?]: X-RAY, RESOLUTION 1.10 ANGSTROMS; ran through RNAview Number of molecules [?]: 4 Length [?]: 44 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 2 Number of unpaired bases [?]: 4 Number of paired bases [?]: 40

Click on any header below for additional features.

Stem features Number of stems [?]: 6 Number of base pairs in stems [?]: 20 Maximum length of a stem [?]: 4 Average length of a stem [?]: 3.33 Minimum length of a stem [?]: 3 Maximum estimated free energy [?]: -2.9 Average estimated free energy [?]: -4.83 Minimum estimated free energy [?]: -5.8

Hairpin loop features Number of hairpin loops [?]: 2 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 [?]: 4 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 [?]: 0

Pseudoknot features