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

General features for molecule NDB_00060 (click to expand/contract all tables) Format: CT RNAML Bpseq Dot-parentheses FASTA Molecule ID [?]: NDB_00060 Molecule name [?]: NDB id udd006 Source [?]: Nucleic Acid Database Source ID [?]: udd006 Reference [?]: M.A.Viswamitra, Z.Shakked, P.G.Jones, G.M.Sheldrick S.A.Salisbury, O.Kennard. Structure of the Deoxytetranucleotide d-pApTpApT and a Sequence-Dependent Model for Poly(dA-dT). Biopolymers V. 21 513 1982 ASTM BIPMAA US ISSN 0006-3525 0161 Type [?]: Unknown [?]     PS figure     PDF figure Figure from original source Organism [?]: N/A Validated by NMR or X-Ray [?]: Yes Method for secondary structure determination [?]: X-Ray; ran through RNAview Number of molecules [?]: 3 Length [?]: 12 Fragments used [?]: No Duplicated sequence [?]: No other molecule in the database has the same sequence Number of domains [?]: 1 Number of unpaired bases [?]: 4 Number of paired bases [?]: 8

Click on any header below for additional features.

Stem features

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

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

Multi-loop features

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

Pseudoknot features Number of pseudoknots [?]: 1 Number of bands: 2 Number of base pairs in bands: 4 Maximum band length: 2 Average band length: 2 Minimum band length: 2 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: 2 Average number of unpaired bases: 2 Minimum number of unpaired bases: 2 Several ways to remove minimum number of base pairs, per molecule: Yes Minimum number of base pairs to remove, per molecule: 2 Maximum number of base pairs to remove, per pseudoknot: 2 Average number of base pairs to remove, per pseudoknot: 2 Minimum number of base pairs to remove, per pseudoknot: 2 Minimum number of bands to remove, per molecule: 1 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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