]> obsolete_relation backbone_connected_to covalently_bonded_to disconnected_from externally_connected_to five_prime_to_five_prime_to five_prime_to_three_prime_to five_prime_to_two_prime_to has_boundary has_non_tangential_proper_part has_tangential_proper_part Pairwise interaction of the sugar edge with a phosphate unit. Only occurs with G. non_tangential_proper_part_of part_of tangential_proper_part_of three_prime_to_five_prime_to three_prime_to_three_prime_to three_prime_to_two_prime_to two_prime_to_five_prime_to two_prime_to_three_prime_to has_quality An RNA base pair consists of a pair of RNA nucleotides that interact by edge-to-edge hydrogen bonding with two of their nucleoside edges. RNA base pair A ribose ring that does not have a hydroxy group at the 2' position. deoxyribose ring 2 2 A family_1_base_pair is an RNAO_base_pair in which the two RNA nucleotides interact by edge-to-edge hydrogen-bonding between the Watson-Crick edges of each base and in which the glycosidic bonds of the two nucleotides are oriented "cis" relative to each other. family_1_base_pair 2 family_2_base_pair A family_2_base_pair is an RNAO_base_pair in which the two RNA nucleotides interact by edge-to-edge hydrogen-bonding between the Watson-Crick edges of each base and in which the glycosidic bonds of the two nucleotides are oriented "trans" relative to each other. 2 family_3_base_pair Forbidden pairings (Watson-Crick edge first); CA, UC, AC, AA, GC, GU. A family_3_base_pair is an RNAO_base_pair in which two RNA nucleotides interact by edge-to-edge hydrogen-bonding between the Watson-Crick edge of one base and the Hoogsteen edge of the other base and in which the glycosidic bonds of the two nucleotides are oriented "cis" relative to each other. 2 Forbidden are the following pairings (Watson-Crick edge first); CU, UC, AC, AU, GC, GA. family_4_base_pair A family_4_base_pair is an RNAO_base_pair in which two RNA nucleotides interact by edge-to-edge hydrogen-bonding between the Watson-Crick edge of one base and the Hoogsteen edge of the other base and in which the glycosidic bonds of the two nucleotides are oriented "trans" relative to each other. 2 A family_5_base_pair is an RNAO_base_pair in which two RNA nucleotides interact by edge-to-edge hydrogen-bonding between the Watson-Crick edge of one base and the Sugar edge of the other base and in which the glycosidic bonds of the two nucleotides are oriented "cis" relative to each other. family_5_base_pair 2 A family_6_base_pair is an RNAO_base_pair in which two RNA nucleotides interact by edge-to-edge hydrogen-bonding between the Watson-Crick edge of one base and the Sugar edge of the other base and in which the glycosidic bonds of the two nucleotides are oriented "trans" relative to each other. Forbidden is the pairing where G presents the Watson-Crick edge and A presents the sugar edge. family_6_base_pair 2 Forbidden pairings are: CC, CU, CA, UA, UC, UG, UU, AC, AU, AA and GU. family_7_base_pair A family_7_base_pair is an RNAO_base_pair in which two RNA nucleotides interact by edge-to-edge hydrogen-bonding between the Hoogsteen edges of each base and in which the glycosidic bonds of the two nucleotides are oriented "cis" relative to each other. 2 family_8_base_pair A family_8_base_pair is an RNAO_base_pair in which two RNA nucleotides interact by edge-to-edge hydrogen-bonding between the Hoogsteen edges of each base and in which the glycosidic bonds of the two nucleotides are oriented "trans" relative to each other. 2 family_9_base_pair A family_9_base_pair is an RNAO_base_pair in which two RNA nucleotides interact by edge-to-edge hydrogen-bonding between the Hoogsteen edge of one base and the Sugar edge of the other base and in which the glycosidic bonds of the two nucleotides are oriented "cis" relative to each other. 2 A family_10_base_pair is an RNAO_base_pair in which two RNA nucleotides interact by edge-to-edge hydrogen-bonding between the Hoogsteen edge of one base and the Sugar edge of the other base and in which the glycosidic bonds of the two nucleotides are oriented "trans" relative to each other. family_10_base_pair 2 A family_11_base_pair is an RNAO_base_pair in which two RNA nucleotides interact by edge-to-edge hydrogen-bonding between the Sugar edges of each base and in which the glycosidic bonds of the two nucleotides are oriented "cis" relative to each other. family_11_base_pair 2 family_12_base_pair A family_12_base_pair is an RNAO_base_pair in which two RNA nucleotides interact by edge-to-edge hydrogen-bonding between the Sugar edges of each base and in which the glycosidic bonds of the two nucleotides are oriented "trans" relative to each other. Excluded are CA, CC, CU, CG, and UA, UC, UU, UG. nucleotide_suite 2 canonical RNA base pair An RNAO_base_pair which has cis-Watson--Crick pairing and where the participating bases are AU, CG, GC or UA. A nucleobase is an N-heterocyclic group that forms part of a nucleotide. nucleobase A phosphate group consists of a phosphorus atom doubly-bonded to two oxygen atoms and singly-bonded to two oxygen atoms, both of which have a free valence. Unlike the phosphate group in ChEBI (CHEBI:32958), the RNAO phosphate group has two free valences. phosphate unit A ribonucleoside consists of a nitrogen heterocycle (a nucleobase) covalently bonded to a ribose ring, with free valences at the 3' and 5' positions on the ring. ribonucleoside A ribonucleotide consists of a nitrogen heterocyclic group covalently bonded to the 4' position of a ribose ring and a phosphate group covalently bonded the 3' position of the ribose ring. There is a free valence on one of the oxygens of the phosphate group and on the 5' position of the ribose ring. ribonucleotide A ribose ring is a furanose ring with free valences at the 4' position (to bond to the nucleobase), and the 3' and 5' positions. ribose ring two_prime_hydroxy_group purine nucleobase A purine nucleobase is a heterocyclic group consisting of a five-membered aromatic ring ortho,para-fused to a six-membered aromatic ring and where the atoms at the 1-, 3-, 7- and 9- positions are nitrogen atoms. A pyrimidine nucleobase is a heterocyclic group consisting of a six-membered ring where the atoms at the 1- and 3-positions are nitrogen atoms. pyrimidine nucleobase cytosine nucleobase A cytosine nucleobase is a pyrimidine that contains a 4-amino group and a 2-oxo group and has a free valence at the 1-position. uracil nucleobase A uracil nucleobase is a pyrimidine nucleobase that contains a 2-oxo group and a 4-oxo group and has a free valence at the 1-position. adenine nucleobase An adenine nucleobase is a purine nucleobase that contains a 6-amino group and a free valence at the 9-position. A guanine nucleobase is a purine nucleobase that contains a 2-amino group, a 6-oxo group and a free valence at the 9-position. guanine nucleobase suite in 22 conformation suite in 22 conformation suite in 23 conformation suite in 23 conformation suite in 32 conformation suite in 32 conformation purine ribonucleoside suite in 33 conformation suite in 33 conformation pyrimidine ribonucleoside cytidine residue uridine residue adenosine residue guanosine residue suite in 1a conformation suite in 1c conformation suite in 1e conformation suite in 1f conformation suite in 1g conformation suite in 1l conformation suite in 1m conformation suite in 3a conformation suite in 3d conformation suite in 5a conformation suite in 5d conformation suite in 5j conformation suite in 5n conformation suite in 7a conformation suite in 7d conformation suite in 9a conformation suite in ampersand-a conformation suite in 1bracket conformation suite in 1o conformation suite in 1t conformation suite in 3b conformation suite in 1z conformation suite in 5p conformation suite in 5q conformation suite in 5r conformation suite in 5z conformation suite in 7p conformation suite in 7r conformation suite in 1b conformation suite in 0a conformation suite in 0i conformation suite in 0k conformation suite in 2a conformation suite in 2g conformation suite in 2h conformation suite in 4a conformation suite in 4d conformation suite in 4g conformation suite in 4n conformation suite in 6d conformation suite in 6g conformation suite in 8d conformation suite in 6n conformation suite in 6j conformation suite in 0b conformation suite in 2bracket conformation suite in 2o conformation suite in 2u conformation suite in 2z conformation suite in 4b conformation suite in 4p conformation suite in 4s conformation suite in 6p conformation A tangential proper part of an RNA molecule is a proper part that shares a boundary with the RNA molecule. tangential proper part of RNA molecule The Watson-Crick edge of a nucleobase is the preferred edge along which it undergoes hydrogen bonding with other nucleobases. Watson-Crick edge Hoogsteen edge The Hoogsteen edge of a nucleobase is the edge of the nucleobase which is not adjacent to the 2'-hydroxyl group on the ribose ring. sugar edge The sugar edge of a nucleoside consists of the edge of the nucleobase adjacent ot the 2'-hydroxyl group on the ribose ring and the 2'-hydroxyl group on the ribose ring. 1 paired_region A collection of one or more sequence regions that contains at least 1 base pair. A collection of one or more sequence regions that contains no base pairs. unpaired_region unbroken_stem A paired_region made up of two regions of sequence, each of which is contiguous, that completely pair with each other (no bulges/mismatches/etc). This form is sometimes colloquially referred to as a "helix", but we have not adopted that term since it implies a level of explicit structural knowledge that is frequently lacking. A contiguous sequence region that directly links the two halves of an unbroken_stem (but does not participate in the stem); this structure is also known as a "hairpin loop". Because a terminal loop may also participate in other inter-base interactions, (a) it is defined relative to a particular unbroken_stem, and (b) it is not implicitly defined as unpaired (or paired). terminal_loop A set consisting of all and only the sequence regions that link two given unbroken_stems; this term encompasses the concepts of "bulge" and "mismatch" as well. Again, this term is defined relative to two particular unbroken_stems and does not imply unpairedness (or pairedness). internal_loop purine ribonucleotide pyrimidine ribonucleotide cytidylate residue uridylate residue adenylate residue guanylate residue The set consisting of all and only the sequence regions that link more than two given unbroken_stems such that each region links exactly two unbroken_stems. This term is defined relative to the particular unbroken_stems involved and, again, does not imply anything about the pairedness/unpairedness of the bases in this region. The degree of a junction is a property (e.g. 3-junction, 4-junction), so the different degrees do not get separate entries in the ontology. stem_junction strand_end A sequence_region bounded at one end by the 5' or 3' end of the molecule, and at the other by an unbroken_stem. Part of an RNA or DNA molecule consisting of one or more sequence_regions. collection_of_sequence_regions three_prime_end 1 nucleic acid fiat part Fiat part of an RNA or DNA molecule containing only nucleotide residues. five_prime_end http://goldbook.iupac.org/C01258.html conformation The spatial arrangement of the atoms in a molecule or molecular part affording distinction between stereoisomers which can be interconverted by rotations about formally single bonds. A conformation that inheres in an RNA base pair. It may be cis- or trans- depending on the orientations of the ribose rings relative to the edge-edge interaction of the nucleobases. base pair orientation PERSON: Colin Batchelor, based on the Leontis-Westhof classification. base pair cis-orientation A base pair conformation where the ribose rings are on the same side of a plane drawn through the middle of the edge-edge hydrogen bonds. PERSON: Colin Batchelor, based on the Leontis-Westhof classification. A base pair conformation where the ribose rings are on opposite sides of a plane drawn through the middle of the edge-edge hydrogen bonds. PERSON: Colin Batchelor, based on the Leontis-Westhof classification. base pair trans-orientation cis-oriented RNA base pair trans-oriented RNA base pair nucleoside conformation PERSON: Michel Dumontier A conformation that inheres in an nucleoside based on the rotation of the nucleobase about the glycosidic torsion angle χ with the furanose. A syn nucleoside conformation is a nucleoside conformation characterized by the nucleobase being oriented towards the ribose due to rotation about the glycosidic torsion angle χ. From χ = 0°, where the plane of the base is aligned with the O4’-C1’ bond in a direction towards the O4’ atom, the syn conformation covers the remaining rotations of ±90°: χ = [-90°, 90°]. syn nucleoside conformation PERSON: Michel Dumontier anti nucleoside conformation PERSON: Michel Dumontier A anti nucleoside conformation is a nucleoside conformation characterized by the nucleobase being oriented away from the ribose due to rotation about the glycosidic torsion angle χ. From χ = 180°, where the plane of the base is aligned with the O4’-C1’ bond in a direction away from the O4’ atom, the anti conformation covers a rotations of ±90°: χ = [-180°, 90°]. An envelope conformation is a furan ring conformation in which only one of the five fruan atoms (C1’, C2’, C3’, C4’ or O4’) is out of the plane formed by the four others. PERSON: Michel Dumontier envelope conformation PERSON: Michel Dumontier An envelope conformation is a furan ring conformation in which two atoms are in opposite sides of the plane formed by the remaining three. twist conformation A furan ring conformation is a conformation that inheres in a furan ring and is characterized by the values of torsion angles: θ0-4. furan ring conformation PERSON: Michel Dumontier C2’-endo pucker C2'-endo pucker (²E conformation) is an envelope conformation in which the C2' atom is above the plane formed by the other 4 atoms. PERSON: Michel Dumontier PERSON: Michel Dumontier C3’-endo pucker C3'-endo pucker (An ³E conformation) is an envelope conformation in which the C3' atom is above the plane formed by the other 4 atoms. PERSON: Michel Dumontier C4'-exo pucker (E₄ conformation) is an envelope conformation in which the C4' atom is below the plane formed by the other 4 atoms. C4’-exo pucker PERSON: Michel Dumontier C3'-endo - C4' -exo pucker C3'-endo - C4' exo pucker (³E₄ conformation) is a twist conformation in which the C3' atom is above the plane and the C4' atom is below the plane. C3'-endo - C2' -exo pucker C3'-endo - C2' exo pucker (³E₂ conformation) is a twist conformation in which the C3' atom is above the plane and the C2' atom is below the plane. PERSON: Michel Dumontier A base stack consists of a pair of nucleotides that interact by London dispersion inter-molecular interactions between their nucleobases such that one base is stacked on top of the other. PERSON: Michel Dumontier base stack PERSON: Michel Dumontier An adjacent base stack is a base stack between a pair of sequence-adjacent nucleotides. adjacent base stack non-adjacent base stack PERSON: Michel Dumontier A non-adjacent base stack is a base stack between a pair of non sequence-adjacent nucleotides. base stack orientation A base stack orientation is a conformation that inheres in a base stack by virtue of the orientation of the nucleobases relative to i) the alignment of base normals and ii) their sequence adjacency. PERSON: Michel Dumontier PERSON: Michel Dumontier base stack straight orientation An base stack straight orientation is a base stack orientation in which the normals of both bases are aligned in the same direction. base stack reverse orientation A base stack reverse orientation is a base stack orientation in which the normals of both bases are aligned in the opposite directions. PERSON: Michel Dumontier base stack base-normal orientation A base stack base-normal orientation is a base stack orientation that depends on the relative orientation of the base normals. base stack above orientation A base stack above orientation is a base stack orientation in which the second base (B) is in the same direction as the normal to the first base (A). PERSON: Michel Dumontier base stack below orientation A base stack below orientation is a base stack orientation in which the normal of the second base (B) is directed towards the first base (A). PERSON: Michel Dumontier base stack sequence adjacency A base stack sequence adjacency is a base stack orientation that depends on whether the stacked nucleobases are part of nucleotides that are sequence adjacent or not. PERSON: Michel Dumontier A base stack adjacent orientation is a base stack orientation in which the stacked nucleobases are part of nucleotides that are sequence adjacent. PERSON: Michel Dumontier base stack adjacent base orientation PERSON: Michel Dumontier base stack non-adjacent base orientation A base stack non-adjacent orientation is a base stack orientation in which the stacked nucleobases are part of nucleotides that are not sequence adjacent. A furanose ring is a ring that consists of four carbon and one oxygen atom and has free valences at each carbon position. furanose ring PERSON: Michel Dumontier An upward base stack is a base stack that exhibits both an straight orientation and an above orientation. PERSON: Michel Dumontier upward base stack PERSON: Michel Dumontier A downward base stack is a base stack that exhibits both an straight orientation and a below orientation. downward base stack An inward base stack is a base stack that exhibits both a reverse orientation and an above orientation. inward base stack PERSON: Michel Dumontier outward base stack PERSON: Michel Dumontier An outward base stack is a base stack that exhibits both a reverse orientation and a below orientation.