]> Francois Major Eric Westhof Jesse Stombaugh Jane S. Richardson The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure Data Neocles Leontis Iga Korneta Colin Batchelor 2010-05-17T23:35:00 Robert Hoehndorf Michel Dumontier Craig L. Zirbel Jose Cruz-Toledo Kristian Rother Rob Knight Thomas Bittner Chris J. Mungall Karen Eilbeck obsolete relation linear RNA backbone of has linear RNA backbone RNA backbone of has RNA backbone has direct part direct part of connected to covalently connected to (transitive) covalently bonded to (transitive) covalently bonded to covalently connected to backbone connected to covalently connected 5prime to 5prime covalently connected 5prime to 3prime covalently connected 5prime to 2prime covalently connected 3prime to 5prime covalently connected 3prime to 3prime covalently connected 3prime to 2prime covalently connected 2prime to 5prime covalently connected 2prime to 3prime weakly interacting with (transitive) weakly interacting with pairs with stacks with stacks 5prime face to 5prime face stacks 5prime face to 3prime face stacks 3prime face to 5prime face stacks 3prime face to 3prime face pairs with HH pairs with CHH pairs with THH pairs with HS pairs with CHS pairs with THS pairs with HW pairs with CHW pairs with THW pairs with SH pairs with CSH pairs with TSH pairs with SS pairs with CSS pairs with TSS pairs with SW pairs with CSW pairs with TSW pairs with WH pairs with CWH pairs with TWH pairs with WS pairs with CWS pairs with TWS pairs with WW pairs with CWW pairs with TWW boundary of external boundary of has boundary has external boundary has member member of subcollection of submolecule of has submolecule has subcollection overlaps covalently bonded sum of same chain corresponds to corresponds to, nucleotide by nucleotide suite of has suite has face face of 5prime face of 3prime face of has 5prime face has 3prime face has edge edge of has sugar edge has Hoogsteen edge has Watson-Crick edge is Hoogsteen edge of is sugar edge of is Watson-Crick edge of sum of collection covalently connected 5prime to 3prime (transitive) synonym: 3prime_to covalently connected 3prime to 5prime (transitive) Synonym: 5prime_to hydrogen bonds with has functional parent Pairwise interaction of the sugar edge with a phosphate unit. Only occurs with G. has quality 5,6-dihydrouracil nucleobase 2 2 1-methyladenosine residue 1 beta-D-galactosyl group hypoxanthine nucleobase 1 inosine residue 1 pseudouridine residue 1-methylguanosine residue 1 1-methylinosine residue 1 1-methylpseudouridine residue 1 2prime-O-methyluridine residue 1 2prime-O-methylcytidine residue 1 2prime-O-methylguanosine residue 1 2prime-O-methylpseudouridine residue 1 N2,N2-dimethylguanosine residue 1 2-methyladenosine residue 1 N2-methylguanosine residue 1 2-thiocytidine residue 1 3-(3-amino-3-carboxypropyl)uridine residue 1 3-methylcytidine residue 1 N4-acetylcytidine residue 1 4-thiouridine residue 1 5-(carboxyhydroxymethyl)uridine residue 1 5-carboxymethylaminomethyl-2-thiouridine residue 1 5-methoxycarbonylmethyl-2-thiouridine residue 1 5-methoxycarbonylmethyluridine residue 1 5-methoxyuridine residue 1 5-methyl-2-thiouridine residue 1 5-methylcytidine residue 1 7-methylguanosine residue 1 N6-methyladenosine residue 1 glutamyl group 2-amino-4-carboxybutanoyl 3-amino-3-carboxypropyl group carbamoyl group -C(O)NH2 dihydrouridine residue 1 group hydroxymethyl group mannosyl group probably a beta-D-mannosyl group oxygen atom from CHEBI hydroperoxyl prenyl group 3-methylbut-2-en-1-yl ribosyl group tauryl group (2-aminoethyl)sulfonyl uridine 5-oxyacetic acid residue 1 carbon atom from CHEBI N6,N6-dimethyladenosine residue 1 phosphorous atom from CHEBI hydrogen atom from CHEBI nitrogen atom from CHEBI methyl group -CH3 phosphate group -O-P(O)(OH)2 atom from CHEBI threonyl group rel-(2R,3S)-2-amino-3-hydroxybutanoyl lysyl group 2,6-diaminohexanoyl acetyl group -(O)C-CH3 carboxymethyl group -CH2-COOH formyl group -CHO hydroxy group -OH methylamino group -NH-CH3 methoxy group CH3-O- oxo group =O glycyl group H2N-CH2-CO- amino group -NH2 carboxy group -C(O)OH cyano group -CN ribonucleic acid 3prime-5prime RNA 5prime-3prime RNA base pair A base pair consists of a pair of nucleotide residues that interact by nucleoside edge to nucleoside edge hydrogen bonds. deoxyribose ring A ribose ring that does not have a hydroxy group at the 2prime position. family 1 base pair 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 2 base pair 2 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. family 3 base pair 2 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. Forbidden pairings (Watson-Crick edge first); CA, UC, AC, AA, GC, GU. family 4 base pair 2 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. Forbidden are the following pairings (Watson-Crick edge first); CU, UC, AC, AU, GC, GA. family 5 base pair 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 6 base pair 2 Forbidden is the pairing where G presents the Watson-Crick edge and A presents the sugar edge. 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. family 7 base pair 2 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. Forbidden pairings are: CC, CU, CA, UA, UC, UG, UU, AC, AU, AA and GU. family 8 base pair 2 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. family 9 base pair 2 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. family 10 base pair 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 11 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 12 base pair 2 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. RNA suite canonical RNA base pair 2 An RNAO_base_pair which has cis-Watson--Crick pairing and where the participating bases are AU, CG, GC or UA. nucleobase A nucleobase is an N-heterocyclic group that forms part of a nucleoside residue. phosphate moiety 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. ribonucleoside residue A ribonucleoside consists of a nitrogen heterocycle (a nucleobase) covalently bonded to a ribose ring, with free valences at the 3prime oxgen and 5prime oxygen atoms on the ring. ribonucleotide residue A ribonucleotide residue consists of a nitrogen heterocyclic group covalently bonded to the 1prime position of a ribose ring and a phosphate group covalently bonded the 5' oxygen of the ribose ring. There are free valances at the 3'-oxygen of the ribose and on the phosphorus atom of the phosphate group where the ribonucleotide is connected to two other ribonucleotides in the chain. ribose ring A ribose ring is a furanose ring with free valences at the 4prime position (to bond to the nucleobase), and the 3prime and 5prime positions. 2prime hydroxyl 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. pyrimidine nucleobase 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. 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. guanine nucleobase 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. 22 conformation 23 conformation 32 conformation purine ribonucleoside residue 33 conformation pyrimidine ribonucleoside residue cytidine residue uridine residue adenosine residue guanosine residue 1a conformation 1c conformation 1e conformation 1f conformation 1g conformation 1l conformation 1m conformation 3a conformation 3d conformation 5a conformation 5d conformation 5j conformation 5n conformation 7a conformation 7d conformation 9a conformation &a conformation 1[ conformation 1o conformation 1t conformation 3b conformation 1z conformation 5p conformation 5q conformation 5r conformation 5z conformation 7p conformation 7r conformation 1b conformation 0a conformation 0i conformation 0k conformation 2a conformation 2g conformation 2h conformation 4a conformation 4d conformation 4g conformation 4n conformation 6d conformation 6g conformation 8d conformation 6n conformation 6j conformation 0b conformation 2[ conformation 2o conformation 2u conformation 2z conformation 4b conformation 4p conformation 4s conformation 6p conformation nucleoside edge A nucleoside edge is either a Watson-Crick edge or a Hoogsteen edge or a sugar edge. Watson-Crick edge The Watson-Crick edge of a nucleobase is the preferred edge along which it undergoes hydrogen bonding with other nucleobases. Hoogsteen edge The Hoogsteen edge of a nucleobase is the edge of the nucleobase which is not adjacent to the 2prime-hydroxyl group on the ribose ring. sugar edge The sugar edge of a nucleoside consists of the edge of the nucleobase adjacent ot the 2prime-hydroxyl group on the ribose ring and the 2prime-hydroxyl group on the ribose ring. paired region A collection of one or more adjacent nucleotide residues in which at least one residue is part of a base pair. unpaired region A collection of one or more nucleotides that are not involved in base pairing. unbroken stem A paired region made up of two contiguous collections of nucleotides, in which each nucleotide forms a base pair. terminal loop A contiguous sequence of nucleotide residues 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). internal loop A collection of nucleotide residues 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). purine ribonucleotide pyrimidine ribonucleotide cytidylate residue uridylate residue adenylate residue guanylate residue stem junction A collection of nucleotide residues consisting of all and only the nucleotide regions that link more than two 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. strand end A sequence_region bounded at one end by the 5prime or 3prime end of the molecule, and at the other by an unbroken_stem. collection of nucleotides residues A collection of nucleotide residues is a part of a nucleic acid consisting of one or more nucleotides. 3prime end collection of material entities 5prime end conformation http://goldbook.iupac.org/C01258.html 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. base pair orientation 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. PERSON: Colin Batchelor, based on the Leontis-Westhof classification. base pair cis-orientation PERSON: Colin Batchelor, based on the Leontis-Westhof classification. 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. base pair trans-orientation 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. cis-oriented base pair trans-oriented base pair collection of atoms covalent boundary non-covalent boundary nucleoside conformation A conformation that inheres in an nucleoside based on the rotation of the nucleobase about the glycosidic torsion angle χ with the furanose. PERSON: Michel Dumontier syn nucleoside conformation PERSON: Michel Dumontier 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°]. anti nucleoside conformation 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°]. PERSON: Michel Dumontier envelope conformation PERSON: Michel Dumontier 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. twist 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. furan ring 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. PERSON: Michel Dumontier C2prime-endo pucker C2prime-endo pucker (²E conformation) is an envelope conformation in which the C2prime atom is above the plane formed by the other 4 atoms. PERSON: Michel Dumontier C3prime-endo pucker C3prime-endo pucker (An ³E conformation) is an envelope conformation in which the C3prime atom is above the plane formed by the other 4 atoms. PERSON: Michel Dumontier C4prime-exo pucker PERSON: Michel Dumontier C4prime-exo pucker (E₄ conformation) is an envelope conformation in which the C4prime atom is below the plane formed by the other 4 atoms. C3prime-endo - C4prime -exo pucker C3prime-endo - C4prime exo pucker (³E₄ conformation) is a twist conformation in which the C3prime atom is above the plane and the C4prime atom is below the plane. PERSON: Michel Dumontier C3prime-endo - C2prime -exo pucker C3prime-endo - C2prime exo pucker (³E₂ conformation) is a twist conformation in which the C3prime atom is above the plane and the C2prime atom is below the plane. PERSON: Michel Dumontier base stack 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. adjacent base stack An adjacent base stack is a base stack between a pair of sequence-adjacent nucleotides. PERSON: Michel Dumontier 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 #a conformation backbone 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. PERSON: Michel Dumontier base stack reverse orientation PERSON: Michel Dumontier A base stack reverse orientation is a base stack orientation in which the normals of both bases are aligned in the opposite directions. 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. molecule CHEBI:36357 base stack above orientation PERSON: Michel Dumontier 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). 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 PERSON: Michel Dumontier 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. base stack adjacent base orientation 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. 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. PERSON: Michel Dumontier furanose ring A furanose ring is a ring that consists of four carbon and one oxygen atom and has free valences at each carbon position. PERSON: Michel Dumontier upward base stack An upward base stack is a base stack that exhibits both an straight orientation and an above orientation. PERSON: Michel Dumontier downward base stack A downward base stack is a base stack that exhibits both an straight orientation and a below orientation. PERSON: Michel Dumontier inward base stack An inward base stack is a base stack that exhibits both a reverse orientation and an above orientation. PERSON: Michel Dumontier outward base stack An outward base stack is a base stack that exhibits both a reverse orientation and a below orientation. PERSON: Michel Dumontier purine Hoogsteen edge pyrimidine Hoogsteen edge purine Watson-Crick edge pyrimidine Watson-Crick edge purine sugar edge pyrimidine sugar edge submolecule a submolecule is a part of a molecule that consists of covalently bonded sum of a collection of atoms. synonym:moiety pyrimidine O4 atom purine C2 atom pyrimidine N4 atom purine N1 atom purine N6 atom pyrimidine O2 atom pyrimidine N3 atom purine N3 atom ribose O2prime atom RNA backbone purine H2 atom pyrimidine H3 atom purine H8 atom purine C8 atom purine N7 atom purine H62 atom purine O6 atom pyrimidine H5 atom pyrimidine C5 atom pyrimidine C4 atom pyrimidine C6 atom purine H61 atom part of molecule a part of molecule is some part of a molecule. collection of biopolymer residues nucleobase face 5prime face 3prime face nucleoside residue nucleotide residue mereologically maximal object linear RNA backbone mereological sum of collection boundary A boundary is a region at which connections can be formed. backbone conformation nucleic acid external boundary ribose O3prime atom ribose C3prime atom terminal boundary of linear biopolymer uracil O4 atom cytosine O2 atom uracil O2 atom guanine O6 atom adenine C2 atom adenine C8 atom guanine C8 atom cytosine C5 atom uracil C5 atom cytosine C4 atom uracil C4 atom uracil C6 atom cytosine C6 atom adenine H2 atom cytosine N4 atom adenine N1 atom adenine N6 atom cytosine N3 atom uracil N3 atom adenine N3 atom guanine C2 atom uracil H3 atom guanine H8 atom adenine H8 atom adenine H62 atom cytosine H5 atom uracil H5 atom adenine H61 atom guanine N1 atom guanine N3 atom adenine N7 atom guanine N7 atom pyrimidine H6 atom cytosine H6 atom uracil H6 atom purine N9 atom adenine N9 atom guanine N9 atom purine N2 atom guanine N2 atom purine H21 atom purine H22 atom guanine H22 atom guanine H21 atom pyrimidine H41 atom pyrimidine H42 atom cytosine H42 atom cytosine H41 atom ribose O4prime atom ribose O5prime atom ribose C1prime atom ribose C2prime atom ribose C4prime atom ribose C5prime atom ribose H1prime atom ribose H2prime atom ribose H3prime atom ribose H4prime atom ribose H51prime atom ribose H52prime atom ribose OH2prime atom ribose OH3prime atom ribose OH5prime atom phosphate moiety O1P atom phosphate moiety O2P atom phosphate moiety phosphate atom adenosine Watson-Crick edge guanosine Watson-Crick edge cytidine Watson-Crick edge uridine Watson-Crick edge adenine nucleobase functional derivative guanine nucleobase functional derivative cytosine nucleobase functional derivative uracil nucleobase functional derivative adenosine Hoogsteen edge guanosine Hoogsteen edge cytidine Hoogsteen edge uridine Hoogsteen edge adenosine sugar edge guanosine sugar edge cytidine sugar edge uridine sugar edge purine C6 atom guanine C6 atom adenine C6 atom purine carbon atom ribose carbon atom imidazopurine carbon atom pyrimidine carbon atom pyrimidine C2 atom cytosine C2 atom uracil C2 atom purine hydrogen atom pyrimidine hydrogen atom phosphate moiety oxygen atom ribose oxygen atom pyrimidine oxygen atom purine nitrogen atom pyrimidine nitrogen atom ribose hydrogen atom purine H1 atom guanine H1 atom cytidine ribose O 2prime atom uridine ribose O 2prime atom pyrimidine N1 atom adenosine ribonucleoside residue functional derivative guanosine ribonucleoside residue functional derivative cytidine ribonucleoside residue functional derivative uridine ribonucleoside residue functional derivative adenylate residue functional derivative guanylate residue functional derivative cytidylate residue functional derivative uridylate residue functional derivative purine nucleobase functional derivative pyrimidine nucleobase functional derivative purine ribonucleoside residue functional derivative pyrimidine ribonucleoside residue functional derivative purine ribonucleotide functional derivative pyrimidine ribonucleotide functional derivative ribose ring functional derivative 1 1 phosphate moiety functional derivative 5prime cap structure N6-methyladenine nucleobase 1 2prime-O-methylribose ring 1 N6-methyladenylate residue 1 Kristian Rother inosylate residue 1 Kristian Rother dihydrouridylate residue 1 Iga Korneta 2prime-O-methyluridylate residue 1 Iga Korneta 2prime-O-methyladenosine residue 1 2prime-O-methyladenylate residue 1 Iga Korneta 1-methyladenine nucleobase 1 1-methyladenylate residue 1 14/06/2010 Iga Korneta 2-methyladenine nucleobase 1 Iga Korneta 2-methyladenylate residue 1 N6,N6-dimethyladenine nucleobase 2 N6,N6-dimethyladenylate residue 1 1,2prime-O-dimethyladenosine residue 1 1 1,2prime-O-methyladenylate residue 1 N6,2prime-O-dimethyladenosine residue 1 1 N6,2prime-O-dimethyladenylate residue 1 N6,N6,2prime-O-trimethyladenosine residue 1 1 N6,N6,2prime-O-trimethyladenylate residue 1 1-methylhypoxanthine nucleobase 1 1 1-methylinosylate residue 1 2prime-O-methylinosine residue 1 1 2prime-O-methylinosylate residue 1 1,2prime-O-dimethylinosylate residue 1 1,2prime-O-dimethylinosine residue 1 1 2prime-O-methylcytidylate residue 1 3-methylcytosine nucleobase 1 3-methylcytidylate residue 1 N4-methylcytosine nucleobase 1 N4-methylcytidine residue 1 N4-methylcytidylate residue 1 5-methylcytosine nucleobase 1 5-methylcytidylate residue 1 N4,2prime-O-dimethylcytidine residue 1 1 N4,2prime-O-dimethylcytidylate residue 1 N4,N4-dimethylcytosine nucleobase 2 N4,N4-dimethylcytidine residue 1 N4,N4-dimethylcytidylate residue 1 N4,N4,2prime-O-trimethylcytidine residue 1 1 N4,N4,2prime-O-trimethylcytidylate residue 1 5,2prime-O-dimethylcytidine residue 1 1 5,2prime-O-dimethylcytidylate residue 1 2prime-O-methylguanylate residue 1 1-methylguanine nucleobase 1 1-methylguanylate residue 1 N2-methylguanine nucleobase 1 N2-methylguanylate residue 1 N2,N2-dimethylguanine nucleobase 2 N2,N2-dimethylguanylate residue 1 N2,N2,2prime-O-trimethylguanosine residue 1 1 N2,N2,2prime-O-trimethylguanylate residue 1 7-methylguanine nucleobase 1 7-methylguanylate residue 1 N2,7-dimethylguanine nucleobase 1 1 N2,7-dimethylguanylate residue 1 N2,N2,7-trimethylguanosine residue 1 N2,N2,7-trimethylguanine nucleobase 1 2 N2,N2,7-trimethylguanylate residue 1 1,2prime-O-dimethylguanosine residue 1 1 1,2prime-O-methylguanylate residue 1 N2,2prime-O-dimethylguanosine residue 1 1 N2,2prime-O-methylguanylate residue 1 3-methyluracil nucleobase 1 3-methyluridine residue 1 3-methyluridylate residue 1 5-methyluracil nucleobase 1 5-methyluridine residue 1 5-methyluridylate residue 1 3,2prime-O-dimethyluridine residue 1 1 3,2prime-O-dimethyluridylate residue 1 5,2prime-O-dimethyluridine residue 1 1 5,2prime-O-dimethyluridylate residue 1 2-methylthio-N6-methyladenine nucleobase 1 1 1 2-methylthio-N6-methyladenosine residue 1 2-methylthio-N6-methyladenylate residue 1 N6-acetyladenine nucleobase 1 N6-acetyladenosine residue 1 N6-acetyladenylate residue 1 2-thiocytosine nucleobase 1 2-thiocytidylate residue 1 N4-acetylcytosine nucleobase 1 N4-acetylcytidylate residue 1 N4-acetyl-2prime-O-methylcytidine residue 1 1 N4-acetyl-2prime-O-methylcytidylate residue 1 5-formylcytosine nucleobase 1 5-formylcytidine residue 1 5-formylcytidylate residue 1 5-formyl-2prime-O-methylcytidine residue 1 1 5-formyl-2prime-O-methylcytidylate residue 1 2-thiouracil nucleobase 1 2-thiouridine residue 1 2-thiouridylate residue 4-thiouracil nucleobase 1 4-thiouridylate residue 2-selenouracil nucleobase 1 2-selenouridine residue 1 2-selenouridylate residue 2-thio-2prime-O-methyluridine residue 1 1 2-thio-2prime-O-methyluridylate residue 5-methyl-2-thiouracil nucleobase 1 1 5-methyl-2-thiouridylate residue 1 5-formyluracil nucleobase 1 5-formyluridine residue 1 5-formyluridylate residue 1 5-formyl-2prime-O-methyluridine residue 1 1 5-formyl-2prime-O-methyluridylate residue 1 5-formyl-2-thiouridine residue 1 5-formyl-2-thiouracil nucleobase 1 1 5-formyl-2-thiouridylate residue 1 5-formyl-2-selenouracil nucleobase 1 1 5-formyl-2-selenouridine residue 1 5-formyl-2-selenouridylate residue 1 5-methyl-5,6-dihydrouracil nucleobase 1 2 5-methyldihydrouridine residue 1 5-methyldihydrouridylate residue 1 5-hydroxymethylcytosine nucleobase 1 5-hydroxymethylcytidine residue 1 5-hydroxymethylcytidylate residue 1 5-hydroxyuracil nucleobase 1 5-hydroxyuridine residue 1 5-hydroxyuridylate residue 1 5-methoxyuracil nucleobase 1 5-methoxyuridylate residue 1 5-carboxymethyluracil nucleobase 1 5-carboxymethyluridine residue 1 5-carboxymethyluridylate residue 1 5-carboxymethyl-2-thiouracil nucleobase 1 1 5-carboxymethyl-2-thiouridine residue 1 5-carboxymethyl-2-thiouridylate residue 1 5-carboxymethylaminomethyluracil nucleobase 1 1 1 5-carboxymethylaminomethyluridine residue 1 5-carboxymethylaminomethyluridylate residue 1 5-carboxymethylaminomethyl-2prime-O-methyluridine residue 1 1 5-carboxymethylaminomethyl-2prime-O-methyluridylate residue 1 5-carboxymethylaminomethyl-2-thiouracil nucleobase 1 1 1 1 5-carboxymethylaminomethyl-2-thiouridylate residue 1 5-carboxymethylaminomethyl-2-selenouracil nucleobase 1 1 1 1 5-carboxymethylaminomethyl-2-selenouridine residue 1 5-carboxymethylaminomethyl-2-selenouridylate residue 1 5-aminomethyluracil nucleobase 1 1 5-aminomethyluridine residue 1 5-aminomethyluridylate residue 1 5-methylaminomethyl-2-thiouracil nucleobase 1 1 1 5-aminomethyl-2-thiouracil nucleobase 1 1 1 5-aminomethyl-2-thiouridine residue 1 5-methylaminomethyl-2-thiouridine residue 1 5-aminomethyl-2-thiouridylate residue 1 5-methylaminomethyl-2-thiouridylate residue 1 5-methylaminomethyluracil nucleobase 1 1 5-methylaminomethyluridine residue 1 5-methylaminomethyluridylate residue 1 5-aminomethyl-2-selenouracil nucleobase 1 1 1 5-aminomethyl-2-selenouridine residue 1 5-aminomethyl-2-selenouridylate residue 1 5-methylaminomethyl-2-selenouracil nucleobase 1 1 1 5-methylaminomethyl-2-selenouridine residue 1 5-methylaminomethyl-2-selenouridylate residue 1 5-carbamoylmethyluracil nucleobase 1 1 5-carbamoylmethyluridine residue 1 5-carbamoylmethyluridylate residue 1 5-carbamoylmethyl-2prime-O-methyluridine residue 1 1 5-carbamoylmethyl-2prime-O-methyluridylate residue 1 N6-threonylcarbamoyladenine nucleobase 1 1 N6-threonylcarbamoyladenosine residue 1 N6-threonylcarbamoyladenylate residue 1 N6-methyl-N6-threonylcarbamoyladenine nucleobase 1 1 1 N6-methyl-N6-threonylcarbamoyladenosine residue 1 N6-methyl-N6-threonylcarbamoyladenylate residue 1 2-methylthio-N6-threonylcarbamoyladenine nucleobase 1 1 1 1 2-methylthio-N6-threonylcarbamoyladenosine residue 1 2-methylthio-N6-threonylcarbamoyladenosylate residue 1 N6-glycinylcarbamoyladenine nucleobase 1 1 N6-glycinylcarbamoyladenosine residue 1 N6-glycinylcarbamoyladenosylate residue 1 pseudouridylate residue 5-taurinomethyluracil nucleobase 1 1 5-taurinomethyluridine residue 1 5-taurinomethyluridylate residue 1 5-taurinomethyl-2-thiouracil nucleobase 1 1 1 5-taurinomethyl-2-thiouridine residue 1 lysidinylate residue 1 5-taurinomethyl-2-thiouridylate residue 1 lysidine residue 1 2prime-O-(5-phosphoribosyl)ribose ring 2prime-O-ribosyladenylate phosphate residue 1 2prime-O-ribosyladenosine phosphate residue 1 2prime-O-ribosylguanosine phosphate residue 1 2prime-O-ribosylguanylate phosphate residue 1 N6-isopentenyladenine nucleobase 1 N6-isopentenyladenosine residue 1 N6-isopentenyladenylate residue 1 2-methylthio-N6-isopentenyladenine nucleobase 1 1 1 2-methylthio-N6-isopentenyladenosine residue 1 2prime-O-methylpseudouridylate residue 1 3-methylpseudouridine residue 1 3-methylpseudouridylate residue 1 1-methyluracil nucleobase 1 1-methylpseudouridylate residue 1 5-methoxycarbonylmethyluracil nucleobase 1 1 5-methoxycarbonylmethyluridylate residue 1 5-methoxycarbonylmethyl-2-thiouracil nucleobase 1 1 1 5-methoxycarbonylmethyl-2-thiouridylate residue 1 5-methoxycarbonylmethyl-2prime-O-methyluridine residue 1 1 5-methoxycarbonylmethyl-2prime-O-methyluridylate residue 1 3-(3-amino-3-carboxypropyl)uridylate residue 1 3-(3-amino-3-carboxypropyl)methyluridine residue 1 1 3-(3-amino-3-carboxypropyl)methyluridylate residue 1 1-methyl-3-(3-amino-3-carboxypropyl)uracil nucleobase 1 1 1-methyl-3-(3-amino-3-carboxypropyl)pseudouridine residue 1 1-methyl-3-(3-amino-3-carboxypropyl)pseudouridylate residue 1 5-(carboxyhydroxymethyl)uracil nucleobase 1 1 5-(carboxyhydroxymethyl)uridylate residue 1 uracil 5-oxyaceticacid nucleobase 1 1 uridylate 5-oxyacetic acid residue 1 uracil 5-oxyaceticacid methyl ester nucleobase 1 1 1 uridine 5-oxyacetic acid methyl ester residue 1 uridylate 5-oxyacetic acid methyl ester residue 1 5-(carboxyhydroxymethyl)uracil methyl ester nucleobase 1 1 1 5-(carboxyhydroxymethyl)uridine methyl ester residue 1 5-(carboxyhydroxymethyl)uridylate methyl ester residue 1 N6-(cis-hydroxyisopentenyl)adenine nucleobase 1 1 N6-(cis-hydroxyisopentenyl)adenosine residue 1 N6-(cis-hydroxyisopentenyl)adenylate residue 1 2-methylthio-N6-(cis-hydroxyisopentenyl)adenine nucleobase 1 1 1 1 2-methylthio-N6-(cis-hydroxyisopentenyl)adenosine residue 1 2-methylthio-N6-(cis-hydroxyisopentenyl)adenylate residue 1 norvalyl group Not in ChEBI. It derives from 2-aminopentanoic acid (norvaline). There are two enantiomers. N6-hydroxynorvalylcarbamoyladenine nucleobase 1 1 1 N6-hydroxynorvalylcarbamoyladenosine residue 1 N6-hydroxynorvalylcarbamoyladenylate residue 1 2-methylthio-N6-hydroxynorvalylcarbamoyladenine nucleobase 1 1 1 1 1 2-methylthio-N6-hydroxynorvalylcarbamoyladenosine residue 1 2-methylthio-N6-hydroxynorvalylcarbamoyladenylate residue 1 agmatinyl group Not in ChEBI. It derives from agmatine (CHEBI:17431; N-(4-aminobutyl)guanidine). agmatidinylate residue 1 agmatidine residue 1 N2,7,2prime-O-trimethylguanosine residue 1 1 N2,7,2prime-O-trimethylguanylate residue 1 5-isopentenylaminomethyluracil nucleobase 1 1 1 5-isopentenylaminomethyluridylate residue 1 5-isopentenylaminomethyl-2prime-O-methyluridine residue 1 1 5-isopentenylaminomethyluridine residue 1 5-isopentenylaminomethyl-2prime-O-methyluridylate residue 1 5-isopentenylaminomethyl-2-thiouracil nucleobase 1 1 1 1 5-isopentenylaminomethyl-2-thiouridine residue 1 5-isopentenylaminomethyl-2-thiouridylate residue 1 wyosine residue 1 1 wyosinylate residue 1 methylwyosine residue 1 1 1 imidazopurine C7 atom methylwyosinylate residue 1 archaeosine residue 1 carboxamidine group not in ChEBI -C(=NH)-NH2 7-deazapurine C7 atom archaeosinylate residue 1 7-cyano-7-deazaguanosine residue 1 7-cyano-7-deazaguanylate residue 1 7-aminomethyl-7-deazaguanosine residue 1 7-aminomethyl-7-deazaguanylate residue 1 preQ1base nucleobase 1 1 cyclopentenediolyl group cyclopent-(2-3-ene-)4,5-diol-1-yl not in ChEBI Qbase nucleobase 1 1 1 queuosine residue 1 queuosinylate residue 1 mannosyl-Qbase nucleobase 1 1 1 1 mannosyl-queuosine residue 1 mannosyl-queuosinylate residue 1 galactosyl-Qbase nucleobase 1 1 1 1 galactosyl-queuosine residue 1 galactosyl-queuosinylate residue 1 glutamyl-Qbase nucleobase 1 1 1 1 gluQ residue 1 gluQylate residue 1 imidazopurine C6 atom imidazopurine N4 atom 4-demethylwyosine residue 1 4-demethylwyosinylate residue 1 isowyosine residue 1 1 isowyosinylate residue 1 undermodified hydroxywybutosine residue 1 1 1 1 undermodified hydroxywybutosinylate residue 1 10-glutamylwyosine residue 1 1 1 10-glutamylwyosinylate residue 1 10-glutamyl-4-demethylwyosine residue 1 1 10-glutamyl-4-demethylwyosinylate residue 1 10-glutamylmethylesterwyosine residue 1 1 1 1 10-glutamylmethylesterwyosinylate residue 1 2,3-epoxycyclopenta-(4,5-diol)-1-yl group not in ChEBI epoxy-Qbase nucleobase 1 1 1 epoxyqueuosine residue 1 epoxyqueuosinylate residue 1 7-methylguanosine cap structure N2,N2,7-trimethylguanosine cap structure gamma-methylphosphate cap structure wybutosine residue 1 1 1 1 1 1 hydroxywybutosine residue 1 1 1 1 1 1 1 peroxywybutosine residue 1 1 1 1 1 1 1 wybutosinyl residue 1 hydroxywybutosinyl residue 1 peroxywybutosinyl residue 1 3-(3-amino-3-carboxypropyl)uracil nucleobase 1 sulfur atom S selenium atom Se N2,7-dimethylguanosine residue 1