Rhea list of ChEBI terms representing the major species at pH 7.3.
Term not to be used for direct annotation
GO ribbon for eukaroytic cellular processes
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
Binding to an RNA molecule or a portion thereof.
Exportin-5 recognizes 3' overhang of pre-miRNA
Generation of force resulting in movement, for example along a microfilament or microtubule, or in torque resulting in membrane scission or rotation of a flagellum. The energy required is obtained either from the hydrolysis of a nucleoside triphosphate or by an electrochemical proton gradient (proton-motive force).
Extension of pseudopodia by myosin-X in a PI3K dependent manner
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
The action of a molecule that contributes to the structural integrity of a complex.
Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, accross or in between cells.
Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules.
Intermediate II binds CYC1, UQCRC1, UQCRC2, UQCRH
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'.
The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
Not to be used for manual annotation. Please choose a more specific term: for bacteria, annotate to GO:0009274; peptidoglycan-based cell wall, for plants: annotate to GO:0009505 ; plant-type cell wall, for fungi: GO:0009277 ; fungal-type cell wall, and for archae, use GO:0030115 S-layer (see PMID:31214995).
A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore.
The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
generation of precursor metabolites and energy
Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
The synthesis of an RNA transcript from a DNA template.
transcription from bacterial-type RNA polymerase promoter
Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
regulation of cellular transcription, DNA-dependent
regulation of transcription, DNA-dependent
regulation of transcription, DNA-templated
regulation of gene-specific transcription
regulation of DNA-templated transcription
NOTCH4 Intracellular Domain Regulates Transcription
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
glycoprotein-specific chaperone activity
non-chaperonin molecular chaperone ATPase activity
protein complex assembly, multichaperone pathway
Formation of tubulin folding intermediates by CCT/TriC
N-glycan trimming in the ER and Calnexin/Calreticulin cycle
The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups.
cellular amino acid and derivative metabolic process
The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein.
Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport.
A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation.
Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
To annotate the plasma (cytoplasmic) membrane, see instead GO:0005886.
A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.
A thylakoid is not considered an organelle, but some thylakoids are part of organelles.
The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered.
Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change.
Binding to a small molecule, any low molecular weight, monomeric, non-encoded molecule.
Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides.
A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).
A prolongation or process extending from a cell, e.g. a flagellum or axon.
Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.
The region of a bacterial cell to which the DNA is confined.
The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
Metabolism of amino acids and derivatives
The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule.
Any molecular function involved in the regulation of initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome.
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
The binding activity of a molecule that brings together two or more molecules through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
4Fe-4S cluster assembles on NUBP2:NUBP1 scaffold
A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cell wall.
cell wall organization or biogenesis at cellular level
cellular cell wall organisation or biogenesis
cellular cell wall organization or biogenesis
Interacting selectively with one or more biological molecules in another (target) organism, initiating pathogenesis (leading to an abnormal, generally detrimental state) in the target organism. The activity should refer to an evolved function of the active gene product, i.e. one that was selected for. Examples include the activity of botulinum toxin, and snake venom.
Any process that reduces or removes the toxicity of a toxic substance. These may include transport of the toxic substance away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance.
A molecular function regulator regulates the activity of its target via non-covalent binding that does not result in covalent modification to the target. Examples of molecular function regulators include regulatory subunits of multimeric enzymes and channels. Mechanisms of regulation include allosteric changes in the target and competitive inhibition.
This term should only be used in cases when the regulator directly interacts with the enzyme, but does not result in a covalent modification.
Directly binding to a specific ion or molecule and delivering it either to an acceptor molecule or to a specific location.
Note that a carrier moves with its substrate/cargo, while a transporter does not move with the cargo, but facilitates the change in localization.
MMADHC targets transport of cytosolic cob(II)alamin to mitochondria
cob(II)alamin is transferred from MMACHC:MMADHC:cob(II)alamin to MTRR:MTR
SERINC3,5,(1,2,4) transport L-Ser from cytosol to plasma membrane
STAR mediates CHOL translocation from cytosol to mitochondrial intermembrane space
A molecular function that controls the rate, timing and/or magnitude of gene transcription. The function of transcriptional regulators is to modulate gene expression at the transcription step so that they are expressed in the right cell at the right time and in the right amount throughout the life of the cell and the organism. Genes are transcriptional units, and include bacterial operons.
A molecular function required for core promoter activity that mediates the assembly of the RNA polymerase holoenzyme at promoter DNA to form the pre-initiation complex (PIC). General transcription factors (GTFs) bind to and open promoter DNA, initiate RNA synthesis and stimulate the escape of the polymerase from the promoter. Not all subunits of the general transcription factor are necessarily present at all promoters to initiate transcription. GTFs act at each promoter, although the exact subunit composition at individual promoters may vary.
Usage guidance: The distinction between general transcription factors and DNA-binding transcription factors is that the latter modulate the selection of which genes are expressed under specific conditions, while general transcription factors are the constitutive machinery required for transcription initiation.
general transcription initiation factor activity
Binding to a molecule and eliciting a change in the protein's activity in response to the intracellular level of that molecule.
Binding to a specific molecule to prevent it from interacting with other partners or to inhibit its localization to the area of the cell or complex where it is active.
eNOS:NOSIP translocation from caveolae to intracellular compartments
TCN1 binds correnoids in the circulation