BP

GO:0000381

regulation of alternative mRNA splicing, via spliceosome

Any process that modulates the frequency, rate or extent of alternative splicing of nuclear mRNAs.

IDA

BP

GO:0002092

positive regulation of receptor internalization

Any process that activates or increases the frequency, rate or extent of receptor internalization.

IDA

BP

GO:0006397

mRNA processing

Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.

IEA

BP

GO:0006974

cellular response to DNA damage stimulus

Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.

IDA

BP

GO:0007215

glutamate receptor signaling pathway

A series of molecular signals initiated by the binding of glutamate to a glutamate receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.

ISS

BP

GO:0008380

RNA splicing

The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.

IEA

BP

GO:0017148

negative regulation of translation

Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA.

IBA

BP

GO:0031047

gene silencing by RNA

Any process in which RNA molecules inactivate expression of target genes.

IEA

BP

GO:0033129

positive regulation of histone phosphorylation

Any process that activates or increases the frequency, rate or extent of the addition of one or more phosphate groups to a histone protein.

IDA

BP

GO:0034644

cellular response to UV

Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.

ISS

BP

GO:0043488

regulation of mRNA stability

Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs.

ISS

BP

GO:0044830

modulation by host of viral RNA genome replication

A process in which a host organism modulates the frequency, rate or extent of viral RNA genome replication.

IMP

BP

GO:0045727

positive regulation of translation

Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA.

IDA

BP

GO:0045947

negative regulation of translational initiation

Any process that stops, prevents, or reduces the frequency, rate or extent of translational initiation.

ISS

BP

GO:0046928

regulation of neurotransmitter secretion

Any process that modulates the frequency, rate or extent of the regulated release of a neurotransmitter from a cell.

ISS

BP

GO:0051028

mRNA transport

The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

ISS

BP

GO:0051489

regulation of filopodium assembly

Any process that modulates the frequency, rate or extent of the assembly of a filopodium, a thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone.

IDA

BP

GO:0051491

positive regulation of filopodium assembly

Any process that activates or increases the frequency, rate or extent of the assembly of a filopodium, a thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone.

ISS

BP

GO:0060964

regulation of gene silencing by miRNA

Any process that modulates the rate, frequency, or extent of the downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: mRNA cleavage or translational repression.

IMP

BP

GO:0060998

regulation of dendritic spine development

Any process that modulates the rate, frequency, or extent of dendritic spine development, the process whose specific outcome is the progression of the dendritic spine over time, from its formation to the mature structure.

IDA

BP

GO:0060999

positive regulation of dendritic spine development

Any process that increases the rate, frequency, or extent of dendritic spine development, the process whose specific outcome is the progression of the dendritic spine over time, from its formation to the mature structure.

ISS

BP

GO:0072711

cellular response to hydroxyurea

Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydroxyurea stimulus.

ISS

BP

GO:0098586

cellular response to virus

Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a virus.

IDA

BP

GO:0098908

regulation of neuronal action potential

Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a neuron. This typically occurs via modulation of the activity or expression of voltage-gated ion channels.

IDA

BP

GO:1900453

negative regulation of long term synaptic depression

Any process that stops, prevents or reduces the frequency, rate or extent of long term synaptic depression.

ISS

BP

GO:1901254

positive regulation of intracellular transport of viral material

Any process that activates or increases the frequency, rate or extent of intracellular transport of viral material.

IMP

BP

GO:1901386

negative regulation of voltage-gated calcium channel activity

Any process that stops, prevents or reduces the frequency, rate or extent of voltage-gated calcium channel activity.

ISS

BP

GO:1901800

positive regulation of proteasomal protein catabolic process

Any process that activates or increases the frequency, rate or extent of proteasomal protein catabolic process.

ISS

BP

GO:1902416

positive regulation of mRNA binding

Any process that activates or increases the frequency, rate or extent of mRNA binding.

IDA

BP

GO:2000301

negative regulation of synaptic vesicle exocytosis

Any process that stops, prevents or reduces the frequency, rate or extent of synaptic vesicle exocytosis.

ISS

BP

GO:2000637

positive regulation of gene silencing by miRNA

Any process that activates or increases the frequency, rate or extent of gene silencing by miRNA.

IDA

BP

GO:2000766

negative regulation of cytoplasmic translation

Any process that stops, prevents or reduces the frequency, rate or extent of cytoplasmic translation.

ISS

BP

GO:2001022

positive regulation of response to DNA damage stimulus

Any process that activates or increases the frequency, rate or extent of response to DNA damage stimulus.

IDA

CC

GO:0000775

chromosome, centromeric region

The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.

IEA

CC

GO:0005634

nucleus

A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

IDA|ISS

CC

GO:0005654

nucleoplasm

That part of the nuclear content other than the chromosomes or the nucleolus.

IDA

CC

GO:0005694

chromosome

A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.

ISS

CC

GO:0005730

nucleolus

A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.

IDA|TAS

CC

GO:0005737

cytoplasm

All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

IDA|TAS

CC

GO:0005844

polysome

A multiribosomal structure representing a linear array of ribosomes held together by messenger RNA. They represent the active complexes in cellular protein synthesis and are able to incorporate amino acids into polypeptides both in vivo and in vitro.

IDA|ISS

CC

GO:0005845

mRNA cap binding complex

Any protein complex that binds to an mRNA cap at any time in the lifetime of the mRNA.

ISS

CC

GO:0010369

chromocenter

A region in which centric, heterochromatic portions of one or more chromosomes form a compact structure.

ISS

CC

GO:0014069

postsynaptic density

The postsynaptic density is a region that lies adjacent to the cytoplasmic face of the postsynaptic membrane at an excitatory synapse. It forms an electron-dense disc that consists of a range of proteins with different functions, some of which contact the cytoplasmic domains of ion channels in the postsynaptic membrane. The proteins making up the disc include structural proteins linked to the actin cytoskeleton and signalling machinery, such as protein kinases and phosphatases.

ISS

CC

GO:0015030

Cajal body

A class of nuclear body, first seen after silver staining by Ramon y Cajal in 1903, enriched in small nuclear ribonucleoproteins, and certain general RNA polymerase II transcription factors; ultrastructurally, they appear as a tangle of coiled, electron-dense threads roughly 0.5 micrometers in diameter; involved in aspects of snRNP biogenesis; the protein coilin serves as a marker for Cajal bodies. Some argue that Cajal bodies are the sites for preassembly of transcriptosomes, unitary particles involved in transcription and processing of RNA.

IEA

CC

GO:0016020

membrane

A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

IDA

CC

GO:0019034

viral replication complex

Specific locations and structures in the virus infected cell involved in replicating the viral genome.

IDA

CC

GO:0019897

extrinsic component of plasma membrane

The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.

ISS

CC

GO:0030054

cell junction

A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.

IEA

CC

GO:0030424

axon

The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.

ISS

CC

GO:0030425

dendrite

A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.

ISS

CC

GO:0030426

growth cone

The migrating motile tip of a growing nerve cell axon or dendrite.

IDA

CC

GO:0030529

intracellular ribonucleoprotein complex

An intracellular macromolecular complex containing both protein and RNA molecules.

IDA

CC

GO:0032433

filopodium tip

The end of a filopodium distal to the body of the cell.

ISS

CC

GO:0032797

SMN complex

A protein complex that contains the survival motor neuron (SMN) protein and at least eight additional integral components, including the Gemin2-8 and Unrip proteins; the complex is found in the cytoplasm and in nuclear Gems, and is involved in spliceosomal snRNP assembly in the cytoplasm and in pre-mRNA splicing in the nucleus.

IDA

CC

GO:0036464

cytoplasmic ribonucleoprotein granule

A ribonucleoprotein granule located in the cytoplasm.

IDA

CC

GO:0042734

presynaptic membrane

A specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane.

IEA

CC

GO:0042788

polysomal ribosome

A ribosome bound to mRNA that forms part of a polysome.

TAS

CC

GO:0042995

cell projection

A prolongation or process extending from a cell, e.g. a flagellum or axon.

IDA

CC

GO:0043005

neuron projection

A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.

IDA

CC

GO:0043197

dendritic spine

A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including thin, stubby, mushroom, and branched, with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.

ISS

CC

GO:0043204

perikaryon

The portion of the cell soma (cell body) that excludes the nucleus.

IDA|ISS

CC

GO:0043679

axon terminus

Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal button is a specialized region of it.

ISS

CC

GO:0045202

synapse

The junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell; the site of interneuronal communication. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

ISS

CC

GO:0045211

postsynaptic membrane

A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.

IEA

CC

GO:0048471

perinuclear region of cytoplasm

Cytoplasm situated near, or occurring around, the nucleus.

IDA

CC

GO:0071598

neuronal ribonucleoprotein granule

A ribonucleoprotein complex that is found in the cytoplasm of axons and dendrites, and transports translationally silenced mRNAs to dendritic synapses, where they are released and translated in response to specific exogenous stimuli.

ISS

CC

GO:0097386

glial cell projection

A prolongation or process extending from a glial cell.

ISS

CC

GO:0098793

presynapse

The part of a synapse that is part of the presynaptic cell.

ISS

CC

GO:0098794

postsynapse

The part of a synapse that is part of the post-synaptic cell.

ISS

CC

GO:1902737

dendritic filopodium

A small, membranous protrusion found primarily on dendritic stretches of developing neurons. May receive synaptic input, and can develop into dendritic spines.

ISS

CC

GO:1990812

growth cone filopodium

A thin, stiff protrusion extended by the leading edge of an axonal or dendritic growth cone.

ISS

CC

GO:1990904

ribonucleoprotein complex

A macromolecular complex containing both protein and RNA molecules.

IDA

MF

GO:0002151

G-quadruplex RNA binding

Interacting selectively and non-covalently with G-quadruplex RNA structures, in which groups of four guanines adopt a flat, cyclic hydrogen-bonding arrangement known as a guanine tetrad.

IDA

MF

GO:0003682

chromatin binding

Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.

ISS

MF

GO:0003723

RNA binding

Interacting selectively and non-covalently with an RNA molecule or a portion thereof.

IDA

MF

GO:0003729

mRNA binding

Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.

IDA

MF

GO:0003730

mRNA 3'-UTR binding

Interacting selectively and non-covalently with the 3' untranslated region of an mRNA molecule.

IDA

MF

GO:0005515

protein binding

Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).

IPI

MF

GO:0008017

microtubule binding

Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.

ISS

MF

GO:0008266

poly(U) RNA binding

Interacting selectively and non-covalently with a sequence of uracil residues in an RNA molecule.

IDA

MF

GO:0030371

translation repressor activity

Antagonizes ribosome-mediated translation of mRNA into a polypeptide.

IDA

MF

GO:0031369

translation initiation factor binding

Interacting selectively and non-covalently with a translation initiation factor, any polypeptide factor involved in the initiation of ribosome-mediated translation.

IPI

MF

GO:0033592

RNA strand annealing activity

Facilitates the base-pairing of complementary single-stranded RNA.

IDA

MF

GO:0034046

poly(G) binding

Interacting selectively and non-covalently with a sequence of guanine residues in an RNA molecule.

IDA

MF

GO:0035064

methylated histone binding

Interacting selectively and non-covalently with a histone protein in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of plant and animal chromosomes.

IDA

MF

GO:0035197

siRNA binding

Interacting selectively and non-covalently with a small interfering RNA, a 21-23 nucleotide RNA that is processed from double stranded RNA (dsRNA) by an RNAse enzyme.

IDA

MF

GO:0035198

miRNA binding

Interacting selectively and non-covalently with a microRNA, a 21-23 nucleotide RNA that is processed from a stem-loop RNA precursor (pre-miRNA) that is encoded within plant and animal genomes.

IDA

MF

GO:0035613

RNA stem-loop binding

Interacting selectively and non-covalently with a stem-loop in an RNA molecule. An RNA stem-loop is a secondary RNA structure consisting of a double-stranded RNA (dsRNA) stem and a terminal loop.

IDA

MF

GO:0042802

identical protein binding

Interacting selectively and non-covalently with an identical protein or proteins.

IDA

MF

GO:0042803

protein homodimerization activity

Interacting selectively and non-covalently with an identical protein to form a homodimer.

IDA

MF

GO:0043022

ribosome binding

Interacting selectively and non-covalently with any part of a ribosome.

IPI

MF

GO:0044325

ion channel binding

Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.

IPI

MF

GO:0044822

poly(A) RNA binding

Interacting non-covalently with a poly(A) RNA, a RNA molecule which has a tail of adenine bases.

IDA

MF

GO:0045502

dynein binding

Interacting selectively and non-covalently with dynein, the multisubunit protein complex that is associated with microtubules.

ISS

MF

GO:0046982

protein heterodimerization activity

Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.

IDA

MF

GO:0048027

mRNA 5'-UTR binding

Interacting selectively and non-covalently with the 5' untranslated region of an mRNA molecule.

IDA

MF

GO:1990825

sequence-specific mRNA binding

Interacting selectively and non-covalently with messenger RNA (mRNA) of a specific nucleotide composition or a specific sequence motif.

IDA