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The table below is automatically generated by a query that lists subcellular parts

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Definition Id Synonym
Actin Filament A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane (Gene Ontology). sao1588493326
Active Zone Cytomatrix Filamentous matrix immediately internal to the plasma membrane docking zone (Zhai and Bellen, 2004). sao1470121605
Active Zone Dense Projection Electron dense projection extending from the cytomatrix into the cytoplasm on which synaptic vesicles are tethered (Zhai and Bellen, 2004). sao494258938
Active Zone Plasma Membrane Plasma membrane juxtaposed to the PSD where synaptic vesicle fusion occurs (Zhai and Bellen, 2004). sao2038461087
Age associated cellular inclusion sao2017162875
Alpha synuclein positive inclusion A cellular inclusion that contains alpha synuclein nlx_143539
Amorphous Vesicle Category of non-SER vesicle described by Clooney et al. (2002) in dendrites, categorized by smooth membranes, electron-lucent interiors and irregular shapes. Sometimes occurrs in clumps. These vesicles contained gold taken up from the extracellular space, suggesting that they may be part of the endosomal pathway. sao1531915298
Autolysosome A type of secondary lysosome in which a primary lysosome has fused with the outer membrane of an autophagosome. It is involved in the second step of autophagy in which it degrades contents with acidic lysosomal hydrolases. GO:0044754 Autophagolysosome
degrading autophagic vacuole
Autophagosome A vesicle with a double membrance derived from the Endoplasmic Reticulum that encloses cytoplasmic material and organelles to be degraded. Its formation is the first step of the process of autophagy. GO:0005776 autophagic vacuole
initial autophagic vacuole
Axoaxonic synapse The synapse made by an axon terminal of one neuron onto the axon of another. oen_0001117 Axo-axonic synapse
Axodendritic synapse The synapse made by an axon terminal of one neuron onto the dendrite of another. oen_0001118 Axo-dendritic synapse
Axolemma The plasma membrane of an axon; it is a specialized trilaminar random mosaic of protein molecules floating within a fluid matrix of highly mobile phospholipid molecules, 7-8 nm in thickness (Gene Ontology). sao250772229
Axon Hillock Cone shaped elevation from which the axon originates; in Nissl stained preparations, the axon hillock usually can be identified as a region of the perikaryon that is distinguished by a deficiency of Nissl substance (Peters, Palay and Webster, 1991). In physiology: A specialized component of the neuron, usually located in the initial segment of the axon where the action potential is initiated. oen_0001187 Trigger zone
Action potential initial zone
initial segment
Axosomatic synapse The synapse made by an axon terminal of one neuron on the cell body of aanother. oen_0001119 Axo-somatic synapse
Barr Body sao1571698684
Bunina Body Bunina bodies are small eosinphilic granular inclusions that are 1-3 microns in diameter in the anterior horn cells, appearing either singly or in a group. Sometimes they are arranded in small beaded chains. They stain bright red with hematoxylin and eosin (H&E) staining, deep blue with phospotungstic acid hematoxylin and blue with Luxol fast blue. They express cystatin C and consist of electron-dense amorphous material that contains tubules or vesicular structures. The amorphous material frequently includes a cytoplasmis island containing neurofilaments and other micro-organelles. nlx_37
Cajal Body A class of nuclear body, first seen after silver staining by 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. GO:0015030 Coiled body
Cellular Inclusion A discrete intracellular part formed of aggregated molecules such as proteins or other biopolymers. GO:0016234 Inclusion Body
Cellular Subcomponent sao628508602
Cellular membrane Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. GO:0016020 membrane
Centriole A cellular organelle, found close to the nucleus in many eukaryotic cells, consisting of a small cylinder with microtubular walls, 300-500 nm long and 150-250 nm in diameter. It contains nine short, parallel, peripheral microtubular fibrils, each fibril consisting of one complete microtubule fused to two incomplete microtubules. Cells usually have two centrioles, lying at right angles to each other. At division, each pair of centrioles generates another pair and the twin pairs form the pole of the mitotic spindle (Gene Ontology). GO:0005814
Centrosome A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle. GO:0005813
Chemical Synapse sao289211478
Chromatin The ordered and organized complex of DNA and protein that forms the chromosome (Gene Ontology). sao1615953555
Cilium Cilia arising from neurons have been described in many different regions of the nervous system. Neuronal cilia have a "9+0" pattern, that is, they are missing the central pair of microtubules that characterizes most cilia (Peters, Palay and Webster, 1991). sao787716553
Cilium basal body A membrane-tethered derivative of the centriole, and the site of assembly and remodelling of the cilium. As well as anchoring the cilium, the basal body is thought to provide a selective gateway regulating the entry of ciliary proteins and vesicles by intraflagellar transport. GO:0036064 ciliary basal body
Cis Face of Golgi Apparatus The network of interconnected tubular and cisternal structures located at the convex side of the Golgi apparatus, which abuts the endoplasmic reticulum. GO:0005801 cis Golgi network
Golgi cis face
Golgi cis-face
forming face
cis face
Classical Lewy Body Eosinophilic cytoplasmic lesion, 5 to 15 micrometers in diameter, with a dense eosinphilic core surrounded by a halo of 10 to 20 nm wide radially oriented alpha-synuclein fibrils. sao4749542545 Brainstem Lewy Body
Clathrin Coat A membrane coat found on coated pits and some coated vesicles; consists of polymerized clathrin triskelions, each comprising three clathrin heavy chains and three clathrin light chains, linked to the membrane via one of the AP adaptor complexes (Gene Ontology). sao879919129
Clathrin Coated Endocytic Vesicle A clathrin-coated, membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance (Gene Ontology). sao1243595998
Coated Tip Coated tips of tubular endosomes that appear to be vesicles in the process of budding off (Clooney et al., 2002). sao694815499
Coated pit A part of the endomembrane system in the form of an invagination of a membrane upon which a clathrin coat forms, and that can be converted by vesicle budding into a clathrin-coated vesicle. Coated pits form on the plasma membrane, where they are involved in receptor-mediated selective transport of many proteins and other macromolecules across the cell membrane, in the trans-Golgi network, and on some endosomes. GO:0005905
Complex laminated body Cytoplasmic organelles described in some lateral geniculate neurons composed of sheets of tubules (25 nm in diameter) separated by dense material (about 75 nm wide), which together with the tubules whorl give a structure resembling a 'finger-print '. In 2 um thick Epon-Araldite sections stained with methylene-blue and Azure II, CLBs are dark blue, round or oval bodies of the same order of size as the nucleolus. nlx_151681
Condensed Chromatin Chromatin that are agglomerated into irregular masses, some attached to the nuclear envelope., A compact and highly condensed form of chromatin (Gene Ontology). sao581845896 heterochromatin
Contractile vacuole A specialized vacuole of eukaryotic cells, especially Protozoa, that fills with water from the cytoplasm and then discharges this externally by the opening of contractile vacuole pores. Its function is probably osmoregulatory. GO:0000331
Cortical Lewy Body Lesion that is less well defined than a Classical Lewy Body and lacks a halo. sao4040591221
Cytoplasmic Vesicle A vesicle formed of membrane or protein, found in the cytoplasm of a cell (Gene Ontology). sao180601769
Cytoskeletal Element sao1635329413
Cytosol The part of the cytoplasm that does not contain membranous or particulate subcellular components (UMLS). sao101633890
Dendritic Microtubule sao110773650
Dendroaxonic synapse The synapse made by an axon terminal of one neuron onto the axon of another. oen_0001116 Dendro-axonic_synapse
Dense Body An electron dense body, some of which contain granules (Peters, Palay and Webster (1991) sao730872736
Dense Core Vesicle 40-60 nm vesicle containing an electron dense granule, 15-20 nm in diameter (Peters, Palay and Webster, 1991). sao772007592
Docked Vesicle Synaptic vesicle docked at the pre-synaptic active zone. sao403156667
Early endosome A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center. GO:0005770 prevacuolar compartment
Electrotonic Synapse Electrotonic synapses are gap junctions that allow the passage of ions directly from cell to cell. Ultrastructurally, it can be recognized as a 7 layered structure with 4 dense lines, two from each of the plasma membranes, alternating with 3 lighter lines. Electrotonic synapses are generally symmetric and display little or no dense material associated with the cytoplasmic face of the plasma membrane (Peters, Palay and Webster, 1991). sao1311109124 Electrical Synapse
Endocytic Vesicle A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance (Gene Ontology). sao1362520468
Endomembrane system A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. GO:0012505
Endoplasmic reticulum The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached) (Gene Ontology). GO:0005783
Endosomal Membrane sao978443756
Endosomal Subcomponent sao1683772610
Endosome A membrane-bounded organelle to which materials ingested by endocytosis are delivered. GO:0005768
Extended Chromatin A dispersed and relatively uncompacted form of chromatin (Gene Ontology). sao445485807 euchromatin
Fibrillary Inclusion Cellular inclusion found in cytoplasm of giant cells of Dieters in lateral vestibular nucleus of the rat consisting of circular areas filled with fine slender filaments about 10 nanometers in diameter, delimited by a wall of varying complexity either a single continuous membrane or a tubular network consisting of a fine filamentous material giving the wall a honeycomb appearance. Similar structures have been discribed in the ventral cochlear nucleus, spinal cord, substantia nigra. First described by Sitelo and Palay, 1968. (from Peters, Palay, and Webster) sao967812059
Flame-shaped Neurofibrillary Tangle nlx_subcell_20090202
Free Ribosome sao1139385046
Glial Cytoplasmic Inclusion A glial cytoplasmic inclusion is a pathological hallmark of multiple system atrophy. GCIs are non-membrane-bound cytoplasmic inclusions composed of 10-40 nm granule-coated fibrils. These inclusions have an abnormal accumulation of alpha-synuclein protein. nlx_84726 Papp-Lantos inclusion
Glial Filament sao-1863852493
Glial Inclusion nlx_54629 Argyrophilic Glial Inclusion
Glycogen Granule Cytoplasmic bead-like structures of animal cells, visible by electron microscope. Each granule is a functional unit with the biosynthesis and catabolism of glycogen being catalyzed by enzymes bound to the granule surface (Gene Ontology). Appears as small, electron dense particles 20-40 nm in diameter. Glycogen is difficult to fix in vivo so amounts may be underestimated (Peters, Palay and Webster). sao1081228141
Golgi Subcomponent sao624292949
Golgi apparatus A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions. GO:0005794 golgi cisternae
Golgi cisternae Any of the thin, flattened membrane-bounded compartments that form the central portion of the Golgi complex. GO:0031985 Golgi lamellae
Golgi-associated vesicle Any vesicles associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell (Gene Ontology). GO:0005798
Granular Vesicle Vesicle of varying size, but usually larger than 45 nm, that has an electron dense "granular" core, associated with noradrenergic and peptidergic cells. sao478230652
Hyaline Inclusion Pale eosinophilic inclusions with halos in H&E (hematoxylin and eosin) preparations. nlx_369 Pale body
Immature Insulin Granule A proinsulin-containing secretory vesicle which occurs within pancreatic beta cells. Immature insulin are also called "pale granules" due to their pale appearance under an transmission electron microscope. Immature insulin granules bud off the trans-most Golgi cisternae as part of the insulin synthesis process. When the proinsulin in converted to a mature form of insulin and clusters into an electron dense core, it is said to become an mature insulin granule. nlx_12553 Pale granule
Insulin Granule Membrane-bound secretory granules which contain insulin and occur inside pancreatic beta cells. nlx_27557 Insulin secretory granule
Inter-Golgi Transport Vesicle A vesicle that mediates transport of cargo within the Golgi complex (for example, between cisternae of the Golgi stack) (Gene Ontology). sao1382918459
Interchromatin Granule A class of nuclear body measuring 20-25 nm in diameter and distributed throughout the interchromatin space, linked together by thin fibrils. They are believed to be storage centers for various snRNAs, snRNPs, serine/arginine-rich proteins and RNA polymerase II. A typical mammalian cell contains 25-50 clusters of interchromatin granules. Interchromatin granule clusters do not contain the heterogeneous nuclear RNA-binding proteins (hnRNPs) (Gene Ontology). sao1049471211
Intermediate filament A cytoskeletal structure that forms a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space. Intermediate filaments may be divided into five chemically distinct classes: Type I, acidic keratins; Type II, basic keratins; Type III, including desmin, vimentin and others; Type IV, neurofilaments and related filaments; and Type V, lamins. GO:0005882
Intracellular Membrane The lipid bilayer surrounding an organelle. GO:0031090 organelle membrane
Junctional fold The specialized membrane in folding at the end plate of a muscle fiber in the region of the motor nerve terminal oen_0001156
Lamellar Body Membranous inclusions composed of stacks of unperforated cisternae derived from the granular endoplasmic reticulum. Cisternae are spaced at intervals of about 30-40 nm (Peters, Palay and Webster, 1991). sao1379604862
Laminated Body Inclusion bodies characterized by regularly spaced sheets of tubules arranged in a whorl pattern resembling a fingerprint. They have been observed in neurons of the lateral geniculate nucleus (Peters, Palay and Webster, The Fine Structure of the Nervous System, 3rd ed., Oxford University Press, 1991, pg. 48, figure.) GO:1990011 Laminated inclusion body
Large Vesicle Vesicles of same size and content of coated vesicles; posited by Clooney et al. (2002) to represent coated vesicles after uncoating. sao1241866791
Late Endosome Late endosomes are vesicular structures that accumulate internalized components after their passage through early endosomes (GO: 0005700). nlx_98851
Lewy Body Neuronal inclusion commonly found in damaged neurons. A spherical mass that dispaces other cells composed of abnormally phosphorylated, neurofilament proteins aggregated with ubiquitin and alpha-synuclein. They are intracytoplasmic. sao4933778419 Cytoplasmic Inclusion
Lewy Body-like Hyaline Inclusion In H&E preparations, neuronal LBHIs show an eosinphilic core with a paler peripheral halo, and their name is derived from their H&E staining features, which resemble those of Lewy bodies in patients with Parkinson's disease. Neuronal Lewy Body-like Hyaline Inclusions consist of filaments and granular materials, exhibit dense cores with rough preipheral halos and lack a limiting membrane. The filaments of these inclusions are composed of approximately 15-25 nm granule-coated fibrils in association with normal 10-nm neurofilaments. nlx_169
Lipofuscin Finely granular yellow-brown pigment granules composed of lipid-containing residues of lysosomal digestion. It accumulates in various normal tissues and apparently increases in quantity with age (Adapted from Wikipedia and MSH). sao941755985
Lumen Cargo Refers to cargo carried in the lumen of the vesicle; may be crystalized or otherwise bound, e.g., insulin. sao976831666
Lysosome A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions. GO:0005764
Lytic vacuole A vacuole that is maintained at an acidic pH and which contains degradative enzymes, including a wide variety of acid hydrolases. GO:0000323
Macular post synaptic density Post synaptic density in which the density is continuous nlx_152898
Mature Insulin Granule Insulin secretory granule which occurs inside pancreatic beta cells and contain a large electron-dense core of tightly clustered insulin hexamers. Mature insulin granules are typically ~200-300 nm in diameter, and each contain 150000-280000 insulin molecules in mouse. The precursor of a mature insulin granule is an immature insulin granule, which is also known as a pale granule, as it lacks an electron dense core and is pale in appearance. nlx_13590 Dense core granule
Mature granule
Membrane Bound Ribosome A ribosome that is attached to a intracellular membrane. Does not itself have a membrane surrounding it. sao1291545653
Membrane Cargo Refers to integral membrane proteins carried via the vesicle membrane. sao1037637579
Membrane bound organelle Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane (Gene Ontology). GO:0043227 membranous organelle
membrane-bounded organelle
membrane bounded organelle
membrane bound organelle
Microfilament birnlex_888
Microtubule Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle. GO:0005874 Neurotubule
Microtubule (sao1846835077) Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle (Gene Ontology). sao1846835077
Mitochondrial Adhaerens Complex An adherens plaque attached by filamentous strands to mitochondrion found in large synaptic terminals in the calyx of Held. The peripheral membrane facing the plaque is flattened and faces the synaptic presynaptic membrane (Perkins and Ellisman, 2005). sao1933817066 mitochondrial-associated adherens complex
Mitochondrial Chromosome A chromosome found in the mitochondrion of a eukaryotic cell (Gene Ontology). sao1186327184
Mitochondrial Matrix The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes concerned with fatty-acid oxidation and enzymes of the tricarboxylic acid cycle (Gene Ontology). sao1804523077
Mitochondrial Membrane sao1045389829
Mitochondrial Membrane Inner The inner membrane of the mitochondria. It is highly folded to form cristae (Gene Ontology). The inner membrane of the mitochondria. It is highly folded to form cristae (Gene Ontology). sao1371347282 inner mitochondrial membrane
Mitochondrial Membrane Outer The membrane on the outer surface of the mitochondrion, interfacing with the cell cytoplasm (Gene Ontology). sao1289741256 outer mitochondrial membrane
Mitochondrial Subcomponent sao666410040
Mitochondrion A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration (Gene Ontology). GO:0005739
Mixed Synapse Existence of both chemical and electrotonic synapses at the same interface (Peters, Palay and Webster, 1991)., Synaptic contact characterized by both electrical and chemical synaptic junctions. sao1506103497
Mossy fiber rosette a synapse of the mossy fiber onto the dendrite of a granule cell; each mossy fiber can have up to 50 rosettes. (source: ( nlx_subcell_091021
Multivesicular body A type of late endosome in which regions of the limiting endosomal membrane invaginate to form internal vesicles; membrane proteins that enter the internal vesicles are sequestered from the cytoplasm (Gene Ontology). GO:0005771
Nematosome Cytoplasmic, ball-like inclusion resembling a nucleolus and consisting of a convoluted network of electron-opaque strands embedded in a less dense matrix. It measures approximately 0.9 microns and lacks a limiting membrane. Its strands (diameter = 400-600 A) appear to be made of an entanglement of tightly packed filaments and particles approximately 25-50 A thick. Cytochemical studies suggest the presence of nonhistone proteins and some RNA. Usually only one such structure is present in a cell, and it appears to occur in most ganglion cells. Although they can be seen anywhere in the cell body, nematosomes are typically located in the perinuclear cytoplasm, where they are often associated with smooth-surfaced and coated vesicles. GO:0097417
Neurofibrillary tangle Intracellular mass of paired, hellically wound protein filaments (PHF) lying in the cytoplasm of neuronal cell bodies and neuritic cell processes. They contain an abnormally phosporylated form of a microtuble associated with protein, tau. sao2409833926
Neurofilament A type of intermediate filament found in the core of neuronal axons. Neurofilaments are heteropolymers composed of three type IV polypeptides: NF-L, NF-M, and NF-H (for low, middle, and high molecular weight). Neurofilaments are responsible for the radial growth of an axon and determine axonal diameter. GO:0005883 type IV intermediate filament
Neuromuscular Junction The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a post-synaptic potential responsible of the muscle contraction (Gene Ontology). sao1124888485
Neuronal Cytoplasmic Inclusion
Neurosecretory Vesicle Large dense cored vesicles, up to 150-200 nm in diameter found in neurosecretory cells in the hypothalamus. The electron dense appearance is dependent upon fixation (Peters, Palay and Webster, 1991). sao2031592629
Neurotubule Refers to a microtubule found in a nerve cell. The term "neurotubule" may now be obselete; however, it was used in earlier findings. sao248349196
Non-membrane bound organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes (Gene Ontology). sao1456184038
Nuclear Body Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins (Gene Ontology). sao505137457
Nuclear Lamina Meshwork of extremely fine filaments composed of polypeptides called lamins that run parallel with the inner surface of the nuclear envelope (Peters, Palay and Webster, 1991)., The fibrous, electron-dense layer lying on the nucleoplasmic side of the inner membrane of a cell nucleus, composed of lamin filaments. The polypeptides of the lamina are thought to be concerned in the dissolution of the nuclear envelope and its re-formation during mitosis. The lamina is composed of lamin A and lamin C filaments cross-linked into an orthogonal lattice, which is attached via lamin B to the inner nuclear membrane through interactions with a lamin B receptor, an IFAP, in the membrane (Gene Ontology). GO:0005652
Nuclear Subcomponent sao1499850686
Nuclear envelope The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). GO:0005635
Nuclear inner membrane The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope (Gene Ontology). GO:0005637
Nuclear membrane Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space (Gene Ontology). GO:0031965
Nuclear outer membrane The outer, i.e. cytoplasm-facing, lipid bilayer of the nuclear envelope; continuous with the endoplasmic reticulum of the cell and sometimes studded with ribosomes (Gene Ontology). GO:0005640
Nuclear pore Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined (Gene Ontology). GO:0005643
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 (Gene Ontology). GO:0005730
Nucleolus-associated heterochromatin Dense particles of heterochromatin, consisting of a loosely twisted strang ~600 A thick, found associated with the nucleolus (Palay and Chan-Palay, 1974). GO:0097424
Nucleoplasm That part of the nuclear content other than the chromosomes or the nucleolus (Gene Ontology). GO:0005654
Nucleus A membrane-bounded organelle of eukaryotic cells that contains the chromosomes. It is the primary site of DNA replication and RNA synthesis in the cell (Gene Ontology). GO:0005634 cell nucleus
Organelle Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane (Gene Ontology). GO:0043226
Perforated post synaptic density A post synaptic density characterized by interruptions in the electron dense portions nlx_152897
Perforated synapse A synapse characterized by interruptions in the post synaptic density in electron micrographs. In three dimensions, these interruptions appear as holes in the post synaptic density nlx_152896
Peroxisome A small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules; contains some enzymes that produce and others that degrade hydrogen peroxide (H2O2) (Gene Ontology). GO:0005777 microbody
peroxisome vesicle
Pick Body Pick Bodies are composed of numerous tau fibrils arranged in a disorderly array. Tau protein is a major component. Pick bodies also stain for ubiquitin, alpha-synuclein, and apolipoprotein E. nlx_448
Pinocytic vesicle A membrane-bounded, uncoated intracellular vesicle formed by the process of pinocytosis. GO:0044352 pinosome
Plasma membrane The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins (Gene Ontology). GO:0005886 cell membrane
Plasmalemmal precursor vesicle A cytoplasmic vesicle approximately 150 nm in diameter thought to be involved in plasma membrane expansion. Most commonly found in growing axons and dendrites as well as regenerating axons (Pfenninger, Nature Reviews Neurosci 10: 251, 2009)
Post-synaptic Component sao1507566336
Post-synaptic Vesicle A synaptic vesicle which has undergone fusion with the membrane of the presynaptic terminal (at the end of an axon) and released its neurotransmitters into the synaptic cleft. nlx_28005
Post-synaptic density Synaptic component; electron dense cytoskeletal specialization located on the post synaptic membrane at the site of synaptic contact. The PSD is particularly prominent in glutamatergic synapses, giving the synapse an asymmetrical appearance. This type of PSD is often referred to as "asymmetrical" or Gray's Type 1 in electron microscopic images (MEMartone). GO:0014069 postsynaptic density
post synaptic density
Pre-synaptic Active Zone Component sao1911631652
Pre-synaptic Component sao386529203
Pre-synaptic Dense Body Electron dense structure anchored to the presynaptic membrane closely associated with large numbers of synaptic vesicles, which appear to be tethered to the dense body by several short filaments (from Parsons and Sterling, 2003). sao1111202255 ribbon
Pre-synaptic Grid A hexagonal array of electron dense particles attched to the cyotplasmic face of the presynaptic membrane, revealed by staining with ethanolic phosphotungstic acid (Peters, Palay and Webster, 1991). sao1730664005
Pre-synaptic Ribbon Dense plate-like structure lying near and perpendicular to the pre-synaptic junction. Usually associated with pre-synaptic vesicles (Peters, Palay, and Webster). sao-1488888179
Primary lysosome A lysosome before it has fused with a vesicle or vacuole (Gene Ontology). GO:0005766
RER Membrane sao3089754107
Ribbon Synapse Type of synapse characterized by an electron-dense ribbon, lamella (bar) or spherical body in the presynaptic process cytoplasm (Sjostrand, 1953; Ladman, 1958; Gray and Pease, 1971). It usually sits in or just above an evaginated ridge of the terminal membrane..." - Dowling (1987) sao1884931180
Ribosome 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 (Gene Ontology). GO:0005840
Rosenthal fiber nlx_144563
Rough endoplasmic reticulum The rough (or granular) ER has ribosomes adhering to the outer surface; the ribosomes are the site of translation of the mRNA for those proteins which are either to be retained within the cisternae (ER-resident proteins), the proteins of the lysosomes, or the proteins destined for export from the cell. Glycoproteins undergo their initial glycosylation within the cisternae (Gene Ontology). GO:0005791 Nissl substance
SER Membrane The lipid bilayer surrounding the smooth endoplasmic reticulum (Gene Ontology). sao1596955044
Secondary lysosome Vacuole formed by the fusion of a lysosome with an organelle (autosome) or with a primary phagosome (Gene Ontology). GO:0005767
Skein-like Inclusion Skein-like inclusions are intracytoplasmic filamentous structures that are frequently encountered in preparations immunostained for ubiquitin. In H&E preparations (staining with hematoxylin and eosin) they are hardly visible or sometimes detected as faintly eosinophilic structures. nlx_subcell_20090103
Skein-like inclusion Skein-like inclusions are intracytoplasmic filamentous structures that are frequently encountered in preparations immunostained for ubiquitin. In H&E preparations (staining with hematoxylin and eosin) they are hardly visible or sometimes detected as faintly eosinophilic structures. (PMID: 18026741)
Smooth Membrane Characterized by a membrane with no indentations. sao1845602529
Smooth endoplasmic reticulum The smooth ER has no ribosomes attached to it. The smooth is the recipient of the proteins synthesized in the rough ER. Those proteins to be exported are passed to the Golgi complex, the resident proteins are returned to the rough ER and the lysosomal proteins after phosphorylation of their mannose residues are passed to the lysosomes. Glycosylation of the glycoproteins also continues. The smooth ER is the site of synthesis of lipids, including the phospholipids. The membranes of the smooth ER also contain enzymes that catalyze a series of reactions to detoxify both lipid-soluble drugs and harmful products of metabolism. Large quantities of certain compounds such as phenobarbital cause an increase in the amount of the smooth ER (Gene Ontology). GO:0005790
Sorting Endosome Multivesicular bodies surrounded by and connected with multiple tubular compartments with associated vesicles. MVB-tubule complexes are posited by Clooney et al. (2002) to correspond to sorting endosomes. "MVB–tubule complexes appear to correspond to the sorting endosomes involved in separating soma-bound material from recyclable material..." GO:0097443 MVB-tubule complex
Spine apparatus A specialization of the endomembrane system found in some classes of spines consisting of two or more closely apposed lamellae with interspersed dense material. GO:0097444
Star-shaped Neurofibrillary Tangle nlx_subcell_20090201
Striated organelle a cytoskeletal structure located in the apical region of cochlear and vestibular hair cells, consisting of alternating, cross-linked, thick and thin filamentous bundles nlx_152870 laminated body
Friedman's body
Friedmann body
Subplasmalemmal Coating Electron dense material observed coating the cytoplasmic face of the plasma membrane in certain regions of a neuron, e.g., the axon initial segment; the nodal membrane at the Node of Ranvier sao1938587839
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 (Gene Ontology). GO:0045202 synaptic junction
Synaptic Component sao1784069613
Synaptic Vesicle Secretory organelles, some 50 nm in diameter, of pre-synaptic nerve terminals; accumulate high concentrations of neurotransmitters and secrete these into the synaptic cleft by fusion with the 'active zone' of the pre-synaptic plasma membrane (Gene Ontology). GO:0008021
Taxi body nlx_152895 postsynaptic dense body of Taxi
postsynaptic dense body
Transport Vesicle Any of the vesicles of the constitutive secretory pathway, which carry cargo from the ER to the Golgi, between Golgi cisternae, and to destinations within or outside the cell (Gene Ontolgoy). sao885490876 secretory vesicle
Tubular Endosome Endosomal component consisting of cylindrical shaped tubues, ~50 nm in diameter, with smooth outer membranes an dark, grainy interiors (Clooney et al., 2002). Clathrin-like protein coats occur at the ends of some tubular compartments. sao1570660411
Vacuole GO:0005773
Vesicle Any small, fluid-filled, spherical organelle enclosed by membrane or protein (Gene Ontology). sao221389602
Vesicle Cargo Refers to the contents contained in the vesicle. sao1490223249
Vesicle Coat Refers to any specialized coating present on a vesicle membrane, e.g., clathrin. sao1177708494
Vesicle Membrane The lipid bilayer surrounding any membrane-bounded vesicle in the cell (Gene Ontology). sao1153182838
Vesicle Other Category for vesicles observed in electron micrographs with unknown function. sao577473346
Vesicle Subcomponent sao1455064842


Akash, Memartone, Slarson


*Note: Neurolex imports many terms and their ids from existing community ontologies, e.g., the Gene Ontology. Neurolex, however, is a dynamic site and any content beyond the identifier should not be presumed to reflect the content or views of the source ontology. Users should consult with the authoritative source for each ontology for current information.