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0CLCN3_HUMAN*   SwissProt (?) | Description Local Annotation Link Reference
General Information
NameCLCN3
DescriptionChloride channel protein 3 (clc-3).
SpeciesHomo sapiens (NCBI taxonomy ID: 9606)
GO0009986 cell surface (NAS)
0005769 early endosome (IDA)
0005794 Golgi apparatus (IDA)
0016021 integral to membrane (TAS)
0005770 late endosome (IDA)
0012506 vesicle membrane (IDA)
0030165 PDZ domain binding (IDA)
0005515 protein binding (IPI)
0046982 protein heterodimerization activity (IDA)
0042803 protein homodimerization activity (NAS)
0005247 voltage-gated chloride channel activity (TAS)
0048388 endosomal lumen acidification (TAS)
0006885 regulation of pH (TAS)
0006810 transport (TAS)

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schematic display of those terms with internal associations, click the node and browse the corresponding GO term
Domain Architecture (Details)
InterPro domains unassigned to SynO:
Chloride channels (CLCs) constitute an evolutionarily well-conserved family of voltage-gated channels that are structurally unrelated to the other known voltage-gated channels. They are found in organisms ranging from bacteria to yeasts and plants.nd also to animals. Their functions in higher animals likely include the regulation of cell volume.ontrol of electrical excitability and trans-epithelial transport .The first member of the family (CLC-0) was expression-cloned from the electric organ of Torpedo marmorata .nd subsequently nine CLC-like proteins have been cloned from mammals. They are thought to function as multimers of two or more identical or homologous subunits.nd they have varying tissue distributions and functional properties. To date.LC-0.LC-1.LC-2.LC-4 and CLC-5 have been demonstrated to form functional Cl- channels; whether the remaining isoforms do so is either contested or unproven. One possible explanation for the difficulty in expressing activatable Cl- channels is that some of the isoforms may function as Cl- channels of intracellular compartments.ather than of the plasma membrane. However.hey are all thought to have a similar transmembrane (TM) topology.nitial hydropathy analysis suggesting 13 hydrophobic stretches long enough to form putative TM domains . Recently.he postulated TM topology has been revised.nd it now seems likely that the CLCs have 10 (or possibly 12) TM domains.ith both N- and C-termini residing in the cytoplasm .A number of human disease-causing mutations have been identified in the genes encoding CLCs. Mutations in CLCN1.he gene encoding CLC-1.he major skeletal muscle Cl- channel.ead to both recessively and dominantly-inherited forms of muscle stiffness or myotonia . Similarly.utations in CLCN5.hich encodes CLC-5. renal Cl- channel.ead to several forms of inherited kidney stone disease . These mutations have been demonstrated to reduce or abolish CLC function.
  IPR001807:Cl- channel, voltage gated
CBS (cystathionine-beta-synthase) domains are small intracellular modules.ostly found in two or four copies within a protein.hat occur in several different proteins in all kingdoms of life. Tandem pairs of CBS domains can act as binding domains for adenosine derivatives and may regulate the activity of attached enzymatic or other domains . In some cases.BS domains may act as sensors of cellular energy status by being activated by AMP and inhibited by ATP . In chloride ion channels.he CBS domains have been implicated in intracellular targeting and trafficking.s well as in protein-protein interactions.ut results vary with different channels: in the CLC-5 channel.he CBS domain was shown to be required for trafficking .hile in the CLC-1 channel.he CBS domain was shown to be critical for channel function.ut not necessary for trafficking . Mutations in conserved residues within CBS domains cause a variety of human hereditary diseases.ncluding (with the gene mutated in parentheses): homocystinuria (cystathionine beta-synthase); Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase); retinitis pigmentosa (IMP dehydrogenase-1); congenital myotonia.diopathic generalized epilepsy.ypercalciuric nephrolithiasis.nd classic Bartter syndrome (CLC chloride channel family members).
  IPR000644:CBS
Chloride channels (CLCs) constitute an evolutionarily well-conserved family of voltage-gated channels that are structurally unrelated to the other known voltage-gated channels. They are found in organisms ranging from bacteria to yeasts and plants.nd also to animals. Their functions in higher animals likely include the regulation of cell volume.ontrol of electrical excitability and trans-epithelial transport .The first member of the family (CLC-0) was expression-cloned from the electric organ of Torpedo marmorata .nd subsequently nine CLC-like proteins have been cloned from mammals. They are thought to function as multimers of two or more identical or homologous subunits.nd they have varying tissue distributions and functional properties. To date.LC-0.LC-1.LC-2.LC-4 and CLC-5 have been demonstrated to form functional Cl- channels; whether the remaining isoforms do so is either contested or unproven. One possible explanation for the difficulty in expressing activatable Cl- channels is that some of the isoforms may function as Cl- channels of intracellular compartments.ather than of the plasma membrane. However.hey are all thought to have a similar transmembrane (TM) topology.nitial hydropathy analysis suggesting 13 hydrophobic stretches long enough to form putative TM domains . Recently.he postulated TM topology has been revised.nd it now seems likely that the CLCs have 10 (or possibly 12) TM domains.ith both N- and C-termini residing in the cytoplasm .A number of human disease-causing mutations have been identified in the genes encoding CLCs. Mutations in CLCN1.he gene encoding CLC-1.he major skeletal muscle Cl- channel.ead to both recessively and dominantly-inherited forms of muscle stiffness or myotonia . Similarly.utations in CLCN5.hich encodes CLC-5. renal Cl- channel.ead to several forms of inherited kidney stone disease . These mutations have been demonstrated to reduce or abolish CLC function.CLC-3 is a member of the CLC family initially cloned from rat kidney and localised to chromosome 4 in humans ; the human isoform contains 762amino acid residues. Together with CLC-4 and CLC-5.t forms a distinctbranch of the CLC gene family.he three members showing ~80% residueidentity. Expression of CLC-3 produces outwardly-rectifying Cl- currentsthat are inhibited by protein kinase C activation .More recently.t has been suggested that CLC-3 may be a ubiquitous swelling-activated Cl- channel that has very similar characteristics to those ofnative volume-regulated Cl- currents .
  IPR002245:Chloride channel CLC-3
IPR001807:Voltage_CLC 
Evalue:-213.244125366211 
Location:159-567IPR000644:CBS 
Evalue:-20.2218494415283 
Location:605-749IPR001807:CLCHANNEL 
Evalue:0 
Location:571-585IPR002245:CLCHANNEL3 
Evalue:0 
Location:1-11IPR002245:CLCHANNEL3 
Evalue:0 
Location:140-150IPR002245:CLCHANNEL3 
Evalue:0 
Location:39-45IPR002245:CLCHANNEL3 
Evalue:0 
Location:56-62
SequencesProtein: CLCN3_HUMAN (762 aa)
mRNA: AB019542 NM_001829 NM_173872 X78520
Local Annotation
Synapse Ontology
transport of vesicles in the presynaptic neuron
sdb:0017 Mobilization: synapsins, CAM kinase I  (Evidence:keywords)
endosome of the presynaptic compartment. A cellular structure that is involved in the transport of proteins in the neuron after the proteins are endocytosed from the outside to the inside of the cell.
sdb:0088 endosome  (Evidence:keywords)
activation of protein kinase C
sdb:0206 activation of protein kinase C  (Evidence:keywords)
KO assignmentK05012
  Level 3 annotation:
    chloride channel 3
  Level 2 annotation:
    Ion channels
Loci Structure (Details)Loci index, Chromosomal location, Length, Possible relational loci clusterExon1: 165 residues, 170778296-170778789Exon2: 60 residues, 170793638-170793814Exon3: 54 residues, 170837775-170837933Exon4: 35 residues, 170845383-170845483Exon5: 64 residues, 170846768-170846956Exon6: 43 residues, 170848255-170848378Exon7: 71 residues, 170849839-170850046Exon8: 29 residues, 170853337-170853418Exon9: 184 residues, 170854914-170855460Exon10: 64 residues, 170861723-170861910Exon11: 135 residues, 170864593-170864992Exon12: 74 residues, 170870804-170871021Exon13: 27 residues, 170875517-170875593Exon14: 368 residues, 170877632-170878731Exon15: 2 residues, -Jump to CLCN3_HUMANExon1: 165 residues, 170778296-170778789Exon2: 60 residues, 170793638-170793814Exon3: 54 residues, 170837775-170837933Exon4: 35 residues, 170845383-170845483Exon5: 64 residues, 170846768-170846956Exon6: 43 residues, 170848255-170848378Exon7: 71 residues, 170849839-170850046Exon8: 29 residues, 170853337-170853418Exon9: 184 residues, 170854914-170855460Exon10: 64 residues, 170861723-170861910Exon11: 135 residues, 170864593-170864992Exon12: 74 residues, 170870804-170871021Exon13: 368 residues, 170877632-170878731Exon14: 2 residues, -Jump to CLCN3_HUMANExon1: 138 residues, 170778378-170778789Exon2: 60 residues, 170793638-170793814Exon3: 54 residues, 170837775-170837933Exon4: 35 residues, 170845383-170845483Exon5: 64 residues, 170846768-170846956Exon6: 43 residues, 170848255-170848378Exon7: 71 residues, 170849839-170850046Exon8: 29 residues, 170853337-170853418Exon9: 184 residues, 170854914-170855460Exon10: 64 residues, 170861723-170861910Exon11: 135 residues, 170864593-170864992Exon12: 74 residues, 170870804-170871021Exon13: 152 residues, 170877632-170878082Exon14: 215 residues, 170878092-170878732Exon15: 2 residues, -Jump to CLCN3_HUMANExon1: 24 residues, 170778718-170778789Exon2: 60 residues, 170793638-170793814Exon3: 54 residues, 170837775-170837933Exon4: 35 residues, 170845383-170845483Exon5: 64 residues, 170846768-170846956Exon6: 43 residues, 170848255-170848378Exon7: 71 residues, 170849839-170850046Exon8: 29 residues, 170853337-170853418Exon9: 184 residues, 170854914-170855460Exon10: 64 residues, 170861723-170861910Exon11: 135 residues, 170864593-170864992Exon12: 74 residues, 170870804-170871021Exon13: 27 residues, 170875517-170875593Exon14: 95 residues, 170877632-170877912Exon15: 2 residues, -Jump to CLCN3_HUMAN  
Tune and view alternative isoforms
Loci Cluster (Details)Loci: 4695 171217948-171247940 ~-30K 28408(AADAT)(-)Loci: 3439 170778296-170878732 ~-100K 28400(CLCN3)(+)Link out to UCSC