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Genome: Caenorhabditis Elegans | mRNA | miRBase 18 (Nov. 2011), ENSEMBL 65 (Dec. 2011) and RNA22v1.0
Description: List of transcripts that are targeted by all of the below miRNA identifiers simultaneously
miRNA's: cel-miR-54-5p (MIMAT0020773)
Filtering By: Base pair min value: 12 | Folding energy max value (Kcal/mol): -21 | Min miRNA targets: 1


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Gene IDTranscript IDCommon Gene Name# of miRNA targets
for specified miRNAs
ChromosomeStrand DirectionTranscript Link to view miRNA target predictionsGene LinkDescription
6R55.26R55.26R55.2123 XForwardView as cDNA map |
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Ensembl
AC8.12AC8.12AC8.12123 XForwardView as cDNA map |
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Ensembl
AC8.7AC8.7AC8.7123 XForwardView as cDNA map |
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Ensembl
AH9.2AH9.2crn-4123 XReverseView as cDNA map |
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Ensembl
AH9.4AH9.4AH9.4223 XReverseView as cDNA map |
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Ensembl
AH9.6AH9.6AH9.6123 XReverseView as cDNA map |
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Ensembl
AH9.6 encodes a novel protein that contains two predicted transmembrane domains and that is conserved in other nematode species. [Source: WormBase]
B0198.1B0198.1tsp-20123 XReverseView as cDNA map |
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Ensembl
B0198.2B0198.2aB0198.2123 XForwardView as cDNA map |
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Ensembl
B0198.3B0198.3aB0198.3123 XReverseView as cDNA map |
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Ensembl
B0272.1B0272.1tbb-4223 XReverseView as cDNA map |
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Ensembl
B0272.4B0272.4B0272.4123 XForwardView as cDNA map |
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Ensembl
B0294.1B0294.1B0294.1223 XReverseView as cDNA map |
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Ensembl
B0302.1B0302.1a.1kin-25223 XForwardView as cDNA map |
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Ensembl
kin-25 encodes a nonreceptor tyrosine kinase that is a member of the Ack subfamily of cytoplasmic tyrosine kinases. [Source: WormBase]
B0302.1B0302.1a.2kin-25123 XForwardView as cDNA map |
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Ensembl
kin-25 encodes a nonreceptor tyrosine kinase that is a member of the Ack subfamily of cytoplasmic tyrosine kinases. [Source: WormBase]
B0302.1B0302.1bkin-25123 XForwardView as cDNA map |
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Ensembl
kin-25 encodes a nonreceptor tyrosine kinase that is a member of the Ack subfamily of cytoplasmic tyrosine kinases. [Source: WormBase]
B0302.2B0302.2B0302.2123 XForwardView as cDNA map |
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Ensembl
B0310.1B0310.1bB0310.1123 XForwardView as cDNA map |
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Ensembl
B0310.1 encodes a nematode-specific transmembrane protein. loss of B0310.1 activity via RNAi results in reduced fat content in wild-type and tub-1 mutant animals, suggesting that B0301.1 plays a role in lipid metabolism. [Source: WormBase]
B0310.3B0310.3B0310.3123 XReverseView as cDNA map |
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Ensembl
B0310.5B0310.5ugt-46123 XReverseView as cDNA map |
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Ensembl
B0395.3B0395.3.1B0395.3123 XReverseView as cDNA map |
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Ensembl
B0395.3 is orthologous to the human gene CHOLINE ACETYLTRANSFERASE ISOFORM R (CHAT. OMIM:118490), which when mutated leads to disease. [Source: WormBase]
B0403.2B0403.2ubc-17323 XForwardView as cDNA map |
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Ensembl
B0403.6B0403.6B0403.6123 XReverseView as cDNA map |
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Ensembl
B0410.3B0410.3B0410.3123 XReverseView as cDNA map |
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Ensembl
B0416.1B0416.1B0416.1323 XForwardView as cDNA map |
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Ensembl
B0416.3B0416.3B0416.3423 XForwardView as cDNA map |
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Ensembl
B0416.5B0416.5aB0416.5123 XReverseView as cDNA map |
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Ensembl
B0416.6B0416.6gly-13223 XReverseView as cDNA map |
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Ensembl
gly-13 encodes an experimentally verified UDP-N-acetylglucosamine alpha-3-D-mannoside beta-1,2-N-acetylglucosaminyltransferase I (GnT I), that is the primary GnT I enzyme in vivo, and that can act on unusual substrates. gly-13 is expressed throughout development in many cell types. gly-13 has no obvious function in vivo, since a deletion allele of gly-13 is phenotypically normal even as a double or triple mutant with gly-12 and gly-14. [Source: WormBase]
B0563.10B0563.10B0563.10123 XReverseView as cDNA map |
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Ensembl
B0563.2B0563.2tsp-11223 XForwardView as cDNA map |
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Ensembl
B0563.4B0563.4.1tmbi-4323 XForwardView as cDNA map |
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Ensembl
B0563.4B0563.4.2tmbi-4323 XForwardView as cDNA map |
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Ensembl
C01C10.1C01C10.1clc-2223 XForwardView as cDNA map |
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Ensembl
clc-2 encodes a claudin homolog, closely similar to CLC-1, that is required for normal cohesion of apical junctions in epithelia. claudins are integral membrane proteins with four transmembrane sequences that are found in mammalian tight junctions (TJs), induce TJs when transgenically expressed in cells normally lacking them, and can mediate the specific conductance of of specific ions (e.g., magnesium or calcium) through TJs while blocking the flow of water. CLC-2 maintains the impermeability ('barrier function') of epithelia, since clc-1(RNAi) animals have abnormal permeability of the hypodermis to dyes. clc-2 is expressed in hypodermal seam cells, with two diffuse lines of CLC-2 protein. [Source: WormBase]
C01C10.3C01C10.3.1acl-12123 XReverseView as cDNA map |
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Ensembl
C01C10.3C01C10.3.2acl-12123 XReverseView as cDNA map |
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Ensembl
C01C4.1C01C4.1nlp-1123 XForwardView as cDNA map |
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Ensembl
nlp-1 encodes a predicted neuropeptide-like protein of the MSFamide family with similarity to Aplysia californica (sea hare) buccalin, a neuropeptide that regulates acetylcholine-induced muscle contraction. NLP-1 is expressed in the phasmid PHB tail sensory neuron, lateral neurons, head neurons, and the intestine. the precise role of NLP-1 in nervous system function and development is not yet known. [Source: WormBase]
C02B4.1C02B4.1adt-1423 XForwardView as cDNA map |
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Ensembl
The adt-1 gene encodes a metalloproteinase with disintegrin-like and metalloproteinase with thrombospondin type I motifs (ADAMTS) that is required for male tail morphogenesis. [Source: WormBase]
C02B4.2C02B4.2nhr-17123 XReverseView as cDNA map |
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Ensembl
nhr-17 encodes a member of the superfamily of nuclear receptors, which is one of the most abundant class of transcriptional regulators. nuclear receptors have a well conserved DNA binding domain and a less conserved C-terminal ligand binding domain. [Source: WormBase]
C02B8.1C02B8.1.1C02B8.1123 XForwardView as cDNA map |
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C02B8.1C02B8.1.2C02B8.1123 XForwardView as cDNA map |
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Ensembl
C02B8.5C02B8.5C02B8.5123 XReverseView as cDNA map |
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C02B8.5 encodes a homolog of the functionally active Fmrf Receptor (FR. CG2114) of D. melanogaster. it is thus possible that C02B8.5 is a receptor for one of the FMRF-like neurotransmitters in C. elegans (e.g., FLP-1 through FLP-12). [Source: WormBase]
C02B8.6C02B8.6C02B8.6123 XReverseView as cDNA map |
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Ensembl
C02C6.1C02C6.1adyn-1423 XForwardView as cDNA map |
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Ensembl
dyn-1 encodes the C. elegans ortholog of the dynamin GTPase. dyn-1 activity is required for endocytosis, synaptic vesicle recycling, cytokinesis, and the CED-1 pathway that regulates engulfment and degradation of apoptotic cells. mutations in dyn-1 affect locomotion, egg-laying, defecation, and embryonic development, indicating that dyn-1's endocytic function is required for a number of diverse processes. dyn-1 reporter fusion constructs are expressed in motor neurons, intestinal cells, and pharyngeal muscle. [Source: WormBase]
C02C6.1C02C6.1bdyn-1423 XForwardView as cDNA map |
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dyn-1 encodes the C. elegans ortholog of the dynamin GTPase. dyn-1 activity is required for endocytosis, synaptic vesicle recycling, cytokinesis, and the CED-1 pathway that regulates engulfment and degradation of apoptotic cells. mutations in dyn-1 affect locomotion, egg-laying, defecation, and embryonic development, indicating that dyn-1's endocytic function is required for a number of diverse processes. dyn-1 reporter fusion constructs are expressed in motor neurons, intestinal cells, and pharyngeal muscle. [Source: WormBase]
C02D4.2C02D4.2aser-2123 XReverseView as cDNA map |
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Ensembl
ser-2 encodes at least four tyramine 7-transmembrane domain receptors (GPCRs), by alternative splicing from three different promoters, that have distinct but partially overlapping expression patterns. ser-2 has at least three alternative promoters that drive SER-2 expression in a set of sensory, inter- and motor neurons (e.g., AIY, AIZ, and RIA) adding up to ~10% of all neurons in the nervous system, as well as pharyngeal cells and head muscles. the deletion ser-2(pk1397) has no obvious mutant phenotype. LIM-4 is required for SER-2 expression, and MAB-23 is required for SER-2 expression at normally high levels. [Source: WormBase]
C02D4.2C02D4.2bser-2123 XReverseView as cDNA map |
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Ensembl
ser-2 encodes at least four tyramine 7-transmembrane domain receptors (GPCRs), by alternative splicing from three different promoters, that have distinct but partially overlapping expression patterns. ser-2 has at least three alternative promoters that drive SER-2 expression in a set of sensory, inter- and motor neurons (e.g., AIY, AIZ, and RIA) adding up to ~10% of all neurons in the nervous system, as well as pharyngeal cells and head muscles. the deletion ser-2(pk1397) has no obvious mutant phenotype. LIM-4 is required for SER-2 expression, and MAB-23 is required for SER-2 expression at normally high levels. [Source: WormBase]
C02D4.2C02D4.2eser-2123 XReverseView as cDNA map |
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Ensembl
ser-2 encodes at least four tyramine 7-transmembrane domain receptors (GPCRs), by alternative splicing from three different promoters, that have distinct but partially overlapping expression patterns. ser-2 has at least three alternative promoters that drive SER-2 expression in a set of sensory, inter- and motor neurons (e.g., AIY, AIZ, and RIA) adding up to ~10% of all neurons in the nervous system, as well as pharyngeal cells and head muscles. the deletion ser-2(pk1397) has no obvious mutant phenotype. LIM-4 is required for SER-2 expression, and MAB-23 is required for SER-2 expression at normally high levels. [Source: WormBase]
C02D4.2C02D4.2fser-2223 XReverseView as cDNA map |
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Ensembl
ser-2 encodes at least four tyramine 7-transmembrane domain receptors (GPCRs), by alternative splicing from three different promoters, that have distinct but partially overlapping expression patterns. ser-2 has at least three alternative promoters that drive SER-2 expression in a set of sensory, inter- and motor neurons (e.g., AIY, AIZ, and RIA) adding up to ~10% of all neurons in the nervous system, as well as pharyngeal cells and head muscles. the deletion ser-2(pk1397) has no obvious mutant phenotype. LIM-4 is required for SER-2 expression, and MAB-23 is required for SER-2 expression at normally high levels. [Source: WormBase]
C02F12.3C02F12.3.1C02F12.3123 XReverseView as cDNA map |
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Ensembl
C02F12.3C02F12.3.2C02F12.3123 XReverseView as cDNA map |
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Ensembl
C02F12.3C02F12.3.3C02F12.3123 XReverseView as cDNA map |
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C02F12.4C02F12.4tag-52123 XReverseView as cDNA map |
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C02F12.7C02F12.7tag-278123 XReverseView as cDNA map |
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C02F12.8C02F12.8C02F12.8123 XReverseView as cDNA map |
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C02F12.9C02F12.9C02F12.9123 XForwardView as cDNA map |
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C02H7.2C02H7.2npr-19123 XReverseView as cDNA map |
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Ensembl
C02H7.3C02H7.3aaex-3223 XReverseView as cDNA map |
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aex-3 encodes a guanine nucleotide exchange factor for the rab-3 GTPase that is orthologous to human MAP kinase activating protein containing death domain (MADD, OMIM:603584). AEX-3 is required for intracellular vesicle trafficking as well as synaptic vesicle release and interacts with CAB-1 and RAB-3 to regulate separate pathways for neural activities such as defecation and male mating, respectively. AEX-3 is also required for egg laying and locomotion. AEX-3 is expressed in nearly all neurons. [Source: WormBase]
C03A3.1C03A3.1aC03A3.1123 XForwardView as cDNA map |
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C03A3.2C03A3.2.1C03A3.2223 XForwardView as cDNA map |
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C03A3.2C03A3.2.2C03A3.2223 XForwardView as cDNA map |
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C03B1.12C03B1.12.1lmp-1123 XReverseView as cDNA map |
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lmp-1 encodes a protein with similarity to vertebrate lysosome-associated membrane proteins CD68, and appears to be the only protein in C. elegans that has a GYXX (phi) vertebrate lysosomal targeting sequence at its carboxy terminus. localized to the periphery of a large population of membrane bound organelles (granules) seen throughout the early embryos and restricted to the cells of the intestine during later stages. [Source: WormBase]
C03B1.14C03B1.14C03B1.14123 XReverseView as cDNA map |
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C03B1.5C03B1.5C03B1.5223 XForwardView as cDNA map |
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C03F11.4C03F11.4.1C03F11.4123 XReverseView as cDNA map |
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C03F11.4C03F11.4.2C03F11.4123 XReverseView as cDNA map |
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C03F11.4C03F11.4.3C03F11.4123 XReverseView as cDNA map |
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C03H12.1C03H12.1C03H12.1123 XForwardView as cDNA map |
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C04A11.1C04A11.1C04A11.1123 XForwardView as cDNA map |
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C04A11.2C04A11.2C04A11.2123 XReverseView as cDNA map |
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C04A11.3C04A11.3gck-4123 XForwardView as cDNA map |
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C04A11.4C04A11.4adm-2123 XForwardView as cDNA map |
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adm-2 encodes a protein containing a snake venom disintegrin-domain and a metalloprotease-like domain (i.e., a protein of the ADAM family). like ADM-1, ADM-2 is homologous to a mammalian sperm glycoprotein (PH-30/fertilin) implicated in sperm-egg fusion, and ADM-2 might thus be a fusogenic protein mediating the merging of plasma membranes during development. [Source: WormBase]
C04B4.2C04B4.2C04B4.2323 XForwardView as cDNA map |
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C04B4.3C04B4.3lips-2223 XForwardView as cDNA map |
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C04C11.1C04C11.1aC04C11.1123 XForwardView as cDNA map |
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C04E7.1C04E7.1C04E7.1323 XForwardView as cDNA map |
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C04E7.2C04E7.2sor-3123 XForwardView as cDNA map |
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sor-3 encodes a novel protein that contains an MBT (malignant brain tumor) domain related to the MBT domains found in the Sex comb on midleg (SCM) and Sfmbt Polycomb group proteins. during development, SOR-3 activity is required to specify the correct number of dopaminergic and serotonergic neurons in males, as well as for proper ray neuron axon guidance, distal tip cell migration, and normal body size. SOR-3 activity is necessary for maintaining repression of Hox gene expression, notably that of egl-5 in many head neurons. in regulating neurotransmitter phenotype, sor-3 functions together with sop-2, which also encodes a Polycomb group protein, and members of the TGF-beta signaling pathway. sor-3 and sop-2 also function together to regulate progression through larval development. a SOR-3::GFP reporter fusion is expressed ubiquitously throughout the life cycle and localizes to both the cytoplasm and the nucleus. [Source: WormBase]
C04E7.3C04E7.3C04E7.3123 XReverseView as cDNA map |
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C04E7.4C04E7.4C04E7.4123 XReverseView as cDNA map |
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C04F6.1C04F6.1vit-5323 XForwardView as cDNA map |
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vit-5 encodes a vitellogenin, a lipid-binding protein precursor related to vertebrate vitellogenins and mammalian ApoB-100, a core LDL particle constituent. by homology, VIT-5 is predicted to function as a lipid transport protein. loss of vit-5 activity via large-scale RNA-mediated interference (RNAi) screens indicates that VIT-5 is required for embryogenesis and normal rates of postembryonic growth. VIT-5 is a major yolk component and is expressed exclusively in the adult hermaphrodite intestine from which it is secreted into the pseudocoelomic space and taken up by oocytes. [Source: WormBase]
C04F6.2C04F6.2C04F6.2123 XForwardView as cDNA map |
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C04F6.3C04F6.3.1cht-1323 XReverseView as cDNA map |
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cht-1 encodes a chitinase orthologous to human chitinase-1 (OMIM:600031, mutations are associated with chitotriosidase deficiency). CHT-1 is predicted to function as an extracellular O-glycosyl hydrolase that hydrolyzes the glycosidic bond between two or more carbohydrates. in C. elegans, CHT-1 may play a role in embryogenesis, and may also be required for cuticle degradation during molting and degradation of chitin-containing pathogens as part of a host defense mechanism. [Source: WormBase]
C04F6.3C04F6.3.2cht-1323 XReverseView as cDNA map |
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cht-1 encodes a chitinase orthologous to human chitinase-1 (OMIM:600031, mutations are associated with chitotriosidase deficiency). CHT-1 is predicted to function as an extracellular O-glycosyl hydrolase that hydrolyzes the glycosidic bond between two or more carbohydrates. in C. elegans, CHT-1 may play a role in embryogenesis, and may also be required for cuticle degradation during molting and degradation of chitin-containing pathogens as part of a host defense mechanism. [Source: WormBase]
C04F6.4C04F6.4aunc-78223 XReverseView as cDNA map |
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The unc-78 gene encodes a homolog of actin-interacting protein 1 (AIP1) that regulates the ordered assembly of actin and cofilin in myofibrils. [Source: WormBase]
C04F6.7C04F6.7C04F6.7123 XReverseView as cDNA map |
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C05A9.1C05A9.1apgp-5423 XReverseView as cDNA map |
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pgp-5 encodes a transmembrane protein that is a member of the P-glycoprotein subclass of the ATP-binding cassette (ABC) transporter superfamily. by homology, PGP-5 is predicted to function as an ATP-dependent efflux pump that protects C. elegans by exporting exogenous toxins. however, as loss of pgp-5 activity via large-scale RNAi screens does not result in any obvious abnormalities, the precise role of PGP-5 in C. elegans development and/or behavior is not yet known. [Source: WormBase]
C05A9.1C05A9.1bpgp-5423 XReverseView as cDNA map |
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pgp-5 encodes a transmembrane protein that is a member of the P-glycoprotein subclass of the ATP-binding cassette (ABC) transporter superfamily. by homology, PGP-5 is predicted to function as an ATP-dependent efflux pump that protects C. elegans by exporting exogenous toxins. however, as loss of pgp-5 activity via large-scale RNAi screens does not result in any obvious abnormalities, the precise role of PGP-5 in C. elegans development and/or behavior is not yet known. [Source: WormBase]
C05C9.2C05C9.2C05C9.2123 XForwardView as cDNA map |
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C05C9.3C05C9.3C05C9.3123 XReverseView as cDNA map |
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The protein product of this gene is predicted to contain a glutamine/asparagine (Q/N)-rich ('prion') domain, by the algorithm of Michelitsch and Weissman (as of the WS77 release of WormBase, i.e., in wormpep77). [Source: WormBase]
C05D9.1C05D9.1.1snx-1123 XForwardView as cDNA map |
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C05D9.1C05D9.1.2snx-1123 XForwardView as cDNA map |
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C05D9.3C05D9.3C05D9.3123 XForwardView as cDNA map |
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C05E11.3C05E11.3C05E11.3223 XForwardView as cDNA map |
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C05E11.5C05E11.5amt-4123 XForwardView as cDNA map |
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amt-4 encodes a member of the ammonium transporter protein family. [Source: WormBase]
C05E11.7C05E11.7C05E11.7123 XReverseView as cDNA map |
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C05E7.2C05E7.2C05E7.2123 XReverseView as cDNA map |
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C05E7.3C05E7.3C05E7.3123 XReverseView as cDNA map |
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C05G5.1C05G5.1C05G5.1123 XReverseView as cDNA map |
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C05G5.5C05G5.5C05G5.5123 XReverseView as cDNA map |
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C06E2.1C06E2.1C06E2.1123 XReverseView as cDNA map |
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C06E2.7C06E2.7ubc-22123 XReverseView as cDNA map |
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ubc-22 encodes an E2 ubiquitin-conjugating enzyme orthologous to Saccharomyces cerevisiae UBC8 and human UBC1/HIP2 (Huntingtin interacting protein 2, OMIM:602846) which are involved in regulating fructose-1,6-bisphosphatase and huntingtin catabolism, respectively. by homology, UBC-22 is likely required for covalent attachment of ubiquitin to select target proteins to facilitate their degradation. however, as loss of UBC-22 activity via RNA-mediated interference (RNAi) does not result in any abnormalities, the precise role of UBC-22 in C. elegans development and/or behavior is not yet known. [Source: WormBase]
C06E2.9C06E2.9C06E2.9223 XForwardView as cDNA map |
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GUI created by the Computational Medicine Center at the Sidney Kimmel Medical College of Thomas Jefferson University
We gratefully acknowledge support of this work by the William M. Keck Foundation