Gene omics information

Query gene ID At3g21240
Gene name 4CL2 (4-COUMARATE:COA LIGASE 2)
Organism Arabidopsis thaliana


Co-expressed genes



As this page just shows up to 10 genes to the query, if you wish to have the complete list of co-expressed genes, click Gene/Probe ID.

VF%ileGene/Probe IDRepr.IDGene NameFunctional DescriptionS.X.H.G.Other DB
1.00100.0At3g212408216784CL2 (4-COUMARATE:COA LIGASE 2)encodes an isoform of 4-coumarate:CoA ligase (4CL), which is involved in the last step of the general phenylpropanoid pathway. The catalytic efficiency was in the following (descending) order: p-coumaric acid, caffeic acid, ferulic acid, 5-OH-ferulic acid and cinnamic acid. At4CL2 was unable to use sinapic acid as substrate.S.X.H.G.
0.8994.6At2g40890818686CYP98A3 (cytochrome P450, family 98, subfamily A, polypeptide 3)encodes coumarate 3-hydroxylase (C3H), a P450-dependent monooxygenase. Involved in lignin biosynthesis and flavonoid biosynthesis. Also affects the biosynthesis of coumarins such as scopoletin and scopolin as a branching-out-pathway from the phenylpropanoid acid level.S.X.H.G.
0.6176.7At1g28680839768transferase family proteinF:transferase activity, transferring acyl groups other than amino-acyl groups, transferase activity;P:biological_process unknown;C:cellular_component unknown;PFS.X.H.G.
0.5773.8At2g37040818280pal1 (Phe ammonia lyase 1)encodes a protein similar to phenylalanine ammonia-lyaseS.X.H.G.
0.4457.2At1g52760841709esterase/lipase/thioesterase family proteinF:catalytic activity;P:unknown;C:cellular_component unknown;BPOMFVAS.X.H.G.
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Specifically expressed experiments



As this page just shows up to 10 assays to the query, if you wish to have the complete list of assays that the query gene/probe was specifically expressed, click here.
Std2 GX%ileGSM IDAssay NameGSE IDExperiment Title
91.399.9GSM184496Endodermis&Pericycle root cells 2hr KCl control treated, biological rep3GSE7631Cell-specific nitrogen responses in the Arabidopsis root
88.399.9GSM265474Arabidopsis, whole roots, -Fe, 72 hour, rep 2GSE10502Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
86.499.9GSM265432Arabidopsis, root, longitudinal zone 4, -Fe conditions, rep 1GSE10497Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
83.399.9GSM184499Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep3GSE7631Cell-specific nitrogen responses in the Arabidopsis root
77.599.9GSM265473Arabidopsis, whole roots, -Fe, 72 hour, rep 1GSE10502Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
74.099.9GSM184900Arabidopsis, root cells, endodermis and quiescent center, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with salt
73.899.9GSM184501Endodermis&Pericycle root cells 2hr continuous KNO3 treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis root
72.899.9GSM184494Endodermis&Pericycle root cells 2hr KCl control treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis root
69.799.9GSM184495Endodermis&Pericycle root cells 2hr KCl control treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis root
64.299.8GSM265472Arabidopsis, whole roots, -Fe, 48 hour, rep 2GSE10502Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
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Homologous genes



Paralogous genes



Click Gene ID to show a list of homologous genes.

HFEvBSGene IDRepr. IDGene NameFunctional descriptionC.G.S.X.Other DB
0.710694At1g516808415934CL1 (4-COUMARATE:COA LIGASE 1)encodes an isoform of 4-coumarate:CoA ligase (4CL), which is involved in the last step of the general phenylpropanoid pathway. In addition to 4-coumarate, it also converts ferulate. The catalytic efficiency was in the following (descending) order: p-coumaric acid, ferulic acid, caffeic acid and 5-OH-ferulic acid. At4CL1 was unable to use sinapic acid as substrate.C.G.S.X.
0.082e-1481At1g650608428144CL3encodes an isoform of 4-coumarate:CoA ligase (4CL), which is involved in the last step of the general phenylpropanoid pathway. mRNA levels are not induced in response to wounding or to fungal infection by P. parasitica. mRNA is expressed in flowers, to a lesser degree in mature leaves and siliques and marginally in seedling roots and bolting stems of mature plants. The catalytic efficiency was in the following (descending) order: p-coumaric acid, caffeic acid, ferulic acid, cinnamic acid and 5-OH-ferulic acid. At4CL3 was unable to use sinapic acid as substrate.C.G.S.X.
0.173e-654At3g212308216774CL5 (4-coumarate:CoA ligase 5)The gene encodes a 4-coumarate coenzyme A ligase being able to use sinapate as substrate. The catalytic efficiency was in the following (descending) order: p-coumaric acid, caffeic acid, 5-OH-ferulic acid, ferulic acid and sinapic acid. At4CL5 was unable to use cinnamic acid as substrate. Knockout of At4CL5 (4cl5) revealed no effect on syringyl lignin content indicating that the activity observed does probably not occur in vivo.C.G.S.X.
0.032e-448At1g20510838639OPCL1 (OPC-8:0 COA LIGASE1)F:4-coumarate-CoA ligase activity;P:phenylpropanoid metabolic process, jasmonic acid biosynthetic process, response to wounding;C:peroxisome;BOFMPAVC.G.S.X.
0.043e-344At4g051608258644-coumarate--CoA ligase, putative / 4-coumaroyl-CoA synthase, putativeEncodes a peroxisomal protein involved in the activation of fatty acids through esterification with CoA. At4g05160 preferentially activates fatty acids with medium chain length (C6:0 and C7:0) as well as even-numbered long-chain fatty acids (C14:0, C16:0 and C18:0). At4g05160 was also able to catalyze the conversion of OPC-6:0 to its CoA ester and is therefore thought to be involved in the peroxisomal β-oxidation steps of jasmonic acid biosynthesis.C.G.S.X.
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Orthologous genes



Click Gene ID to show a list of orthologous genes.

HFEvBSSpeciesGene IDRepr. IDGene NameFunctional descriptionEvAGI codeArabidopsis gene nameC.G.S.X.Other DB
0.145e-963Glycine maxGma.8472.1.S1_atBI9420984-coumarate:Coenzyme A ligase isoenzyme 4-2e-8At1g516804CL1 (4-COUMARATE:COA LIGASE 1)C.G.S.X.
0.071e-1067Hordeum vulgareContig15844_atContig15844--2e-10At3g212404CL2 (4-COUMARATE:COA LIGASE 2)C.G.S.X.
0.092e-656Oryza sativaOs08g0448000AK120964.1-4-coumarate--CoA ligase 1 (EC 6.2.1.12) (4CL 1)(4-coumaroyl-CoA synthase 1) (Clone 4CL14) (Fragment)1e-6At3g212404CL2 (4-COUMARATE:COA LIGASE 2)C.G.S.X.
0.173e-757Populus trichocarpaPtp.3043.1.S1_atAF041049.14-Coumarate:CoA ligase-3e-13At1g516804CL1 (4-COUMARATE:COA LIGASE 1)C.G.S.X.
0.062e-448Triticum aestivumTaAffx.30205.2.S1_s_atCA627137--1e-4At3g212404CL2 (4-COUMARATE:COA LIGASE 2)C.G.S.X.
0.227e-1787Vitis vinifera1609307_atCD715818hypothetical protein LOC100254698-3e-16At3g212404CL2 (4-COUMARATE:COA LIGASE 2)C.G.S.X.
0.036e-652Zea maysZm.1390.1.A1_atAY106966.1--3e-3At3g212304CL5 (4-coumarate:CoA ligase 5)C.G.S.X.
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Biological processes



Click GO ID to show a list of genes that are associated with the GO ID.

ECCGO IDProcess Name
XGO:0009411A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.
XGO:0009611A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism.
XGO:0009620A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a fungus.
SGO:0009698The chemical reactions and pathways involving aromatic derivatives of trans-cinnamic acid.
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Metabolic pathways



Click KaPPA-View ID to show a list of genes that are assigned to the KaPPA-View ID.

KaPPA-View IDLink to Kappa-ViewPathway Name
00061Link to KaPPA-View 4Flavonoids biosynthesis
00064Link to KaPPA-View 4The cinnamate-monolignol pathway/sinapoyl ester biosynthesis
00420Link to KaPPA-View 4Ubiquinone biosynthesis



Click KEGG PATHWAY ID to show a list of genes that are assigned to the KEGG PATHWAY ID.

KEGG PATHWAY IDLink to KEGG PATHWAYPathway Name
00130Link to KEGG PATHWAYUbiquinone and other terpenoid-quinone biosynthesis
00940Link to KEGG PATHWAYPhenylpropanoid biosynthesis
01061Link to KEGG PATHWAYBiosynthesis of phenylpropanoids
01063Link to KEGG PATHWAYBiosynthesis of alkaloids derived from shikimate pathway
01100Link to KEGG PATHWAYMetabolic pathways
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