Gene omics information

Query gene ID At1g65060
Gene name 4CL3
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
0.8994.6At1g650608428144CL3encodes 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.S.X.H.G.
0.8994.6At3g51240824287F3H (FLAVANONE 3-HYDROXYLASE)Encodes flavanone 3-hydroxylase that is coordinately expressed with chalcone synthase and chalcone isomerases. Regulates flavonoid biosynthesis.S.X.H.G.
0.8994.6At5g05270830409chalcone-flavanone isomerase family proteinF:chalcone isomerase activity;P:flavonoid biosynthetic process;C:cellular_component unknown;PS.X.H.G.
0.8994.6At5g13930831241TT4 (TRANSPARENT TESTA 4)Encodes chalcone synthase (CHS), a key enzyme involved in the biosynthesis of flavonoids. Required for the accumulation of purple anthocyanins in leaves and stems. Also involved in the regulation of auxin transport and the modulation of root gravitropism.S.X.H.G.
0.7385.5At5g08640830765FLS (FLAVONOL SYNTHASE)Encodes a flavonol synthase that catalyzes formation of flavonols from dihydroflavonols.S.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
102.599.9E-MEXP-449-raw-cel-676423253
58.999.8GSM184895Arabidopsis, root cells, cortex, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with salt
57.199.8GSM131590ATGE_35_CGSE5632AtGenExpress: Developmental series (flowers and pollen)
56.399.8GSM131588ATGE_35_AGSE5632AtGenExpress: Developmental series (flowers and pollen)
52.999.8GSM131589ATGE_35_BGSE5632AtGenExpress: Developmental series (flowers and pollen)
47.099.8GSM184896Arabidopsis, root cells, cortex, standard conditions, replicate 2GSE7641Expression analysis of root cell-types after treatment with salt
45.599.8GSM147965lec1-1 Globular Stage Seed 1GSE1051Seed development in LEAFY COTYLEDON1 mutants
44.599.8GSM147966lec1-1 Globular Stage Seed 2GSE1051Seed development in LEAFY COTYLEDON1 mutants
38.299.8GSM147964WT Globular Stage Seed 2GSE680Transcript Profiling of Arabidopsis Plant Life Cycle
35.599.7E-MEXP-449-raw-cel-676423133
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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
0.154e-1583At1g516808415934CL1 (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-1481At3g212408216784CL2 (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.C.G.S.X.
0.142e-1377At3g212308216774CL5 (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.
0.041e-552At1g62940842596ACOS5 (ACYL-COA SYNTHETASE 5)encodes an acyl-CoA synthetase, has in vitro activity towards medium- to long-chain fatty acids and their hydroxylated derivatives. Expressed in the tapetum. Involved in pollen wall exine formation. Null mutants were devoid of pollen grains at anther maturity and were completely male sterile.C.G.S.X.
0.032e-448At4g051608258644-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.
0.015e-240At1g62760842574invertase/pectin methylesterase inhibitor family proteinF:enzyme inhibitor activity, pectinesterase inhibitor activity, pectinesterase activity;P:unknown;C:unknown;MOFBPVAC.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
0.122e-1481Glycine maxGma.8449.1.S1_atAF002258.14-coumarate:CoA ligase isoenzyme 3-2e-14At1g650604CL3C.G.S.X.
0.077e-342Hordeum vulgareContig4677_atContig4677--8e-3At1g650604CL3C.G.S.X.
0.071e-450Oryza sativaOs02g0697400AK105636.1-4-coumarate--CoA ligase 2 (EC 6.2.1.12) (4CL 2)(4-coumaroyl-CoA synthase 2)8e-5At1g650604CL3C.G.S.X.
0.241e-21105Populus trichocarpaPtpAffx.12056.3.S1_a_atCV2594944-Coumarate:CoA ligase-5e-22At1g650604CL3C.G.S.X.
0.042e-448Triticum aestivumTaAffx.30205.2.S1_s_atCA627137--1e-4At3g212404CL2 (4-COUMARATE:COA LIGASE 2)C.G.S.X.
0.123e-1375Vitis vinifera1619320_atCB974305--7e-13At1g650604CL3C.G.S.X.
0.044e-136Zea maysZm.11845.1.A1_atCO532590--3e-1At1g650604CL3C.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:0010584The formation of the pollen exine. The reticulate pollen wall pattern consists of two layers, exine and intine.
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:0050832Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
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.
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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