Gene omics information

Query gene ID At4g37930
Gene name SHM1 (SERINE TRANSHYDROXYMETHYLTRANSFERASE 1)
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
0.114.1At4g37930829949SHM1 (SERINE TRANSHYDROXYMETHYLTRANSFERASE 1)Encodes a protein with mitochondrial serine hydroxymethyltransferase activity, which functions in the photorespiratory pathway, catalyzes the conversion of serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. Involved in controlling cell damage caused by abiotic stress, such as high light and salt and the hypersensitive defense response of plants.S.X.H.G.
0.2217.5At4g38970830052fructose-bisphosphate aldolase, putativeProtein is tyrosine-phosphorylated and its phosphorylation state is modulated in response to ABA in Arabidopsis thaliana seeds.S.X.H.G.
0.1710.2At2g39730818558RCA (RUBISCO ACTIVASE)Rubisco activase, a nuclear-encoded chloroplast protein that consists of two isoforms arising from alternative splicing in most plants. Required for the light activation of rubisco.S.X.H.G.
0.168.8At5g54770835567THI1Encodes a thiamine biosynthetic gene that has a dual function in thiamine biosynthesis and mitochondrial DNA damage tolerance. It appears to be involved in producing the thiazole portion of thiamine (vitamin B1). A crystal structure of the protein reveals that it forms a 2-ring homo-octamer.S.X.H.G.
0.157.8At3g61470825320LHCA2Encodes a component of the light harvesting antenna complex of photosystem I.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
6.298.6E-ATMX-33-raw-cel-1562596264
6.198.5GSM131103Broadley_1-1_A1-Bo+P-nutrient-replete_Rep1_ATH1GSE5614Changes in Gene Expression in Brassica oleracea Shoots during Phosphate Starvation (Cross-species study)
5.998.5E-ATMX-35-raw-cel-1574334896
5.298.2E-ATMX-33-raw-cel-1562596310
5.198.2GSM269824T8 leaf-well watered-rep2GSE10670Global expression profiling of wild type and transgenic Arabidopsis plants in response to water stress
4.898.0E-MEXP-1573-raw-cel-1617523321
4.697.9GSM216899ga1-3_shoots_1h_GA4_repl1GSE8739Early gibberellin responses in Arabidopsis
4.697.9GSM128688Helenius_1-1_control-non-treated_Rep1_ATH1GSE5521Comparative ABA-treatment of Col-O vector control and transgenic plants
4.497.8GSM269816T8 leaf-well watered-rep1GSE10670Global expression profiling of wild type and transgenic Arabidopsis plants in response to water stress
4.397.7GSM128689Helenius_1-2_control-ABA-treated_Rep1_ATH1GSE5521Comparative ABA-treatment of Col-O vector control and transgenic plants
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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
0.591e-141504At5g26780832736SHM2 (SERINE HYDROXYMETHYLTRANSFERASE 2)Encodes a protein with serine hydroxymethyltransferase activity which is thought to be localized in the mitochondrial matrix. SHM2 expression fails to rescue the conditional lethal phenotype of the shm1-1 mutant, defective in SHM1.C.G.S.X.
0.051e-552At4g13930827027SHM4 (serine hydroxymethyltransferase 4)Encodes a serine hydroxymethyltransferase maximally expressed in rootC.G.S.X.
0.015e-240At2g24210816955TPS10 (terpene synthase 10)F:myrcene synthase activity, (E)-beta-ocimene synthase activity;P:response to jasmonic acid stimulus, monoterpenoid biosynthetic process, response to wounding;C:unknown;POC.G.S.X.
0.028e-136At5g66280836760GMD1 (GDP-D-MANNOSE 4,6-DEHYDRATASE 1)GDP-D-mannose 4,6-dehydrataseC.G.S.X.
0.018e-136At4g33500829488protein phosphatase 2C-related / PP2C-relatedF:protein serine/threonine phosphatase activity, catalytic activity;P:unknown;C:chloroplast;MOBFPAVC.G.S.X.
0.013e+034At5g18320831950armadillo/beta-catenin repeat family protein / U-box domain-containing proteinF:ubiquitin-protein ligase activity, binding;P:protein ubiquitination;C:ubiquitin ligase complex;PFOMBVC.G.S.X.
0.023e+034At5g03370831859acylphosphatase familyF:acylphosphatase activity;P:biological_process unknown;C:unknown;BOMAPFC.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
0.465e-114412Glycine maxGma.7214.1.S1_atCD412786--3e-114At4g37930SHM1 (SERINE TRANSHYDROXYMETHYLTRANSFERASE 1)C.G.S.X.
0.575e-90331Hordeum vulgareContig1824_s_atContig1824--1e-89At4g37930SHM1 (SERINE TRANSHYDROXYMETHYLTRANSFERASE 1)C.G.S.X.
0.601e-109398Oryza sativaOs03g0738400AK119226.1-Serine hydroxymethyltransferase, mitochondrialprecursor (EC 2.1.2.1) (Serine methylase) (Glycinehydroxymethyltransferase) (SHMT)6e-110At4g37930SHM1 (SERINE TRANSHYDROXYMETHYLTRANSFERASE 1)C.G.S.X.
0.531e-114414Populus trichocarpaPtpAffx.41585.1.S1_atCX660062precursor of transferase serine hydroxymethyltransferase 3-0At5g26780SHM2 (SERINE HYDROXYMETHYLTRANSFERASE 2)C.G.S.X.
0.478e-75282Triticum aestivumTa.27135.1.S1_atBJ241323--1e-74At4g37930SHM1 (SERINE TRANSHYDROXYMETHYLTRANSFERASE 1)C.G.S.X.
0.630817Vitis vinifera1618636_atCB976802hypothetical protein LOC100261289-0At4g37930SHM1 (SERINE TRANSHYDROXYMETHYLTRANSFERASE 1)C.G.S.X.
0.552e-58226Zea maysZm.4908.1.S1_atBG316794IDP527 protein-5e-58At4g37930SHM1 (SERINE TRANSHYDROXYMETHYLTRANSFERASE 1)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:0046686A 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 cadmium (Cd) ion stimulus.
XGO:0009409A 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 cold stimulus, a temperature stimulus below the optimal temperature for that organism.
XGO:0009853A light-dependent catabolic process occurring concomitantly with photosynthesis in plants (especially C3 plants) whereby dioxygen (O2) is consumed and carbon dioxide (CO2) is evolved. The substrate is glycolate formed in large quantities in chloroplasts from 2-phosphoglycolate generated from ribulose 1,5-bisphosphate by the action of ribulose-bisphosphate carboxylase; the glycolate enters the peroxisomes where it is converted by glycolate oxidase to glyoxylate which undergoes transamination to glycine. This then passes into the mitochondria where it is decarboxylated forming one molecule of serine for every two molecules of glycine. This pathway also exists in photosynthetic bacteria.
XGO:0019464
SGO:0006800The chemical reactions and pathways involving dioxygen (O2), or any of the reactive oxygen species, e.g. superoxide anions (O2-), hydrogen peroxide (H2O2), and hydroxyl radicals (-OH).
SGO:0009626The rapid, localized death of plant cells in response to invasion by a pathogen.
CGO:0006544The chemical reactions and pathways involving glycine, aminoethanoic acid.
CGO:0006563The chemical reactions and pathways involving L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic 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
00008Link to KaPPA-View 4Serine and glycine metabolism
00118Link to KaPPA-View 4Glycolate pathway
00144Link to KaPPA-View 4Formyl THF 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
00260Link to KEGG PATHWAYGlycine, serine and threonine metabolism
00460Link to KEGG PATHWAYCyanoamino acid metabolism
00670Link to KEGG PATHWAYOne carbon pool by folate
00680Link to KEGG PATHWAYMethane metabolism
01100Link to KEGG PATHWAYMetabolic pathways
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