CoP: Co-expressed Biological Processes

Gene omics information

Query gene ID At5g17790

Gene name VAR3 (VARIEGATED 3)

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 %ile Gene/Probe ID Repr.ID Gene Name Functional Description S.X. H.G. Other DB
1.00 100.0 At5g17790 831647 VAR3 (VARIEGATED 3) Encodes a 85.9 kDa protein containing novel repeats and zinc fingers described as protein interaction domains. VAR3 is a part of a protein complex required for normal chloroplast and palisade cell development. Mutants display a variegated phenotype due to somatic areas lacking or containing developmentally retarded chloroplasts and greatly reduced numbers of palisade cells. S.X. H.G.
0.45 58.3 At3g23020 821876 pentatricopeptide (PPR) repeat-containing protein F:binding;P:biological_process unknown;C:chloroplast;POMFBA S.X. H.G.
0.39 48.4 At5g39710 833967 EMB2745 (EMBRYO DEFECTIVE 2745) F:unknown;P:embryonic development ending in seed dormancy;C:unknown;POMFBA S.X. H.G.
0.37 45.0 At1g17850 838364 - F:molecular_function unknown;P:biological_process unknown;C:chloroplast;OBPMF S.X. H.G.
0.36 43.6 At4g14605 827109 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMO S.X. H.G.
0.31 33.8 At4g30000 829123 dihydropterin pyrophosphokinase, putative / dihydropteroate synthase, putative / DHPS, putative F:2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity, dihydropteroate synthase activity;P:cellular metabolic process, folic acid and derivative biosynthetic process;C:unknown;BOFAPM S.X. H.G.
0.28 30.3 At4g14510 827098 RNA binding F:RNA binding;P:biological_process unknown;C:chloroplast;POMFBVA S.X. H.G.
0.28 30.3 At1g09820 837514 pentatricopeptide (PPR) repeat-containing protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFBA S.X. H.G.
0.27 26.2 At2g38570 818439 - F:molecular_function unknown;P:biological_process unknown;C:unknown;BPO S.X. H.G.
0.26 24.4 At4g15820 827263 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMFPBV 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 %ile GSM ID Assay Name GSE ID Experiment Title
187.1 100.0 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
139.4 99.9 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
136.4 99.9 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
130.3 99.9 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
129.9 99.9 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
121.7 99.9 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
117.4 99.9 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
116.4 99.9 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
110.5 99.9 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
98.5 99.9 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
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Homologous genes

Paralogous genes

Click Gene ID to show a list of homologous genes.

HF Ev BS Gene ID Repr. ID Gene Name Functional description C.G. S.X. Other DB
0.01 3e-1 38 At3g27410 822362 unknown protein F:molecular_function unknown;P:biological_process unknown;C:anchored to membrane;P C.G. S.X.
0.01 1e+0 36 At4g37180 829872 myb family transcription factor myb family transcription factor, contains Pfam domain, PF00249: Myb-like DNA-binding domain l; also isolated as a putative cytoskeletal protein in a yeast screen C.G. S.X.
0.01 1e+0 36 At4g21120 827860 AAT1 (AMINO ACID TRANSPORTER 1) Encodes a member of the cationic amino acid transporter (CAT) subfamily of amino acid polyamine choline transporters. Mediates efficient uptake of Lys, Arg and Glu in a yeast system. C.G. S.X.
0.01 1e+0 36 At3g09560 820113 lipin family protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BMOFPVA C.G. S.X.
0.01 1e+0 36 At1g76680 844001 OPR1 Encodes a a member of an alpha/beta barrel fold family of FMN-containing oxidoreductases. One of two closely related 12-oxophytodienoic acid reductases. This enzyme is not expected to participate in jasmonic acid biosynthesis because during in vitro assays, it shows very little activity with the naturally occurring OPDA isomer. Up-regulated by senescence and jasmonic acid. Induced by salicylic acid. Independent of NPR1 for their induction by salicylic acid. C.G. S.X.
0.01 1e+0 36 At1g68050 843133 FKF1 (FLAVIN-BINDING, KELCH REPEAT, F BOX 1) Encodes FKF1, a flavin-binding kelch repeat F box protein, is clock-controlled, regulates transition to flowering. Forms a complex with GI on the CO promoter to regulate CO expression. C.G. S.X.
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Orthologous genes

Click Gene ID to show a list of orthologous genes.

HF Ev BS Species Gene ID Repr. ID Gene Name Functional description Ev AGI code Arabidopsis gene name C.G. S.X. Other DB
0.08 3e-8 61 Glycine max GmaAffx.69683.1.S1_at CA799656 - - 7e-9 At5g17790 VAR3 (VARIEGATED 3) C.G. S.X.
0.01 6e-1 36 Hordeum vulgare Contig25150_at Contig25150 - - 3e-1 At3g23400 plastid-lipid associated protein PAP / fibrillin family protein C.G. S.X.
0.05 6e-10 67 Oryza sativa Os01g0815700 AK073519.1 - Zn-finger, Ran-binding domain containing protein 5e-10 At5g17790 VAR3 (VARIEGATED 3) C.G. S.X.
0.06 6e-3 44 Populus trichocarpa PtpAffx.158573.1.S1_at CX658654 hypothetical protein - 1e-3 At5g17790 VAR3 (VARIEGATED 3) C.G. S.X.
0.02 1e+0 36 Triticum aestivum Ta.18833.1.S1_at CA642739 - - 2e+0 At5g19260 unknown protein C.G. S.X.
0.10 7e-21 101 Vitis vinifera 1617399_at CB342525 hypothetical protein LOC100262132 - 5e-21 At5g17790 VAR3 (VARIEGATED 3) C.G. S.X.
0.01 3e-2 40 Zea mays Zm.12657.1.A1_at CA826570 - - 1e-1 At1g11580 PMEPCRA (METHYLESTERASE PCR A) 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.

ECC GO ID Process Name
X GO:0009658 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the chloroplast.
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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 ID Link to Kappa-View Pathway Name

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

KEGG PATHWAY ID Link to KEGG PATHWAY Pathway Name
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