CoP: Co-expressed Biological Processes

Gene omics information

Query gene ID At5g53950

Gene name CUC2 (CUP-SHAPED COTYLEDON 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 %ile Gene/Probe ID Repr.ID Gene Name Functional Description S.X. H.G. Other DB
0.72 84.8 At5g53950 835478 CUC2 (CUP-SHAPED COTYLEDON 2) Transcriptional activator of the NAC gene family, with CUC1 redundantly required for embryonic apical meristem formation, cotyledon separation and expression of STM. Proper timing of CUC2 expression is required to maintain the phyllotactic pattern initiated in the meristem. CUC2 expression in leaf sinus region is required for serration and the extent of serration is modulated by mir164A mediated repression of CUC2. S.X. H.G.
0.35 41.6 At4g27510 828860 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;P S.X. H.G.
0.34 39.8 At2g21800 816716 ATEME1A (ARABIDOPSIS ESSENTIAL MEIOTIC ENDONUCLEASE 1A) Forms a complex with MUS81 that functions as endonuclease in DNA recombination and repair processes. S.X. H.G.
0.30 32.1 At5g48820 834940 ICK6 (INHIBITOR/INTERACTOR WITH CYCLIN-DEPENDENT KINASE) Kip-related protein (KRP) gene, encodes CDK (cyclin-dependent kinase) inhibitor (CKI), negative regulator of cell division. Binds to D type and CDC2A cyclins and may inhibit cell cycle. Seven KRP genes were found in Arabidopsis thaliana. Differential expression patterns for distinct KRPs were revealed by in situ hybridization. S.X. H.G.
0.29 30.3 At3g10310 820193 ATP binding / microtubule motor F:microtubule motor activity, ATP binding;P:microtubule-based movement;C:microtubule associated complex;MOFP S.X. H.G.
0.29 30.3 At3g48910 - - - S.X. H.G.
0.28 30.3 At1g17920 838371 HDG12 (HOMEODOMAIN GLABROUS 12) Encodes a homeobox-leucine zipper family protein belonging to the HD-ZIP IV family. Together with HDG11, it is involved in trichome branching. S.X. H.G.
0.28 30.3 At1g27880 839681 ATP-dependent DNA helicase, putative F:helicase activity, nucleic acid binding, ATP-dependent helicase activity, ATP binding;P:DNA recombination;C:cellular_component unknown;BOMFPVA S.X. H.G.
0.25 22.6 At3g58770 825046 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO S.X. H.G.
0.23 19.3 At1g01370 839104 HTR12 Encodes a centromere-identifying protein histone H3 variant. Localized at centromeres in both mitotic and meiotic cells. 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
347.3 100.0 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
317.4 100.0 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
302.1 100.0 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
190.4 100.0 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
144.4 99.9 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
115.1 99.9 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
87.3 99.9 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
82.5 99.9 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
80.7 99.9 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
65.8 99.8 GSM184551 Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
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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
0.30 7e-59 228 At3g15170 820748 CUC1 (CUP-SHAPED COTYLEDON1) Encodes a transcription factor involved in shoot apical meristem formation and auxin-mediated lateral root formation. The gene is thought not to be involved in stress responses (NaCl, auxins, ethylene). Cuc mutant was first recognized at the heart stage, where embryos lacking two distinct bulges of cotyledonary primordia were observed. C.G. S.X.
0.14 3e-24 113 At5g18270 831945 ANAC087 F:transcription factor activity;P:multicellular organismal development, regulation of transcription;C:cellular_component unknown;P C.G. S.X.
0.08 7e-19 95 At3g04060 819561 anac046 (Arabidopsis NAC domain containing protein 46) F:transcription factor activity;P:multicellular organismal development, regulation of transcription;C:cellular_component unknown;P C.G. S.X.
0.18 1e-14 81 At3g18400 821369 anac058 (Arabidopsis NAC domain containing protein 58) F:transcription factor activity;P:multicellular organismal development, regulation of transcription;C:cellular_component unknown;PO C.G. S.X.
0.16 2e-13 77 At2g24430 816979 ANAC038 (ARABIDOPSIS NAC DOMAIN CONTAINING PROTEIN 38) F:transcription factor activity;P:multicellular organismal development, regulation of transcription;C:cellular_component unknown;PMF C.G. S.X.
0.15 6e-13 75 At5g39610 833957 ATNAC6 (ARABIDOPSIS NAC DOMAIN CONTAINING PROTEIN 6) Encodes a NAC-domain transcription factor. Positively regulates aging-induced cell death and senescence in leaves. This gene is upregulated in response to salt stress in wildtype as well as NTHK1 transgenic lines although in the latter case the induction was drastically reduced. It was also upregulated by ABA, ACC and NAA treatment, although in the latter two cases, the induction occurred relatively late when compared with NaCl or ABA treatments. Note: this protein (AtNAC6) on occasion has also been referred to as AtNAC2, not to be confused with the AtNAC2 found at locus AT3G15510. C.G. S.X.
0.14 3e-12 73 At1g76420 843975 CUC3 (CUP SHAPED COTYLEDON3) Identified in an enhancer trap line; member of the NAC family of proteins. Expressed at the boundary between the shoot meristem and lateral organs and the polar nuclei in the embryo sac. 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
0.17 9e-13 75 Glycine max GmaAffx.90313.1.S1_at CF806038 NAC domain protein - 9e-11 At5g39610 ATNAC6 (ARABIDOPSIS NAC DOMAIN CONTAINING PROTEIN 6) C.G. S.X.
0.05 7e-2 38 Hordeum vulgare Contig8993_at Contig8993 - - 1e-2 At5g61430 ANAC100 (ARABIDOPSIS NAC DOMAIN CONTAINING PROTEIN 100) C.G. S.X.
0.13 5e-9 63 Oryza sativa Os09g0497900 AK102511.1 - No apical meristem (NAM) protein domain containingprotein 1e-21 At3g18400 anac058 (Arabidopsis NAC domain containing protein 58) C.G. S.X.
0.32 8e-44 178 Populus trichocarpa PtpAffx.214805.1.S1_at pmrna28658 NAC domain protein, IPR003441 - 3e-34 At3g15170 CUC1 (CUP-SHAPED COTYLEDON1) C.G. S.X.
0.13 1e-5 52 Triticum aestivum Ta.9333.3.S1_a_at BJ288880 - - 5e-6 At5g53950 CUC2 (CUP-SHAPED COTYLEDON 2) C.G. S.X.
0.04 1e-8 59 Vitis vinifera 1610480_at CA809362 hypothetical protein LOC100254239 - 3e-9 At1g56010 NAC1 C.G. S.X.
0.06 4e-3 42 Zea mays Zm.5914.1.A1_at CA402103 nac4 protein - 4e-12 At3g04060 anac046 (Arabidopsis NAC domain containing protein 46) 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:0010072 The specification of the meristem which will give rise to all post-embryonic above-ground structures of the plant as well as the non-root below-ground structures, such as rhizomes and tubers.
X GO:0010160 The regionalization process that specifies organ primordium boundaries resulting in a restriction of organogenesis to a limited spatial domain and keeping the organ separate from surrounding tissues.
X GO:0010223 The process that gives rise to secondary (or auxiliary or axillary) shoots in plants. This process pertains to the initial formation of a structure from unspecified parts. These secondary shoots originate from secondary meristems initiated in the axils of leaf primordia. Axillary meristems function like the shoot apical meristem of the primary shoot initating the development of lateral organs.
X GO:0048366 The process whose specific outcome is the progression of the leaf over time, from its formation to the mature structure.
X GO:0048504 Any process that modulates the rate, frequency or extent of organ formation at a consistent predetermined time point during development.
C GO:0007275 The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
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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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