CoP: Co-expressed Biological Processes

Gene omics information

Query gene ID At3g13940

Gene name DNA binding / DNA-directed RNA polymerase

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
0.79 89.1 At3g13940 820607 DNA binding / DNA-directed RNA polymerase F:DNA-directed RNA polymerase activity, DNA binding;P:transcription;C:nucleus;FMPOB S.X. H.G.
0.96 97.3 At2g20740 816603 - F:molecular_function unknown;P:biological_process unknown;C:endomembrane system, integral to membrane;PO S.X. H.G.
0.96 97.3 At4g01570 828133 pentatricopeptide (PPR) repeat-containing protein F:unknown;P:biological_process unknown;C:unknown;POFMBA S.X. H.G.
0.96 97.3 At5g32450 833204 RNA recognition motif (RRM)-containing protein F:oxidoreductase activity, nucleotide binding, nucleic acid binding;P:oxidation reduction;C:unknown;PFMO S.X. H.G.
0.92 96.0 At2g36990 818273 SIGF (RNA POLYMERASE SIGMA-SUBUNIT F) Encodes a general sigma factor in chloroplasts and is probably responsible for the recognition of sigma 70 type standard bacteria-type multi-subunit RNA polymerase (PEP) promoters in young cotyledons. S.X. H.G.
0.92 96.0 At3g62330 825406 zinc knuckle (CCHC-type) family protein F:zinc ion binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MOFPBV S.X. H.G.
0.89 94.6 At2g21195 816656 unknown protein F:molecular_function unknown;P:response to oxidative stress;C:cellular_component unknown;P S.X. H.G.
0.89 94.6 At5g18570 831975 GTP1/OBG family protein F:GTP binding, nucleotide binding;P:unknown;C:intracellular, chloroplast;BOMFAPV S.X. H.G.
0.89 94.6 At5g24400 832511 emb2024 (embryo defective 2024) F:6-phosphogluconolactonase activity, catalytic activity;P:embryonic development ending in seed dormancy, carbohydrate metabolic process;C:peroxisome, chloroplast stroma, chloroplast;BOMFP S.X. H.G.
0.86 93.1 At1g07970 837312 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;MPFOB S.X. H.G.
Click here to hide the above table.

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
456.6 100.0 GSM133757 Lindsey_1-8_heart-stage-cotyledon_Rep2_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
25.9 99.7 GSM184556 Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
23.7 99.6 GSM133319 RIKEN-LI5A GSE5701 AtGenExpress: Basic hormone treatment of seeds
23.0 99.6 GSM133120 RIKEN-YAMAUCHI2B GSE5687 AtGenExpress: Different temperature treatment of seeds
21.4 99.6 GSM133313 RIKEN-LI2A GSE5701 AtGenExpress: Basic hormone treatment of seeds
20.3 99.6 GSM133307 RIKEN-NAKABAYASHI3A GSE5700 AtGenExpress: Effect of ABA during seed imbibition
20.1 99.6 E-MEXP-849-raw-cel-1181981038
19.8 99.6 GSM133119 RIKEN-YAMAUCHI2A GSE5687 AtGenExpress: Different temperature treatment of seeds
18.9 99.5 E-MEXP-849-raw-cel-1181981022
18.9 99.5 E-MEXP-849-raw-cel-1181981046
Click here to hide the above table.

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 4e-2 40 At2g16470 - C.G. S.X.
0.02 2e-1 38 At5g03050 831689 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P C.G. S.X.
0.01 2e-1 38 At2g14910 815980 unknown protein F:unknown;P:unknown;C:chloroplast;BOPM C.G. S.X.
0.01 2e-1 38 At1g64280 842733 NPR1 (NONEXPRESSER OF PR GENES 1) This gene is a key regulator of the salicylic acid (SA)-mediated systemic acquired resistance (SAR) pathway. It is similar to the transcription factor inhibitor I kappa B, and contains ankyrin repeats. It confers resistance to the pathogens Pseudomonas syringae and Peronospora parasitica in a dosage-dependent fashion. Although transgenic Arabidopsis plants overexpressing NPR1 acquire enhanced sensitivity to SA and (benzothiadiazole) BTH, they display no obvious detrimental morphological changes and do not have elevated pathogenesis-related gene expression until activated by inducers or pathogens. C.G. S.X.
0.01 2e-1 38 At1g07330 837244 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMPFBA C.G. S.X.
0.01 7e-1 36 At5g55130 835604 CNX5 (CO-FACTOR FOR NITRATE, REDUCTASE AND XANTHINE DEHYDROGENASE 5) putative molybdopterin synthase sulphurylase (cnx5) C.G. S.X.
Click here to hide the above table.

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
0.02 9e-1 36 Glycine max GmaAffx.47359.1.S1_at BU964713 - - 3e-25 At3g04820 pseudouridine synthase C.G. S.X.
0.02 1e+0 34 Hordeum vulgare HVSMEf0015I06r2_at HVSMEf0015I06r2 - - 4e+0 At4g36590 MADS-box protein (AGL40) C.G. S.X.
0.02 3e-1 38 Oryza sativa OsAffx.30923.1.S1_at - - - 0 C.G. S.X.
0.02 6e-2 40 Populus trichocarpa PtpAffx.25334.2.S1_at CV262387 hypothetical protein - 1e+1 At5g44574 unknown protein C.G. S.X.
0.02 7e-1 36 Triticum aestivum TaAffx.89766.1.S1_at CA657290 - - 4e-1 At3g13940 DNA binding / DNA-directed RNA polymerase C.G. S.X.
0.02 3e+0 32 Vitis vinifera 1622652_at CD004838 - - 9e-1 At5g53070 ribosomal protein L9 family protein C.G. S.X.
0.01 1e+0 34 Zea mays Zm.821.1.A1_at CO524526 - - 2e+0 At1g38790 unknown protein C.G. S.X.
Click here to hide the above table.

Biological processes

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

ECC GO ID Process Name
L GO:0006350 The synthesis of either RNA on a template of DNA or DNA on a template of RNA.
Click here to hide the above table.

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
Click here to hide the above table.

Back to the CoP portal site

Back to the KAGIANA project homepage