CoP: Co-expressed Biological Processes

Gene omics information

Query gene ID At3g49170

Gene name EMB2261 (embryo defective 2261)

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
0.83 91.4 At3g49170 824078 EMB2261 (embryo defective 2261) F:unknown;P:embryonic development ending in seed dormancy;C:chloroplast;POMFB S.X. H.G.
0.87 93.5 At2g13900 815874 DC1 domain-containing protein F:protein binding, zinc ion binding;P:unknown;C:unknown;PMO S.X. H.G.
0.87 93.5 At4g26020 828708 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPAV S.X. H.G.
0.81 90.4 At5g26620 832728 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P S.X. H.G.
0.80 89.8 At4g14670 827117 CLPB2 This locus was originally annotated as encoding ClpB2 (also referred to as Hsp92.7), which belongs to the Casein lytic proteinase/heat shock protein 100 (Clp/Hsp100) family. However, according to Lee et al. (2007, Plant Journal, 49:115-127), there is no evidence for expression of an appropriate-sized mRNA from this locus. Re-annotation of the genome indicates that this locus potentially encodes a 68.8-kDa protein, containing only the N-terminal two thirds of the originally predicted open reading frame. This locus contains a 626-bp deletion in WS ecotype compared with the Col ecotype, which eliminates residues 1-86 of the predicted protein. S.X. H.G.
0.80 89.8 At4g02970 828121 AT7SL-1 (Arabidopsis 7SL RNA 1) Signal recognition particle. Type 4 of RNA polymerase III dependent genes. S.X. H.G.
0.80 89.8 At1g46912 841119 F-box family protein-related F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P S.X. H.G.
0.79 89.1 At5g14560 831307 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P S.X. H.G.
0.77 88.0 At2g32050 817765 cell cycle control protein-related F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOP S.X. H.G.
0.76 87.4 At2g40440 818638 BTB/POZ domain-containing protein F:protein binding;P:biological_process unknown;C:cellular_component unknown;PMO 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
387.1 100.0 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
381.5 100.0 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
348.5 100.0 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
334.3 100.0 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
333.7 100.0 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
315.9 100.0 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
315.8 100.0 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
301.7 100.0 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
288.0 100.0 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
263.3 100.0 GSM143306 High_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
0.03 9e-8 59 At4g14850 827142 LOI1 (lovastatin insensitive 1) Encodes a pentatricopeptide (PPR) protein that binds single-stranded RNA. The N-terminal portion of the protein can localize to the mitochondria. Mutations in this gene make plants less sensitive to inhibitors of the MEP and MVA pathways of isoprenoid biosynthesis and increase the activity of HMG CoA reductase. C.G. S.X.
0.03 1e-6 56 At4g02750 828187 pentatricopeptide (PPR) repeat-containing protein F:unknown;P:unknown;C:mitochondrion;POMFB C.G. S.X.
0.05 2e-5 52 At5g52630 835340 MEF1 (MITOCHONDRIAL RNA EDITING FACTOR 1) Encodes a member of the DYW subfamily of pentatricopeptide repeat (PPR) proteins. Loss of MEF1 function affects RNA editing at specific sites in the mitochondrial genome but do not exhibit obvious phenotypes. C.G. S.X.
0.01 2e-5 52 At4g13650 826999 pentatricopeptide (PPR) repeat-containing protein F:unknown;P:biological_process unknown;C:cellular_component unknown;POMFBA C.G. S.X.
0.02 2e-5 52 At1g28690 839769 pentatricopeptide (PPR) repeat-containing protein F:unknown;P:biological_process unknown;C:unknown;POMFBA C.G. S.X.
0.01 9e-5 50 At4g33170 829454 pentatricopeptide (PPR) repeat-containing protein F:unknown;P:unknown;C:chloroplast;POMFB C.G. S.X.
0.01 9e-5 50 At3g22690 821840 pentatricopeptide (PPR) repeat-containing protein F:unknown;P:regulation of chlorophyll biosynthetic process, photosystem II assembly, photosystem I assembly, thylakoid membrane organization, RNA modification;C:chloroplast;POMFBA C.G. S.X.
0.01 9e-5 50 At2g02980 814827 pentatricopeptide (PPR) repeat-containing protein F:unknown;P:biological_process unknown;C:chloroplast;POFMBA C.G. S.X.
0.02 3e-4 48 At1g04840 839402 pentatricopeptide (PPR) repeat-containing protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFB 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
0.05 2e-9 65 Glycine max Gma.7862.1.A1_at BU550720 - - 4e-10 At3g49170 EMB2261 (embryo defective 2261) C.G. S.X.
0.01 6e-1 36 Hordeum vulgare Contig24943_at Contig24943 - - 3e-1 At5g05990 mitochondrial glycoprotein family protein / MAM33 family protein C.G. S.X.
0.03 2e-4 50 Oryza sativa OsAffx.23612.1.S1_at - - - 0 C.G. S.X.
0.21 4e-17 91 Populus trichocarpa PtpAffx.212618.1.S1_at pmrna24702 hypothetical protein - 2e-17 At3g49170 EMB2261 (embryo defective 2261) C.G. S.X.
0.04 6e-6 54 Triticum aestivum Ta.8735.1.A1_at BQ162296 - - 1e-6 At3g49170 EMB2261 (embryo defective 2261) C.G. S.X.
0.02 3e-5 50 Vitis vinifera 1620095_at CF403669 hypothetical protein LOC100260539 - 2e-5 At2g15690 pentatricopeptide (PPR) repeat-containing protein C.G. S.X.
0.02 2e+0 34 Zea mays Zm.4090.1.A1_at AI834563 - - 4e-1 At2g41080 pentatricopeptide (PPR) repeat-containing protein 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:0009793 The process whose specific outcome is the progression of the embryo over time, from zygote formation to the end of seed dormancy. An example of this process is found in Arabidopsis thaliana.
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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
00400 Homogalacturonan degradation
00412 Glycoside Hydrolase
00442 Rhamnogalacturonan II degradation

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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