CoP: Co-expressed Biological Processes

Biological process to genes

Query process ID GO:0006511

Process name The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin moiety, or multiple ubiquitin moieties, to the protein.

Organism Oryza sativa

Click Gene ID to show a list of co-expressed genes.

ECC Gene ID Repr. ID Gene name Functional description Ev AGI code Arabidopsis gene name O.I. H.G. Other DB
C Os02g0770000 AB026563.1 - Beta 1 subunit of 20S proteasome 6e-13 At4g31300 PBA1 O.I. H.G.
C Os05g0187000 AB026564.1 - 20S proteasome beta2 subunit 1e-23 At5g40580 PBB2 O.I. H.G.
C Os06g0153800 AB026567.1 - Beta 5 subunit of 20S proteasome 3e-28 At1g13060 PBE1 O.I. H.G.
C Os07g0614100 AB032062.1 - Alpha 1-2 subunit of 20S proteasome 2e+0 At1g76050 pseudouridine synthase family protein O.I. H.G.
C Os09g0515200 AB026568.1 - Beta 7 subunit of 20S proteasome 2e-3 At1g56450 PBG1 O.I. H.G.
L Os01g0121900 - - - 0 - - O.I. H.G.
L Os01g0123700 9629.m00244 - - 2e+0 At5g49480 ATCP1 (Ca2+-binding protein 1) O.I. H.G.
L Os01g0123800 - - - 0 - - O.I. H.G.
L Os01g0144500 - - - 0 - - O.I. H.G.
L Os01g0177200 AK103230.1 - Ubiquitin-specific protease 14 3e-11 At3g20630 UBP14 (UBIQUITIN-SPECIFIC PROTEASE 14) O.I. H.G.
L Os01g0534800 AK104278.1 - PRLI-interacting factor K (Fragment) 2e-2 At4g15420 PRLI-interacting factor K O.I. H.G.
L Os01g0550100 AK066233.1 - Ubiquitin-specific protease 6 5e-21 At1g51710 UBP6 (UBIQUITIN-SPECIFIC PROTEASE 6) O.I. H.G.
L Os01g0761900 - - - 0 - - O.I. H.G.
L Os02g0128800 AK119901.1 - Seven in absentia protein family protein 3e-15 At4g27880 seven in absentia (SINA) family protein O.I. H.G.
L Os02g0180100 AK067359.1 - Peptidase C12, ubiquitin carboxyl-terminalhydrolase 1 family protein 8e-10 At1g65650 UCH2 O.I. H.G.
L Os02g0181800 AK121784.1 - Ubiquitin fusion degradation protein 1 homolog (UBfusion protein 1). Splice isoform Short 5e-8 At4g38930 ubiquitin fusion degradation UFD1 family protein O.I. H.G.
L Os02g0182500 AU068225 - Proteasome subunit beta type 3 (EC 3.4.25.1) (20Sproteasome alpha subunit C) (20S proteasome subunitbeta-3) 2e-16 At1g77440 PBC2 O.I. H.G.
L Os02g0293400 AK072985.1 - Ubiquitin ligase SINAT5 (EC 6.3.2.-) (Seven inabsentia homolog 5). Splice isoform 2 6e-45 At3g61790 seven in absentia (SINA) family protein O.I. H.G.
L Os02g0573400 9630.m03475 - Peptidase C19, ubiquitin carboxyl-terminalhydrolase 2 family protein 1e-11 At2g22310 ATUBP4 (ARABIDOPSIS THALIANA UBIQUITIN-SPECIFIC PROTEASE 4) O.I. H.G.
L Os02g0634900 AK059769.1 - Proteasome subunit alpha type 2 (EC 3.4.25.1) (20Sproteasome alpha subunit B) (20S proteasome subunitalpha-2) 2e-59 At1g16470 PAB1 (PROTEASOME SUBUNIT PAB1) O.I. H.G.
L Os02g0654500 9630.m04217 - Peptidase C12, ubiquitin carboxyl-terminalhydrolase 1 family protein 2e+0 At5g62770 unknown protein O.I. H.G.
L Os02g0795000 - - - 0 - - O.I. H.G.
L Os02g0822200 AK069150.1 - - 6e-18 At1g65650 UCH2 O.I. H.G.
L Os03g0190800 AK069100.1 - - 1e-36 At4g39910 ATUBP3 (ARABIDOPSIS THALIANA UBIQUITIN-SPECIFIC PROTEASE 3) O.I. H.G.
L Os04g0429100 AK073414.1 - Nuclear protein SET domain containing protein 7e-11 At1g76710 SDG26 (SET DOMAIN GROUP 26) O.I. H.G.
L Os04g0546400 AK059677.1 - Peptidase C12, ubiquitin carboxyl-terminalhydrolase 1 family protein 3e-1 At5g35540 unknown protein O.I. H.G.
L Os04g0647400 - - - 0 - - O.I. H.G.
L Os04g0667500 AK103595.1 - Peptidase C12, ubiquitin carboxyl-terminalhydrolase 1 family protein 1e+0 At4g17510 UCH3 (UBIQUITIN C-TERMINAL HYDROLASE 3) O.I. H.G.
L Os05g0238200 9633.m01306 - Ubiquitin ligase SINAT5 (EC 6.3.2.-) (Seven inabsentia homolog 5) 6e-20 At3g61790 seven in absentia (SINA) family protein O.I. H.G.
L Os05g0510300 AK120186.1 - Peptidase C19, ubiquitin carboxyl-terminalhydrolase 2 family protein 1e-3 At3g14400 UBP25 (UBIQUITIN-SPECIFIC PROTEASE 25) O.I. H.G.
L Os06g0139900 AK104152.1 - Beta 1 subunit of 20S proteasome 6e-19 At4g31300 PBA1 O.I. H.G.
L Os06g0167600 AB026560.1 - Proteasome subunit alpha type 4 (EC 3.4.25.1) (20Sproteasome alpha subunit C) (20S proteasome subunitalpha-3) 2e-13 At3g22110 PAC1 O.I. H.G.
L Os06g0184300 AK073840.1 - Peptidase C19, ubiquitin carboxyl-terminalhydrolase 2 family protein 6e-15 At5g57990 UBP23 (UBIQUITIN-SPECIFIC PROTEASE 23) O.I. H.G.
L Os06g0311300 CA760158 - Seven in absentia protein family protein 4e-3 At3g07080 membrane protein O.I. H.G.
L Os06g0654000 AK067618.1 - Peptidase C19, ubiquitin carboxyl-terminalhydrolase 2 family protein 1e-13 At2g24640 UBP19 (UBIQUITIN-SPECIFIC PROTEASE 19) O.I. H.G.
L Os07g0160000 NM_186392.1 - Peptidase C19, ubiquitin carboxyl-terminalhydrolase 2 family protein 2e-15 At5g22030 UBP8 (UBIQUITIN-SPECIFIC PROTEASE 8) O.I. H.G.
L Os07g0659800 AK107155.1 - Ubiquitin ligase SINAT5 (EC 6.3.2.-) (Seven inabsentia homolog 5). Splice isoform 2 5e-8 At3g61790 seven in absentia (SINA) family protein O.I. H.G.
L Os07g0661300 AK060418.1 - Peptidase C19, ubiquitin carboxyl-terminalhydrolase 2 family protein 1e-6 At4g30890 UBP24 (UBIQUITIN-SPECIFIC PROTEASE 24) O.I. H.G.
L Os08g0478500 AK099704.1 - Peptidase C19, ubiquitin carboxyl-terminalhydrolase 2 family protein 2e-3 At4g24560 UBP16 (UBIQUITIN-SPECIFIC PROTEASE 16) O.I. H.G.
L Os08g0527100 AK119411.1 - - 2e+0 At1g07220 - O.I. H.G.
L Os08g0527300 AK121686.1 - Peptidase C19, ubiquitin carboxyl-terminalhydrolase 2 family protein 4e-2 At5g48750 auxin-responsive protein, putative O.I. H.G.
L Os08g0527800 AK063392.1 - - 1e+0 At2g28130 unknown protein O.I. H.G.
L Os08g0527900 9636.m04228 - Peptidase C19, ubiquitin carboxyl-terminalhydrolase 2 family protein 3e-1 At3g49540 unknown protein O.I. H.G.
L Os08g0528100 9636.m04230 - Peptidase C19, ubiquitin carboxyl-terminalhydrolase 2 family protein 9e-2 At2g04840 F-box family protein O.I. H.G.
L Os08g0529100 AK071019.1 - - 4e-5 At3g60820 PBF1 O.I. H.G.
L Os08g0548900 U92540.1 - Proteasome subunit alpha type 7 (EC 3.4.25.1) (20Sproteasome alpha subunit D) (20S proteasome subunitalpha-4) 2e-40 At5g66140 PAD2 (PROTEASOME ALPHA SUBUNIT D 2) O.I. H.G.
L Os09g0407900 AK070971.1 - Peptidase C19, ubiquitin carboxyl-terminalhydrolase 2 family protein 2e-33 At4g22285 ubiquitin thiolesterase/ zinc ion binding O.I. H.G.

ECC	Gene ID	Repr. ID	Gene name	Functional description	Ev	AGI code	Arabidopsis gene name	O.I.	H.G.
C	Os02g0770000	AB026563.1	-	Beta 1 subunit of 20S proteasome	6e-13	At4g31300	PBA1	O.I.	H.G.
C	Os05g0187000	AB026564.1	-	20S proteasome beta2 subunit	1e-23	At5g40580	PBB2	O.I.	H.G.
C	Os06g0153800	AB026567.1	-	Beta 5 subunit of 20S proteasome	3e-28	At1g13060	PBE1	O.I.	H.G.
C	Os07g0614100	AB032062.1	-	Alpha 1-2 subunit of 20S proteasome	2e+0	At1g76050	pseudouridine synthase family protein	O.I.	H.G.
C	Os09g0515200	AB026568.1	-	Beta 7 subunit of 20S proteasome	2e-3	At1g56450	PBG1	O.I.	H.G.
L	Os01g0121900	-	-	-	0	-	-	O.I.	H.G.
L	Os01g0123700	9629.m00244	-	-	2e+0	At5g49480	ATCP1 (Ca2+-binding protein 1)	O.I.	H.G.
L	Os01g0123800	-	-	-	0	-	-	O.I.	H.G.
L	Os01g0144500	-	-	-	0	-	-	O.I.	H.G.
L	Os01g0177200	AK103230.1	-	Ubiquitin-specific protease 14	3e-11	At3g20630	UBP14 (UBIQUITIN-SPECIFIC PROTEASE 14)	O.I.	H.G.
L	Os01g0534800	AK104278.1	-	PRLI-interacting factor K (Fragment)	2e-2	At4g15420	PRLI-interacting factor K	O.I.	H.G.
L	Os01g0550100	AK066233.1	-	Ubiquitin-specific protease 6	5e-21	At1g51710	UBP6 (UBIQUITIN-SPECIFIC PROTEASE 6)	O.I.	H.G.
L	Os01g0761900	-	-	-	0	-	-	O.I.	H.G.
L	Os02g0128800	AK119901.1	-	Seven in absentia protein family protein	3e-15	At4g27880	seven in absentia (SINA) family protein	O.I.	H.G.
L	Os02g0180100	AK067359.1	-	Peptidase C12, ubiquitin carboxyl-terminalhydrolase 1 family protein	8e-10	At1g65650	UCH2	O.I.	H.G.
L	Os02g0181800	AK121784.1	-	Ubiquitin fusion degradation protein 1 homolog (UBfusion protein 1). Splice isoform Short	5e-8	At4g38930	ubiquitin fusion degradation UFD1 family protein	O.I.	H.G.
L	Os02g0182500	AU068225	-	Proteasome subunit beta type 3 (EC 3.4.25.1) (20Sproteasome alpha subunit C) (20S proteasome subunitbeta-3)	2e-16	At1g77440	PBC2	O.I.	H.G.
L	Os02g0293400	AK072985.1	-	Ubiquitin ligase SINAT5 (EC 6.3.2.-) (Seven inabsentia homolog 5). Splice isoform 2	6e-45	At3g61790	seven in absentia (SINA) family protein	O.I.	H.G.
L	Os02g0573400	9630.m03475	-	Peptidase C19, ubiquitin carboxyl-terminalhydrolase 2 family protein	1e-11	At2g22310	ATUBP4 (ARABIDOPSIS THALIANA UBIQUITIN-SPECIFIC PROTEASE 4)	O.I.	H.G.
L	Os02g0634900	AK059769.1	-	Proteasome subunit alpha type 2 (EC 3.4.25.1) (20Sproteasome alpha subunit B) (20S proteasome subunitalpha-2)	2e-59	At1g16470	PAB1 (PROTEASOME SUBUNIT PAB1)	O.I.	H.G.
L	Os02g0654500	9630.m04217	-	Peptidase C12, ubiquitin carboxyl-terminalhydrolase 1 family protein	2e+0	At5g62770	unknown protein	O.I.	H.G.
L	Os02g0795000	-	-	-	0	-	-	O.I.	H.G.
L	Os02g0822200	AK069150.1	-	-	6e-18	At1g65650	UCH2	O.I.	H.G.
L	Os03g0190800	AK069100.1	-	-	1e-36	At4g39910	ATUBP3 (ARABIDOPSIS THALIANA UBIQUITIN-SPECIFIC PROTEASE 3)	O.I.	H.G.
L	Os04g0429100	AK073414.1	-	Nuclear protein SET domain containing protein	7e-11	At1g76710	SDG26 (SET DOMAIN GROUP 26)	O.I.	H.G.
L	Os04g0546400	AK059677.1	-	Peptidase C12, ubiquitin carboxyl-terminalhydrolase 1 family protein	3e-1	At5g35540	unknown protein	O.I.	H.G.
L	Os04g0647400	-	-	-	0	-	-	O.I.	H.G.
L	Os04g0667500	AK103595.1	-	Peptidase C12, ubiquitin carboxyl-terminalhydrolase 1 family protein	1e+0	At4g17510	UCH3 (UBIQUITIN C-TERMINAL HYDROLASE 3)	O.I.	H.G.
L	Os05g0238200	9633.m01306	-	Ubiquitin ligase SINAT5 (EC 6.3.2.-) (Seven inabsentia homolog 5)	6e-20	At3g61790	seven in absentia (SINA) family protein	O.I.	H.G.
L	Os05g0510300	AK120186.1	-	Peptidase C19, ubiquitin carboxyl-terminalhydrolase 2 family protein	1e-3	At3g14400	UBP25 (UBIQUITIN-SPECIFIC PROTEASE 25)	O.I.	H.G.
L	Os06g0139900	AK104152.1	-	Beta 1 subunit of 20S proteasome	6e-19	At4g31300	PBA1	O.I.	H.G.
L	Os06g0167600	AB026560.1	-	Proteasome subunit alpha type 4 (EC 3.4.25.1) (20Sproteasome alpha subunit C) (20S proteasome subunitalpha-3)	2e-13	At3g22110	PAC1	O.I.	H.G.
L	Os06g0184300	AK073840.1	-	Peptidase C19, ubiquitin carboxyl-terminalhydrolase 2 family protein	6e-15	At5g57990	UBP23 (UBIQUITIN-SPECIFIC PROTEASE 23)	O.I.	H.G.
L	Os06g0311300	CA760158	-	Seven in absentia protein family protein	4e-3	At3g07080	membrane protein	O.I.	H.G.
L	Os06g0654000	AK067618.1	-	Peptidase C19, ubiquitin carboxyl-terminalhydrolase 2 family protein	1e-13	At2g24640	UBP19 (UBIQUITIN-SPECIFIC PROTEASE 19)	O.I.	H.G.
L	Os07g0160000	NM_186392.1	-	Peptidase C19, ubiquitin carboxyl-terminalhydrolase 2 family protein	2e-15	At5g22030	UBP8 (UBIQUITIN-SPECIFIC PROTEASE 8)	O.I.	H.G.
L	Os07g0659800	AK107155.1	-	Ubiquitin ligase SINAT5 (EC 6.3.2.-) (Seven inabsentia homolog 5). Splice isoform 2	5e-8	At3g61790	seven in absentia (SINA) family protein	O.I.	H.G.
L	Os07g0661300	AK060418.1	-	Peptidase C19, ubiquitin carboxyl-terminalhydrolase 2 family protein	1e-6	At4g30890	UBP24 (UBIQUITIN-SPECIFIC PROTEASE 24)	O.I.	H.G.
L	Os08g0478500	AK099704.1	-	Peptidase C19, ubiquitin carboxyl-terminalhydrolase 2 family protein	2e-3	At4g24560	UBP16 (UBIQUITIN-SPECIFIC PROTEASE 16)	O.I.	H.G.
L	Os08g0527100	AK119411.1	-	-	2e+0	At1g07220	-	O.I.	H.G.
L	Os08g0527300	AK121686.1	-	Peptidase C19, ubiquitin carboxyl-terminalhydrolase 2 family protein	4e-2	At5g48750	auxin-responsive protein, putative	O.I.	H.G.
L	Os08g0527800	AK063392.1	-	-	1e+0	At2g28130	unknown protein	O.I.	H.G.
L	Os08g0527900	9636.m04228	-	Peptidase C19, ubiquitin carboxyl-terminalhydrolase 2 family protein	3e-1	At3g49540	unknown protein	O.I.	H.G.
L	Os08g0528100	9636.m04230	-	Peptidase C19, ubiquitin carboxyl-terminalhydrolase 2 family protein	9e-2	At2g04840	F-box family protein	O.I.	H.G.
L	Os08g0529100	AK071019.1	-	-	4e-5	At3g60820	PBF1	O.I.	H.G.
L	Os08g0548900	U92540.1	-	Proteasome subunit alpha type 7 (EC 3.4.25.1) (20Sproteasome alpha subunit D) (20S proteasome subunitalpha-4)	2e-40	At5g66140	PAD2 (PROTEASOME ALPHA SUBUNIT D 2)	O.I.	H.G.
L	Os09g0407900	AK070971.1	-	Peptidase C19, ubiquitin carboxyl-terminalhydrolase 2 family protein	2e-33	At4g22285	ubiquitin thiolesterase/ zinc ion binding	O.I.	H.G.

The upper GO terms

Process ID Gene number Process name
GO:0019941 0 The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent modification of the target protein.

Process ID	Gene number	Process name
GO:0019941	0	The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent modification of the target protein.

The lower GO terms

Process ID Gene number Process name
GO:0016598 1 The posttranslational conjugation of arginine to the N-terminal aspartate or glutamate of a protein; required for the degradation of the protein via the ubiquitin pathway.
GO:0030579 0 The chemical reactions and pathways resulting in the breakdown of SMAD signaling proteins by ubiquitination and targeting to the proteasome.
GO:0042787 0 The process by which a ubiquitin moiety, or multiple moieties, are covalently attached to the target protein, thereby initiating the degradation of that protein.
GO:0043161 0 The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
GO:0043162 0 The chemical reactions and pathways resulting in the breakdown of a protein or peptide covalently tagged with ubiquitin, via the multivesicular body (MVB) sorting pathway; ubiquitin-tagged proteins are sorted into MVBs, and delivered to a lysosome/vacuole for degradation.

Process ID	Gene number	Process name
GO:0016598	1	The posttranslational conjugation of arginine to the N-terminal aspartate or glutamate of a protein; required for the degradation of the protein via the ubiquitin pathway.
GO:0030579	0	The chemical reactions and pathways resulting in the breakdown of SMAD signaling proteins by ubiquitination and targeting to the proteasome.
GO:0042787	0	The process by which a ubiquitin moiety, or multiple moieties, are covalently attached to the target protein, thereby initiating the degradation of that protein.
GO:0043161	0	The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
GO:0043162	0	The chemical reactions and pathways resulting in the breakdown of a protein or peptide covalently tagged with ubiquitin, via the multivesicular body (MVB) sorting pathway; ubiquitin-tagged proteins are sorted into MVBs, and delivered to a lysosome/vacuole for degradation.

Comparison with co-expressed genes

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Query process ID	GO:0006511
Process name	The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin moiety, or multiple ubiquitin moieties, to the protein.
Organism	Oryza sativa

Biological process to genes

Query process ID GO:0006511 Process name The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin moiety, or multiple ubiquitin moieties, to the protein. Organism Oryza sativa

The upper GO terms

Process ID Gene number Process name GO:00199410The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent modification of the target protein.

The lower GO terms

Comparison with co-expressed genes

Query process ID GO:0006511

Process name The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin moiety, or multiple ubiquitin moieties, to the protein.

Organism Oryza sativa

Process ID Gene number Process name
GO:0019941 0 The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent modification of the target protein.