CoP: Co-expressed Biological Processes

Microarray experiments to specifically-expressed genes

GSM ID GSM318627

Assay name Apex_BLS>>TCP4_14DAS_2

GSE experiment GSE12691: Knockdown and overexpression of CIN-TCP genes

Click Gene ID to show a list of GSM assays in which the gene are specifically expressed.

Std2 GX %ile Std GX Gene ID Repr. ID Gene name Functional description O.I. C.G. H.G. Other DB
111.8 99.9 101.1 At5g59330 836052 lipid binding F:lipid binding;P:lipid transport;C:endomembrane system O.I. C.G. H.G.
71.1 99.9 23.6 At5g60780 836199 ATNRT2.3 member of High affinity nitrate transporter family O.I. C.G. H.G.
59.6 99.8 42.1 At2g14580 815945 ATPRB1 pathogenesis related protein, encodes a basic PR1-like protein. Expresses in flowers, roots, and not in leaves and responses to ethylene and methyl jasmonate. Salicylic acid represses gene expression. O.I. C.G. H.G.
33.9 99.7 16.7 At1g11300 837672 ATP binding / carbohydrate binding / kinase/ protein kinase/ protein serine/threonine kinase/ protein tyrosine kinase/ sugar binding F:in 7 functions;P:protein amino acid phosphorylation, recognition of pollen;C:endomembrane system;MPOBFVA O.I. C.G. H.G.
33.4 99.7 56.1 At4g33000 829437 CBL10 (CALCINEURIN B-LIKE 10) Encodes a member of the calcineurin B-like calcium sensor gene family. Mediates salt tolerance by regulating ion homeostasis in Arabidopsis. O.I. C.G. H.G.
28.9 99.7 18.7 At4g34650 829617 SQS2 (SQUALENE SYNTHASE 2) Encodes a protein with similarity to squalene synthase which catalyzes the first committed step in sterol biosynthesis. To date no experimental evidence exists that SQS2 functions as a squalene synthase and some experiments indicate it does not have this function. O.I. C.G. H.G.
24.9 99.6 136.1 At3g54500 824615 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOFB O.I. C.G. H.G.
24.5 99.6 29.8 At3g63510 825526 FAD binding / catalytic/ tRNA dihydrouridine synthase F:tRNA dihydrouridine synthase activity, FAD binding, catalytic activity;P:regulation of nitrogen utilization, tRNA processing, oxidation reduction, metabolic process;C:unknown;BOMFPA O.I. C.G. H.G.
23.9 99.6 48.9 At5g64050 836526 ERS (GLUTAMATE TRNA SYNTHETASE) Glutamate-tRNA ligase. Targeted to mitochondria and chloroplast. Its inactivation causes developmental arrest of chloroplasts and mitochondria in Nicotiana benthamiana. O.I. C.G. H.G.
23.2 99.6 36.7 At4g30720 829195 electron carrier/ oxidoreductase F:electron carrier activity, oxidoreductase activity;P:unknown;C:chloroplast;BOAPF O.I. C.G. H.G.
21.4 99.6 54.8 At5g10690 830933 pentatricopeptide (PPR) repeat-containing protein / CBS domain-containing protein F:unknown;P:biological_process unknown;C:chloroplast;POMFBA O.I. C.G. H.G.
20.6 99.6 67.4 At1g12860 837843 SCRM2 (SCREAM 2) Encodes ICE2 (Inducer of CBF Expression 2), a transcription factor of the bHLH family that participates in the response to deep freezing through the cold acclimation-dependent pathway. Overexpression of ICE2 results in increased tolerance to deep freezing stress after cold acclimation. O.I. C.G. H.G.
20.6 99.6 66.5 At1g30520 839932 AAE14 (Acyl-Activating Enzyme 14) Encodes a chloroplast O-succinylbenzoyl-CoA ligase. Involved in phylloquinone biosynthesis. Knock mutant is seedling lethal. O.I. C.G. H.G.
20.0 99.6 194.1 At1g01060 839341 LHY (LATE ELONGATED HYPOCOTYL) LHY encodes a myb-related putative transcription factor involved in circadian rhythm along with another myb transcription factor CCA1 O.I. C.G. H.G.
17.8 99.5 175.7 At1g08520 837374 CHLD F:magnesium chelatase activity, nucleoside-triphosphatase activity, nucleotide binding, ATP binding;P:chlorophyll biosynthetic process;C:magnesium chelatase complex, chloroplast;MOBFPVA O.I. C.G. H.G.
17.2 99.5 24.6 At4g38950 830050 kinesin motor family protein F:microtubule motor activity, ATP binding;P:microtubule-based process, microtubule-based movement;C:microtubule associated complex;MOPF O.I. C.G. H.G.
16.5 99.5 78.6 At3g59780 825147 - F:molecular_function unknown;P:biological_process unknown;C:nucleus, chloroplast;OBMFPV O.I. C.G. H.G.
15.7 99.5 231.4 At5g48490 834905 protease inhibitor/seed storage/lipid transfer protein (LTP) family protein F:lipid binding;P:lipid transport;C:endomembrane system;P O.I. C.G. H.G.
13.6 99.4 34.3 At3g13180 820508 NOL1/NOP2/sun family protein / antitermination NusB domain-containing protein F:RNA binding;P:regulation of transcription, DNA-dependent;C:chloroplast;BOMFAP O.I. C.G. H.G.
12.8 99.3 33.1 At4g23940 828494 FtsH protease, putative F:in 7 functions;P:proteolysis;C:chloroplast;OBMFPAV O.I. C.G. H.G.
12.7 99.3 40.1 At1g14030 837964 ribulose-1,5 bisphosphate carboxylase oxygenase large subunit N-methyltransferase, putative F:[ribulose-bisphosphate carboxylase]-lysine N-methyltransferase activity;P:unknown;C:chloroplast, chloroplast stroma;MPFO O.I. C.G. H.G.
11.8 99.3 158.6 At5g51720 835246 unknown protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast stroma, chloroplast;MPO O.I. C.G. H.G.
11.5 99.3 41.5 At5g16715 831533 EMB2247 (embryo defective 2247) F:valine-tRNA ligase activity, nucleotide binding, aminoacyl-tRNA ligase activity, ATP binding;P:embryonic development ending in seed dormancy, tRNA aminoacylation for protein translation;C:chloroplast stroma, chloroplast;OBMAFP O.I. C.G. H.G.
11.4 99.3 28.6 At2g38780 818460 unknown protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast;POBM O.I. C.G. H.G.
11.3 99.3 28.3 At3g13490 820551 OVA5 (OVULE ABORTION 5) Encodes a dual targeted lysyl-tRNA ligase that is found both in the mitochondrion and the chloroplast. Plants mutated in this gene exhibit an ovule abortion phenotype. O.I. C.G. H.G.
11.3 99.3 10.5 At5g60880 836209 unknown protein F:unknown;P:unknown;C:cellular_component unknown;OPMF O.I. C.G. H.G.
10.7 99.2 15.9 At5g24000 832465 unknown protein F:unknown;P:unknown;C:chloroplast;BOPA O.I. C.G. H.G.
10.4 99.2 72.0 At3g47295 823883 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P O.I. C.G. H.G.
10.4 99.2 44.1 At5g51100 835183 FSD2 (FE SUPEROXIDE DISMUTASE 2) Fe superoxide dismutase whose mRNA levels are increased in response to exposure to UV-B. O.I. C.G. H.G.
10.4 99.2 35.1 At1g64150 842719 unknown protein F:unknown;P:unknown;C:chloroplast, membrane;BOMFPA O.I. C.G. H.G.
10.3 99.2 99.2 At4g24750 828577 - F:molecular_function unknown;P:biological_process unknown;C:chloroplast;PBOA O.I. C.G. H.G.
10.3 99.2 60.2 At5g05740 830458 EGY2 S2P-like putative metalloprotease, also contain transmembrane helices near their C-termini and many of them, five of seven, contain a conserved zinc-binding motif HEXXH. Homolog of EGY1. Each of the EGY1 and EGY-like proteins share two additional highly conserved motifs, the previously reported NPDG motif (aa 442�454 in EGY1, Rudner et al., 1999) and a newly defined GNLR motif (aa 171�179 in EGY1). The GNLR motif is a novel signature motif unique to EGY1 and EGY-like proteins as well as other EGY1 orthologs found in cyanobacteria. O.I. C.G. H.G.
10.3 99.2 40.9 At3g52340 824399 SPP2 (SUCROSE-6F-PHOSPHATE PHOSPHOHYDROLASE 2) sucrose-phosphatase (SPP2) O.I. C.G. H.G.
10.2 99.2 64.8 At4g15110 827177 CYP97B3 member of CYP97B O.I. C.G. H.G.
10.2 99.2 22.4 At3g01490 821136 protein kinase, putative F:protein serine/threonine/tyrosine kinase activity, kinase activity;P:protein amino acid phosphorylation;C:cellular_component unknown;MPOBFVA O.I. C.G. H.G.
9.8 99.1 53.6 At5g17670 831633 hydrolase, acting on ester bonds F:hydrolase activity, acting on ester bonds;P:intracellular protein transport, GPI anchor metabolic process;C:chloroplast, chloroplast envelope;BOP O.I. C.G. H.G.
9.6 99.1 124.5 At2g47940 819406 DEGP2 Encodes DegP2 protease (DEGP2); nuclear gene for chloroplast product. O.I. C.G. H.G.
9.6 99.1 22.2 At2g45270 819135 glycoprotease M22 family protein F:endopeptidase activity, metalloendopeptidase activity, zinc ion binding;P:proteolysis;C:unknown;OBMFAP O.I. C.G. H.G.
9.5 99.1 125.0 At5g62790 836400 DXR (1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE) 1-Deoxy-d-xylulose 5-phosphate reductoisomerase (DXR) catalyzes the first committed step of the 2-C-methyl-d-erythritol 4-phosphate pathway for isoprenoid biosynthesis. In Arabidopsis, DXR is encoded by a single-copy gene. Arabidopsis DXR is targeted to plastids and localizes into chloroplasts of leaf cells. DXR knockout or strongly silenced lines have a seedling lethal, albino phenotype. Transgenic, partially silenced lines expressing 35S:DXR have a variegated phenotype. O.I. C.G. H.G.
9.5 99.1 46.0 At2g25840 817126 OVA4 (ovule abortion 4) F:nucleotide binding, aminoacyl-tRNA ligase activity, tryptophan-tRNA ligase activity, ATP binding;P:N-terminal protein myristoylation, ovule development, tRNA aminoacylation for protein translation;C:mitochondrion, chloroplast;OBMFAP O.I. C.G. H.G.
9.5 99.1 37.0 At3g01370 821288 ATCFM2 (CRM FAMILY MEMBER 2) Encodes a protein containing a CRM domain that is involved in group I and group II intron splicing. O.I. C.G. H.G.
9.5 99.1 28.6 At1g73830 843719 BEE3 (BR ENHANCED EXPRESSION 3) F:transcription factor activity, DNA binding;P:regulation of transcription;C:nucleus;PFMBO O.I. C.G. H.G.
9.5 99.1 27.1 At2g40960 818696 nucleic acid binding F:nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MPFO O.I. C.G. H.G.
9.2 99.1 66.4 At5g22640 832327 emb1211 (embryo defective 1211) F:molecular_function unknown;P:embryonic development ending in seed dormancy;C:chloroplast thylakoid membrane, chloroplast, chloroplast envelope;OMFBPVA O.I. C.G. H.G.
9.1 99.1 75.7 At3g02380 821298 COL2 (constans-like 2) homologous to the flowering-time gene CONSTANS (CO) encoding zinc-finger proteins O.I. C.G. H.G.
9.1 99.1 75.6 At3g25660 822154 glutamyl-tRNA(Gln) amidotransferase, putative F:glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity, carbon-nitrogen ligase activity, with glutamine as amido-N-donor;P:translation;C:chloroplast, chloroplast stroma;OBFMPA O.I. C.G. H.G.
9.1 99.1 71.9 At2g46830 819296 CCA1 (CIRCADIAN CLOCK ASSOCIATED 1) Encodes a transcriptional repressor that performs overlapping functions with LHY in a regulatory feedback loop that is closely associated with the circadian oscillator of Arabidopsis. Binds to the evening element in the promoter of TOC1 and represses TOC1 transcription. CCA1 and LHY colocalize in the nucleus and form heterodimers in vivo. CCA1 and LHY function synergistically in regulating circadian rhythms of Arabidopsis. O.I. C.G. H.G.
9.0 99.1 28.9 At1g09420 837465 G6PD4 (GLUCOSE-6-PHOSPHATE DEHYDROGENASE 4) Encodes a protein similar to glucose-6-phosphate dehydrogenase but, based on amino acid differences in the active site and lack of activity, does not encode a functional G6PDH. The amino acid sequence for the consensus sequence of the G6PDH active site (DHYLGKE) differs in three places in this protein. gc exon splice site at 20574 is based on protein alignment, and is not confirmed experimentally. O.I. C.G. H.G.
9.0 99.1 25.4 At1g26180 839159 unknown protein F:unknown;P:unknown;C:unknown;BOP O.I. C.G. H.G.
8.9 99.0 197.8 At4g12420 826851 SKU5 Encodes a protein of unknown function involved in directed root tip growth. It is a member of 19-member gene family and is distantly related structurally to the multiple-copper oxidases ascorbate oxidase and laccase, though it lacks the copper-binding domains. The protein is glycosylated and GPI-anchored. It is localized to the plasma membrane and the cell wall. The gene is expressed most strongly in expanding tissues. O.I. C.G. H.G.
8.9 99.0 44.7 At1g17650 838342 GLYR2 (GLYOXYLATE REDUCTASE 2) Glyoxylate reductase located in chloroplasts. O.I. C.G. H.G.
8.9 99.0 21.3 At2g26550 817196 HO2 (HEME OXYGENASE 2) encodes a heme oxygenase that catalyzes the oxidation of heme to biliverdin IXalpha, CO and Fe(2+), a committed step in the biosynthesis of the phytochrome chromophore phytochromobilin. O.I. C.G. H.G.
8.8 99.0 40.7 At1g71720 843502 S1 RNA-binding domain-containing protein F:RNA binding;P:unknown;C:chloroplast;BOPMAF O.I. C.G. H.G.
8.8 99.0 19.6 At3g15030 820732 TCP4 (TCP family transcription factor 4) Arabidopsis thaliana TCP family transcription factor. Regulated by miR319. Involved in heterchronic regulation of leaf differentiation. O.I. C.G. H.G.
8.7 99.0 69.0 At1g70940 843432 PIN3 (PIN-FORMED 3) A regulator of auxin efflux and involved in differential growth. PIN3 is expressed in gravity-sensing tissues, with PIN3 protein accumulating predominantly at the lateral cell surface. PIN3 localizes to the plasma membrane and to vesicles. In roots, PIN3 is expressed without pronounced polarity in tiers two and three of the columella cells, at the basal side of vascular cells, and to the lateral side of pericycle cells of the elongation zone. PIN3 overexpression inhibits root cell growth. Protein phosphorylation plays a role in PIN3 trafficking to the plasma membrane. O.I. C.G. H.G.
8.7 99.0 36.1 At1g75100 843847 JAC1 (J-DOMAIN PROTEIN REQUIRED FOR CHLOROPLAST ACCUMULATION RESPONSE 1) Contains a J-domain at the C-terminus which is similar to the J-domain of auxilin, a clathrin-uncoating factor in cow, yeast and worm. Arabidopsis contains 6 other proteins similar to auxilin. Expressed in leaves and stems, but not in roots. Localized in the cytoplasm. Required for the chloroplast accumulation response, but not for the avoidance response. No molecular function known. O.I. C.G. H.G.
8.7 99.0 13.9 At4g15430 827214 - F:molecular_function unknown;P:biological_process unknown;C:endomembrane system, membrane;FPMO O.I. C.G. H.G.
8.6 99.0 34.7 At3g28460 822476 unknown protein F:unknown;P:biological_process unknown;C:chloroplast;BOPA O.I. C.G. H.G.
8.6 99.0 21.3 At5g64580 836579 AAA-type ATPase family protein F:nucleoside-triphosphatase activity, metalloendopeptidase activity, nucleotide binding, zinc ion binding, ATP binding;P:unknown;C:chloroplast, chloroplast envelope;BOMFPAV O.I. C.G. H.G.

Std2 GX	%ile	Std GX	Gene ID	Repr. ID	Gene name	Functional description	O.I.	C.G.	H.G.
111.8	99.9	101.1	At5g59330	836052	lipid binding	F:lipid binding;P:lipid transport;C:endomembrane system	O.I.	C.G.	H.G.
71.1	99.9	23.6	At5g60780	836199	ATNRT2.3	member of High affinity nitrate transporter family	O.I.	C.G.	H.G.
59.6	99.8	42.1	At2g14580	815945	ATPRB1	pathogenesis related protein, encodes a basic PR1-like protein. Expresses in flowers, roots, and not in leaves and responses to ethylene and methyl jasmonate. Salicylic acid represses gene expression.	O.I.	C.G.	H.G.
33.9	99.7	16.7	At1g11300	837672	ATP binding / carbohydrate binding / kinase/ protein kinase/ protein serine/threonine kinase/ protein tyrosine kinase/ sugar binding	F:in 7 functions;P:protein amino acid phosphorylation, recognition of pollen;C:endomembrane system;MPOBFVA	O.I.	C.G.	H.G.
33.4	99.7	56.1	At4g33000	829437	CBL10 (CALCINEURIN B-LIKE 10)	Encodes a member of the calcineurin B-like calcium sensor gene family. Mediates salt tolerance by regulating ion homeostasis in Arabidopsis.	O.I.	C.G.	H.G.
28.9	99.7	18.7	At4g34650	829617	SQS2 (SQUALENE SYNTHASE 2)	Encodes a protein with similarity to squalene synthase which catalyzes the first committed step in sterol biosynthesis. To date no experimental evidence exists that SQS2 functions as a squalene synthase and some experiments indicate it does not have this function.	O.I.	C.G.	H.G.
24.9	99.6	136.1	At3g54500	824615	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOFB	O.I.	C.G.	H.G.
24.5	99.6	29.8	At3g63510	825526	FAD binding / catalytic/ tRNA dihydrouridine synthase	F:tRNA dihydrouridine synthase activity, FAD binding, catalytic activity;P:regulation of nitrogen utilization, tRNA processing, oxidation reduction, metabolic process;C:unknown;BOMFPA	O.I.	C.G.	H.G.
23.9	99.6	48.9	At5g64050	836526	ERS (GLUTAMATE TRNA SYNTHETASE)	Glutamate-tRNA ligase. Targeted to mitochondria and chloroplast. Its inactivation causes developmental arrest of chloroplasts and mitochondria in Nicotiana benthamiana.	O.I.	C.G.	H.G.
23.2	99.6	36.7	At4g30720	829195	electron carrier/ oxidoreductase	F:electron carrier activity, oxidoreductase activity;P:unknown;C:chloroplast;BOAPF	O.I.	C.G.	H.G.
21.4	99.6	54.8	At5g10690	830933	pentatricopeptide (PPR) repeat-containing protein / CBS domain-containing protein	F:unknown;P:biological_process unknown;C:chloroplast;POMFBA	O.I.	C.G.	H.G.
20.6	99.6	67.4	At1g12860	837843	SCRM2 (SCREAM 2)	Encodes ICE2 (Inducer of CBF Expression 2), a transcription factor of the bHLH family that participates in the response to deep freezing through the cold acclimation-dependent pathway. Overexpression of ICE2 results in increased tolerance to deep freezing stress after cold acclimation.	O.I.	C.G.	H.G.
20.6	99.6	66.5	At1g30520	839932	AAE14 (Acyl-Activating Enzyme 14)	Encodes a chloroplast O-succinylbenzoyl-CoA ligase. Involved in phylloquinone biosynthesis. Knock mutant is seedling lethal.	O.I.	C.G.	H.G.
20.0	99.6	194.1	At1g01060	839341	LHY (LATE ELONGATED HYPOCOTYL)	LHY encodes a myb-related putative transcription factor involved in circadian rhythm along with another myb transcription factor CCA1	O.I.	C.G.	H.G.
17.8	99.5	175.7	At1g08520	837374	CHLD	F:magnesium chelatase activity, nucleoside-triphosphatase activity, nucleotide binding, ATP binding;P:chlorophyll biosynthetic process;C:magnesium chelatase complex, chloroplast;MOBFPVA	O.I.	C.G.	H.G.
17.2	99.5	24.6	At4g38950	830050	kinesin motor family protein	F:microtubule motor activity, ATP binding;P:microtubule-based process, microtubule-based movement;C:microtubule associated complex;MOPF	O.I.	C.G.	H.G.
16.5	99.5	78.6	At3g59780	825147	-	F:molecular_function unknown;P:biological_process unknown;C:nucleus, chloroplast;OBMFPV	O.I.	C.G.	H.G.
15.7	99.5	231.4	At5g48490	834905	protease inhibitor/seed storage/lipid transfer protein (LTP) family protein	F:lipid binding;P:lipid transport;C:endomembrane system;P	O.I.	C.G.	H.G.
13.6	99.4	34.3	At3g13180	820508	NOL1/NOP2/sun family protein / antitermination NusB domain-containing protein	F:RNA binding;P:regulation of transcription, DNA-dependent;C:chloroplast;BOMFAP	O.I.	C.G.	H.G.
12.8	99.3	33.1	At4g23940	828494	FtsH protease, putative	F:in 7 functions;P:proteolysis;C:chloroplast;OBMFPAV	O.I.	C.G.	H.G.
12.7	99.3	40.1	At1g14030	837964	ribulose-1,5 bisphosphate carboxylase oxygenase large subunit N-methyltransferase, putative	F:[ribulose-bisphosphate carboxylase]-lysine N-methyltransferase activity;P:unknown;C:chloroplast, chloroplast stroma;MPFO	O.I.	C.G.	H.G.
11.8	99.3	158.6	At5g51720	835246	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast stroma, chloroplast;MPO	O.I.	C.G.	H.G.
11.5	99.3	41.5	At5g16715	831533	EMB2247 (embryo defective 2247)	F:valine-tRNA ligase activity, nucleotide binding, aminoacyl-tRNA ligase activity, ATP binding;P:embryonic development ending in seed dormancy, tRNA aminoacylation for protein translation;C:chloroplast stroma, chloroplast;OBMAFP	O.I.	C.G.	H.G.
11.4	99.3	28.6	At2g38780	818460	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;POBM	O.I.	C.G.	H.G.
11.3	99.3	28.3	At3g13490	820551	OVA5 (OVULE ABORTION 5)	Encodes a dual targeted lysyl-tRNA ligase that is found both in the mitochondrion and the chloroplast. Plants mutated in this gene exhibit an ovule abortion phenotype.	O.I.	C.G.	H.G.
11.3	99.3	10.5	At5g60880	836209	unknown protein	F:unknown;P:unknown;C:cellular_component unknown;OPMF	O.I.	C.G.	H.G.
10.7	99.2	15.9	At5g24000	832465	unknown protein	F:unknown;P:unknown;C:chloroplast;BOPA	O.I.	C.G.	H.G.
10.4	99.2	72.0	At3g47295	823883	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	C.G.	H.G.
10.4	99.2	44.1	At5g51100	835183	FSD2 (FE SUPEROXIDE DISMUTASE 2)	Fe superoxide dismutase whose mRNA levels are increased in response to exposure to UV-B.	O.I.	C.G.	H.G.
10.4	99.2	35.1	At1g64150	842719	unknown protein	F:unknown;P:unknown;C:chloroplast, membrane;BOMFPA	O.I.	C.G.	H.G.
10.3	99.2	99.2	At4g24750	828577	-	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;PBOA	O.I.	C.G.	H.G.
10.3	99.2	60.2	At5g05740	830458	EGY2	S2P-like putative metalloprotease, also contain transmembrane helices near their C-termini and many of them, five of seven, contain a conserved zinc-binding motif HEXXH. Homolog of EGY1. Each of the EGY1 and EGY-like proteins share two additional highly conserved motifs, the previously reported NPDG motif (aa 442�454 in EGY1, Rudner et al., 1999) and a newly defined GNLR motif (aa 171�179 in EGY1). The GNLR motif is a novel signature motif unique to EGY1 and EGY-like proteins as well as other EGY1 orthologs found in cyanobacteria.	O.I.	C.G.	H.G.
10.3	99.2	40.9	At3g52340	824399	SPP2 (SUCROSE-6F-PHOSPHATE PHOSPHOHYDROLASE 2)	sucrose-phosphatase (SPP2)	O.I.	C.G.	H.G.
10.2	99.2	64.8	At4g15110	827177	CYP97B3	member of CYP97B	O.I.	C.G.	H.G.
10.2	99.2	22.4	At3g01490	821136	protein kinase, putative	F:protein serine/threonine/tyrosine kinase activity, kinase activity;P:protein amino acid phosphorylation;C:cellular_component unknown;MPOBFVA	O.I.	C.G.	H.G.
9.8	99.1	53.6	At5g17670	831633	hydrolase, acting on ester bonds	F:hydrolase activity, acting on ester bonds;P:intracellular protein transport, GPI anchor metabolic process;C:chloroplast, chloroplast envelope;BOP	O.I.	C.G.	H.G.
9.6	99.1	124.5	At2g47940	819406	DEGP2	Encodes DegP2 protease (DEGP2); nuclear gene for chloroplast product.	O.I.	C.G.	H.G.
9.6	99.1	22.2	At2g45270	819135	glycoprotease M22 family protein	F:endopeptidase activity, metalloendopeptidase activity, zinc ion binding;P:proteolysis;C:unknown;OBMFAP	O.I.	C.G.	H.G.
9.5	99.1	125.0	At5g62790	836400	DXR (1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE)	1-Deoxy-d-xylulose 5-phosphate reductoisomerase (DXR) catalyzes the first committed step of the 2-C-methyl-d-erythritol 4-phosphate pathway for isoprenoid biosynthesis. In Arabidopsis, DXR is encoded by a single-copy gene. Arabidopsis DXR is targeted to plastids and localizes into chloroplasts of leaf cells. DXR knockout or strongly silenced lines have a seedling lethal, albino phenotype. Transgenic, partially silenced lines expressing 35S:DXR have a variegated phenotype.	O.I.	C.G.	H.G.
9.5	99.1	46.0	At2g25840	817126	OVA4 (ovule abortion 4)	F:nucleotide binding, aminoacyl-tRNA ligase activity, tryptophan-tRNA ligase activity, ATP binding;P:N-terminal protein myristoylation, ovule development, tRNA aminoacylation for protein translation;C:mitochondrion, chloroplast;OBMFAP	O.I.	C.G.	H.G.
9.5	99.1	37.0	At3g01370	821288	ATCFM2 (CRM FAMILY MEMBER 2)	Encodes a protein containing a CRM domain that is involved in group I and group II intron splicing.	O.I.	C.G.	H.G.
9.5	99.1	28.6	At1g73830	843719	BEE3 (BR ENHANCED EXPRESSION 3)	F:transcription factor activity, DNA binding;P:regulation of transcription;C:nucleus;PFMBO	O.I.	C.G.	H.G.
9.5	99.1	27.1	At2g40960	818696	nucleic acid binding	F:nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MPFO	O.I.	C.G.	H.G.
9.2	99.1	66.4	At5g22640	832327	emb1211 (embryo defective 1211)	F:molecular_function unknown;P:embryonic development ending in seed dormancy;C:chloroplast thylakoid membrane, chloroplast, chloroplast envelope;OMFBPVA	O.I.	C.G.	H.G.
9.1	99.1	75.7	At3g02380	821298	COL2 (constans-like 2)	homologous to the flowering-time gene CONSTANS (CO) encoding zinc-finger proteins	O.I.	C.G.	H.G.
9.1	99.1	75.6	At3g25660	822154	glutamyl-tRNA(Gln) amidotransferase, putative	F:glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity, carbon-nitrogen ligase activity, with glutamine as amido-N-donor;P:translation;C:chloroplast, chloroplast stroma;OBFMPA	O.I.	C.G.	H.G.
9.1	99.1	71.9	At2g46830	819296	CCA1 (CIRCADIAN CLOCK ASSOCIATED 1)	Encodes a transcriptional repressor that performs overlapping functions with LHY in a regulatory feedback loop that is closely associated with the circadian oscillator of Arabidopsis. Binds to the evening element in the promoter of TOC1 and represses TOC1 transcription. CCA1 and LHY colocalize in the nucleus and form heterodimers in vivo. CCA1 and LHY function synergistically in regulating circadian rhythms of Arabidopsis.	O.I.	C.G.	H.G.
9.0	99.1	28.9	At1g09420	837465	G6PD4 (GLUCOSE-6-PHOSPHATE DEHYDROGENASE 4)	Encodes a protein similar to glucose-6-phosphate dehydrogenase but, based on amino acid differences in the active site and lack of activity, does not encode a functional G6PDH. The amino acid sequence for the consensus sequence of the G6PDH active site (DHYLGKE) differs in three places in this protein. gc exon splice site at 20574 is based on protein alignment, and is not confirmed experimentally.	O.I.	C.G.	H.G.
9.0	99.1	25.4	At1g26180	839159	unknown protein	F:unknown;P:unknown;C:unknown;BOP	O.I.	C.G.	H.G.
8.9	99.0	197.8	At4g12420	826851	SKU5	Encodes a protein of unknown function involved in directed root tip growth. It is a member of 19-member gene family and is distantly related structurally to the multiple-copper oxidases ascorbate oxidase and laccase, though it lacks the copper-binding domains. The protein is glycosylated and GPI-anchored. It is localized to the plasma membrane and the cell wall. The gene is expressed most strongly in expanding tissues.	O.I.	C.G.	H.G.
8.9	99.0	44.7	At1g17650	838342	GLYR2 (GLYOXYLATE REDUCTASE 2)	Glyoxylate reductase located in chloroplasts.	O.I.	C.G.	H.G.
8.9	99.0	21.3	At2g26550	817196	HO2 (HEME OXYGENASE 2)	encodes a heme oxygenase that catalyzes the oxidation of heme to biliverdin IXalpha, CO and Fe(2+), a committed step in the biosynthesis of the phytochrome chromophore phytochromobilin.	O.I.	C.G.	H.G.
8.8	99.0	40.7	At1g71720	843502	S1 RNA-binding domain-containing protein	F:RNA binding;P:unknown;C:chloroplast;BOPMAF	O.I.	C.G.	H.G.
8.8	99.0	19.6	At3g15030	820732	TCP4 (TCP family transcription factor 4)	Arabidopsis thaliana TCP family transcription factor. Regulated by miR319. Involved in heterchronic regulation of leaf differentiation.	O.I.	C.G.	H.G.
8.7	99.0	69.0	At1g70940	843432	PIN3 (PIN-FORMED 3)	A regulator of auxin efflux and involved in differential growth. PIN3 is expressed in gravity-sensing tissues, with PIN3 protein accumulating predominantly at the lateral cell surface. PIN3 localizes to the plasma membrane and to vesicles. In roots, PIN3 is expressed without pronounced polarity in tiers two and three of the columella cells, at the basal side of vascular cells, and to the lateral side of pericycle cells of the elongation zone. PIN3 overexpression inhibits root cell growth. Protein phosphorylation plays a role in PIN3 trafficking to the plasma membrane.	O.I.	C.G.	H.G.
8.7	99.0	36.1	At1g75100	843847	JAC1 (J-DOMAIN PROTEIN REQUIRED FOR CHLOROPLAST ACCUMULATION RESPONSE 1)	Contains a J-domain at the C-terminus which is similar to the J-domain of auxilin, a clathrin-uncoating factor in cow, yeast and worm. Arabidopsis contains 6 other proteins similar to auxilin. Expressed in leaves and stems, but not in roots. Localized in the cytoplasm. Required for the chloroplast accumulation response, but not for the avoidance response. No molecular function known.	O.I.	C.G.	H.G.
8.7	99.0	13.9	At4g15430	827214	-	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system, membrane;FPMO	O.I.	C.G.	H.G.
8.6	99.0	34.7	At3g28460	822476	unknown protein	F:unknown;P:biological_process unknown;C:chloroplast;BOPA	O.I.	C.G.	H.G.
8.6	99.0	21.3	At5g64580	836579	AAA-type ATPase family protein	F:nucleoside-triphosphatase activity, metalloendopeptidase activity, nucleotide binding, zinc ion binding, ATP binding;P:unknown;C:chloroplast, chloroplast envelope;BOMFPAV	O.I.	C.G.	H.G.

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GSM ID	GSM318627
Assay name	Apex_BLS>>TCP4_14DAS_2
GSE experiment	GSE12691: Knockdown and overexpression of CIN-TCP genes

Microarray experiments to specifically-expressed genes

GSM ID GSM318627 Assay name Apex_BLS>>TCP4_14DAS_2 GSE experiment GSE12691: Knockdown and overexpression of CIN-TCP genes

GSM ID GSM318627

Assay name Apex_BLS>>TCP4_14DAS_2

GSE experiment GSE12691: Knockdown and overexpression of CIN-TCP genes