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["Additional Table 3.  Orthologous Arabidopsis genes and a description of their expression profile from Birnbaum et al. [15]"]
["Operon ID","score","evalue","Arabidopsis ID","*cluster ID from Birnbaum et al. (2002)","*localized expression domains","NR Annotation","AthAnno"]
["MZ00019538",432,1e-121,"At5g24530.1",6,"all zones peaking in lateral root cap stage 3","Putative flavanone 3-hydroxylase [Oryza sativa (japonica cultivar-group)]","\"oxidoreductase, 2OG-Fe(II) oxygenase family protein similar to flavanone 3-hydroxylase [Persea americana][GI:727410]; contains PF03171 2OG-Fe(II) oxygenase superfamily domain  \""]
["MZ00025623",386,1e-107,"At5g02230.2",6,"all zones peaking in lateral root cap stage 3","catalytic/ hydrolase [Arabidopsis thaliana]","haloacid dehalogenase-like hydrolase family protein contains InterPro accession IPR005834: Haloacid dehalogenase-like hydrolase"]
["MZ00014257",649,0,"At1g27680.1",8,"all zones stage 1","ADP-glucose pyrophosphorylase [Zea mays]","glucose-1-phosphate adenylyltransferase large subunit 2 (APL2) / ADP-glucose pyrophosphorylase identical to SP|P55230"]
["MZ00015371",161,9e-40,"At3g15790.1",8,"all zones stage 1","methyl binding domain protein MBD109 [Zea mays]","methyl-CpG-binding domain-containing protein contains Pfam profile PF01429: Methyl-CpG binding domain"]
["MZ00018836",295,4e-80,"At5g47240.1",8,"all zones stage 1","hydrolase [Arabidopsis thaliana]","MutT/nudix family protein similar to SP|P53370 Nucleoside diphosphate-linked moiety X motif 6 {Homo sapiens}; contains Pfam profile PF00293: NUDIX domain"]
["MZ00027605",276,1e-74,"At3g60360.1",8,"all zones stage 1","putative CGI-94 protein [Oryza sativa (japonica cultivar-group)]","expressed protein"]
["MZ00029210",410,1e-114,"At4g38810.2",8,"all zones stage 1","putative calcium-binding protein [Oryza sativa (japonica cultivar-group)]","calcium-binding EF hand family protein contains INTERPRO:IPR002048 calcium-binding EF-hand domain"]
["MZ00050206",450,1e-127,"At4g11640.1",8,"all zones stage 1","putative serine/threonine dehydratase [Sorghum bicolor]","\"serine racemase, putative similar to serine racemase [Mus musculus] GI:6448865; contains Pfam profile PF00291: Pyridoxal-phosphate dependent enzyme  \""]
["MZ00027530",178,8e-45,"At4g40060.1",7,"all zones stage 3","PREDICTED OJ1595_D08.21 gene product [Oryza sativa (japonica cultivar-group)]","homeobox-leucine zipper protein 16 (HB-16) / HD-ZIP transcription factor 16 identical to homeodomain leucine-zipper protein ATHB-16 (GP:5668909|) {Arabidopsis thaliana}"]
["MZ00029080",192,3e-49,"At1g08500.1",7,"all zones stage 3","copper ion binding / electron transporter [Arab...","plastocyanin-like domain-containing protein"]
["MZ00036008",395,1e-110,"At5g10770.1",7,"all zones stage 3","putative nucleoid DNA-binding protein cnd41 [Oryza sativa (japonica cultivar-group)]","\"chloroplast nucleoid DNA-binding protein, putative similar to CND41, chloroplast nucleoid DNA binding protein [Nicotiana tabacum] GI:2541876; contains Pfam profile PF00026: Eukaryotic aspartyl protease \""]
["MZ00010122",264,9e-71,"At1g56010.2",null,"stage1 and 3","putative NAC domain protein NAC1 [Oryza sativa (japonica cultivar-group)]","transcription activator NAC1 (NAC1) contains Pfam PF02365: No apical meristem (NAM) domain; identical to NAC1 GB:AAF21437 GI:6649236 from [Arabidopsis thaliana]"]
["MZ00028553",735,0,"At3g07130.1",null,"epidermis and stele","putative phytase [Oryza sativa (japonica cultivar-group)]","serine/threonine protein phosphatase family protein contains similarity to purple acid phosphatase [Arabidopsis thaliana] gi|20257489|gb|AAM15914"]
["MZ00014665",755,0,"At4g39660.1",4,"epidermis stage 2","alanine:glyoxylate aminotransferase 2 homolog [Arabidopsis thaliana]","\"alanine--glyoxylate aminotransferase, putative / beta-alanine-pyruvate aminotransferase, putative / AGT, putative similar to SP|Q64565 Alanine--glyoxylate aminotransferase 2, mitochon drial precursor (EC 2.6.1.44) (AGT 2) (Beta-alanine-pyruvate aminotransferase) {Rattus norvegicus}; contains Pfam profile PF00202: aminotransferase, class III\""]
["MZ00024840",403,1e-112,"At1g04020.2",4,"epidermis stage 2","putative protein (fragment) [Arabidopsis thaliana]","\"zinc finger (C3HC4-type RING finger) family protein / BRCT domain-containing protein contains Pfam domain, PF00533: BRCA1 C Terminus (BRCT) domain  \""]
["MZ00044305",624,1e-179,"At4g12910.1",5,"lateral root cap stage 1","serine carboxypeptidase i precursor [Oryza sativa (japonica cultivar-group)]","\"serine carboxypeptidase S10 family protein SERINE CARBOXYPEPTIDASE I PRECURSOR - Hordeum vulgare, SWall:CBP1_HORVU  \""]
["MZ00025001",620,1e-177,"At1g02260.1",null,"stage 2","Putative anion transporter [Oryza sativa]","\"transmembrane protein, putative similar to P protein (Melanocyte-specific transporter protein) (SP:Q04671) {Homo sapiens}; contains 8 transmembrane domains  \""]
["MZ00025596",649,0,"At3g55610.1",null,"stage 3","putative delta l pyrroline-5-carboxylate synthetase [Oryza sativa (japonica cultivar-group)]","delta 1-pyrroline-5-carboxylate synthetase B / P5CS B (P5CS2) identical to SP|P54888"]
["MZ00026815",217,1e-56,"At1g18970.1",null,"stage 3","putative oxalate oxidase [Oryza sativa (japonica cultivar-group)]","germin-like protein (GLP1) (GLP4) identical to germin-like protein subfamily T member 1 [SP|P92995]"]
["MZ00027872",392,1e-109,"At5g38710.1",null,"stage 1","\"proline oxidase, putative [Oryza sativa (japonica cultivar-group)]\"","\"proline oxidase, putative / osmotic stress-responsive proline dehydrogenase, putative similar to proline oxidase, mitochondrial precursor (Osmotic stress- induced proline dehydrogenas e) [Arabidopsis tha liana] SWISS-PROT:P92983\""]
["MZ00026383",1341,0,"At4g02280.1",null,"stage 3 ","sucrose synthase 3 [Zea mays]","\"sucrose synthase, putative / sucrose-UDP glucosyltransferase, putative strong similarity to sucrose synthase GI:6682841 from [Citrus unshiu]  \""]
["MZ00043587",110,9e-25,"At5g22580.1",null,"stele and cortex, stages 1 and 2","COG1796: DNA polymerase IV (family X) [Burkho...","expressed protein"]
["MZ00018690",432,1e-121,"At5g51810.1",2,"stele and ground tissue stage 2","gibberellin 20-oxidase 1 [Lolium perenne]","\"gibberellin 20-oxidase, putative similar to gibberellin 20-oxidase GI:1109695, GI:9791186  \""]
["MZ00026366",248,5e-66,"At3g55120.1",2,"stele and ground tissue stage 2","chalcone flavonone isomerase [Zea mays]","chalcone-flavanone isomerase / chalcone isomerase (CHI) identical to SP|P41088"]
["MZ00041461",581,1e-166,"At5g46110.1",2,"stele and ground tissue stage 2","triose phosphate/phosphate translocator [Zea mays]","\"phosphate/triose-phosphate translocator, putative identical to phosphate/triose-phosphate translocator precursor [Arabidopsis thaliana] gi|3983125|gb|AAC83815; similar to triose phosp hate/phosphate tran slocator, chloroplast precursor (CTPT)[Cauliflower]{Brassica oleracea} SWISS-PROT:P52177\""]
["MZ00017681",191,4e-49,"At3g11660.1",3,"stele and ground tissue stage 3","\"Harpin-induced protein 1 (Hin1), putative [Oryza sativa (japonica cultivar-group)]\"","harpin-induced family protein / HIN1 family protein / harpin-responsive family protein similar to harpin-induced protein hin1 (GI:1619321) [Nicotiana tabacum]"]
["MZ00029319",143,2e-34,"At1g72830.1",null,"stele and lateral root cap","putative transcription factor [Oryza sativa (japonica cultivar-group)]","CCAAT-binding transcription factor (CBF-B/NF-YA) family protein contains Pfam profile: PF02045 CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B"]
["MZ00015895",184,4e-47,"At1g71050.1",1,"stele stage 3","farnesylated protein 3 [Hordeum vulgare subsp. vulgare]","heavy-metal-associated domain-containing protein / copper chaperone (CCH)-related low similarity to copper homeostasis factor [GI:3168840][PMID:9701579]; similar to farnesylated prote in ATFP7 [GI:409755 5]; contains heavy-metal-associated domain PF00403"]
["MZ00041440",139,3e-33,"At1g20440.1",1,"stele stage 3","dehydrin [Zea mays]","dehydrin (COR47) identical to dehydrin COR47 (Cold-induced COR47 protein) [Arabidopsis thaliana] SWISS-PROT:P31168"]
["MZ00046781",335,2e-92,"At1g71960.1",1,"stele stage 3","\"ABC transporter protein, putative [Oryza sativa (japonica cultivar-group)]\"","ABC transporter family protein similar to breast cancer resistance protein GB:AAC97367 from [Homo sapiens]"]
["MZ00000937",162,1e-40,"At2g14760.1",null,null,"transcription factor [Arabidopsis thaliana]","basic helix-loop-helix protein / bHLH protein contains Pfam profile PF00010: Helix-loop-helix DNA-binding domain; PMID: 12679534; putative bHLH084 transcription factor"]
["MZ00002621",473,1e-133,"At1g23070.1",null,null,"Hypothetical protein [Arabidopsis thaliana]","hypothetical protein contains Pfam profile PF03619: Domain of unknown function"]
["MZ00002722",451,1e-127,"At5g22500.1",null,null,"putative fatty acyl coA reductase [Oryza sativa (japonica cultivar-group)]","\"acyl CoA reductase, putative / male-sterility protein, putative similar to acyl CoA reductase [Simmondsia chinensis] GI:5020215; contains Pfam profile PF03015: Male sterility protein; identical to cDNA male sterility 2-like protein GI:1491614\""]
["MZ00003049",662,0,"At3g15130.1",null,null,"pentatricopeptide (PPR) repeat-containing protein-like [Oryza sativa (japonica cultivar-group)]","pentatricopeptide (PPR) repeat-containing protein contains INTERPRO:IPR002885 PPR repeats"]
["MZ00013901",135,3e-32,"At2g33830.2",null,null,"\"dormancy-associated protein, putative [Oryza sativa (japonica cultivar-group)]\"","dormancy/auxin associated family protein contains Pfam profile: PF05564 dormancy/auxin associated protein"]
["MZ00015060",2615,0,"At5g04140.1",null,null,"\"GLTB_MAIZE Ferredoxin-dependent glutamate synthase, chloroplast precursor (Fd-GOGAT) \"","glutamate synthase (GLU1) / ferredoxin-dependent glutamate synthase (Fd-GOGAT 1) identical to ferredoxin-dependent glutamate synthase precursor [Arabidopsis thaliana] GI:3869251"]
["MZ00015192",486,1e-137,"At1g14520.1",null,null,"putative myo-inositol oxygenase [Oryza sativa (japonica cultivar-group)]","oxygenase-related similar to myo-inositol oxygenase [Sus scrofa] gi|17432544|gb|AAL39076"]
["MZ00015328",212,7e-55,"At1g72410.1",null,null,"COP1-interacting protein 7 (CIP7)-like [Oryza sativa (japonica cultivar-group)]","COP1-interacting protein-related similar to COP1-Interacting ProteinI 7 (CIP7) [Arabidopsis thaliana] GI:3327870"]
["MZ00015405",701,0,"At2g21520.1",null,null,"putative SEC14 protein [Oryza sativa (japonica cultivar-group)]","\"SEC14 cytosolic factor, putative / phosphoglyceride transfer protein, putative contains Pfam PF00650 : CRAL/TRIO domain; contains Pfam PF03765 : CRAL/TRIO, N-terminus; similar to phos phatidylinositol tr ansfer-like protein IV (GI:14486707) [Lotus japonicus]\""]
["MZ00015682",236,5e-63,"At1g43710.1",null,null,"putative phosphoethanolamine N-methyltransferase [Zea mays]","serine decarboxylase identical to serine decarboxylase [Arabidopsis thaliana] GI:15011302; contains Pfam profile PF00282: Pyridoxal-dependent decarboxylase conserved domain"]
["MZ00016125",437,1e-122,"At1g17550.1",null,null,"protein phosphatase 2C-like protein [Oryza sativa (japonica cultivar-group)]","protein phosphatase 2C-related / PP2C-related similar to protein phosphatase 2C GI:3242077 from (Arabidopsis thaliana)"]
["MZ00016532",328,6e-90,"At2g19810.1",null,null,"putative zinc finger transcription factor [Oryza sativa (japonica cultivar-group)]","\"zinc finger (CCCH-type) family protein contains Pfam domain, PF00642: Zinc finger C-x8-C-x5-C-x3-H type (and similar)  \""]
["MZ00016959",200,1e-51,"At5g58720.1",null,null,"putative PRLI-interacting factor N [Oryza sativa (japonica cultivar-group)]","\"PRLI-interacting factor, putative similar to PRLI-interacting factor N [Arabidopsis thaliana] GI:11139276; contains Pfam profile PF01713: Smr domain  \""]
["MZ00018962",389,1e-108,"At4g16440.1",null,null,"putative hydrogenase [Oryza sativa]","\"iron hydrogenase family protein contains Pfam profiles: PF02906 Iron only hydrogenase large subunit, C-terminal domain, PF02256 Iron hydrogenase small subunit  \""]
["MZ00019671",239,3e-63,"At3g05330.1",null,null,"microtubule-binding protein TANGLED1 [Zea mays]","\"cyclin family low similarity to microtubule-binding protein TANGLED1 [Zea mays] GI:11228986; contains Pfam profile PF00134: Cyclin, N-terminal domain  \""]
["MZ00020555",735,0,"At5g24710.1",null,null,"WD-40 repeat family protein-like [Oryza sativa (japonica cultivar-group)]","\"WD-40 repeat family protein contains 3 Pfam PF00400: WD domain, G-beta repeats;  \""]
["MZ00021761",228,6e-60,"At1g31490.1",null,null,"Transferase family [Oryza sativa (japonica cultivar-group)]","\"transferase family protein contains similarity to anthranilate N-hydroxycinnamoyl benzoyltransferase GI:3288180, GI:2239091 from (Dianthus caryophyllus); contains Pfam profile PF02458 transferase family \""]
["MZ00024656",344,7e-95,"At2g31820.1",null,null,"ankyrin-like protein [Oryza sativa (japonica cultivar-group)]","\"ankyrin repeat family protein contains ankyrin repeat domains, Pfam:PF00023  \""]
["MZ00026037",154,1e-37,"At1g60670.1",null,null,"Hypothetical protein [Arabidopsis thaliana]","\"expressed protein contains similarity to D-ala,D-ala ligase GI:6634594 from [Streptococcus pneumoniae]  \""]
["MZ00026698",268,3e-72,"At2g16390.1",null,null,"putative DNA repair protein [Oryza sativa (japonica cultivar-group)]","\"SNF2 domain-containing protein / helicase domain-containing protein low similarity to RAD54 [Drosophila melanogaster] GI:1765914; contains Pfam profiles PF00271: Helicase conserved C- terminal domain, PF 00176: SNF2 family N-terminal domain\""]
["MZ00026965",407,1e-113,"At5g10460.1",null,null,"Putative sulfate transporter [Oryza sativa (japonica cultivar-group)]","haloacid dehalogenase-like hydrolase family protein contains InterPro accession IPR005834: Haloacid dehalogenase-like hydrolase"]
["MZ00027281",159,4e-39,"At5g12840.4",null,null,"putative CCAAT-binding transcription factor [Oryza sativa (japonica cultivar-group)]","CCAAT-binding transcription factor (CBF-B/NF-YA) family protein contains Pfam profile: PF02045 CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B"]
["MZ00028118",499,1e-141,"At5g06950.2",null,null,"ocs-element binding factor 3.2 [Zea mays]","bZIP transcription factor HBP-1b homolog identical to transcription factor HBP-1b homolog SP:P43273 from [Arabidopsis thaliana]"]
["MZ00031101",322,2e-88,"At1g09140.1",null,null,"ASF/SF2-like pre-mRNA splicing factor SRP30' [Zea mays]","SF2/ASF-like splicing modulator (SRP30) nearly identical to SF2/ASF-like splicing modulator Srp30 [Arabidopsis thaliana] GI:4775270"]
["MZ00031309",501,1e-142,"At3g19990.1",null,null,"Acetylglutamate kinase [Anaeromyxobacter deha...","expressed protein"]
["MZ00041257",166,2e-41,"At1g26750.1",null,null,"Putative RNA-binding protein [Oryza sativa (japonica cultivar-group)]","expressed protein"]
["MZ00041649",310,9e-85,"At2g40300.1",null,null,"ferritin [Zea mays]","\"ferritin, putative similar to ferritin subunit cowpea2 precursor [Vigna unguiculata] GI:2970654; contains Pfam profile PF00210: Ferritin-like domain  \""]
["MZ00044009",241,1e-105,"At4g31340.1",null,null,"BRI1-KD interacting protein 129 [Oryza sativa (japonica cultivar-group)]","\"myosin heavy chain-related contains weak similarity to Myosin heavy chain, nonmuscle type A (Cellular myosin heavy chain, type A) (Nonmuscle myosin heavy chain-A) (NMMHC-A) (Swiss-Pro t:P35579) [Homo sap iens]\""]
["MZ00044292",169,8e-48,"At1g74410.1",null,null,"PREDICTED OJ1734_E02.21-2 gene product [Oryza sativa (japonica cultivar-group)]","\"zinc finger (C3HC4-type RING finger) family protein contains Pfam profile: PF00097 zinc finger, C3HC4 type (RING finger)  \""]
["MZ00050071",156,1e-38,"At4g34410.1",null,null,"ethylene-binding protein-like [Oryza sativa (japonica cultivar-group)]","\"AP2 domain-containing transcription factor, putative ethylene-responsive element binding protein homolog, Stylosanthes hamata, U91857  \""]
["MZ00052484",387,1e-108,"At2g34770.1",null,null,"putative fatty acid hydroxylase [Oryza sativa (japonica cultivar-group)]","fatty acid hydroxylase (FAH1) identical to fatty acid hydroxylase Fah1p GB:AF021804 GI:2736147 from [Arabidopsis thaliana]"]
[]
["*The cluster ID is taken from Birnbaum et al . [15]  The localized expression domain descriptions are from Birnbaum et al [15] whenever the cluster ID is present, otherwise they are interpreted from the Birnbaum data by the present authors."]