====Fixing references between polypeptides and genes==== Adding TrnR as a synonym for 11562.PRE-TRNA-ARG-1-MONOMER (ORF) Adding TrnA as a synonym for 11562.PRE-TRNA-ARG-2-MONOMER (ORF) Adding TrnR as a synonym for 11562.PRE-TRNA-ARG-3-MONOMER (ORF) Adding TrnN as a synonym for 11562.PRE-TRNA-ASN-1-MONOMER (ORF) Adding TrnN as a synonym for 11562.PRE-TRNA-ASN-2-MONOMER (ORF) Adding TrnD as a synonym for 11562.PRE-TRNA-ASP-1-MONOMER (ORF) Adding TrnC as a synonym for 11562.PRE-TRNA-CYS-1-MONOMER (ORF) Adding TrnE as a synonym for 11562.PRE-TRNA-GLU-1-MONOMER (ORF) Adding TrnG as a synonym for 11562.PRE-TRNA-GLY-1-MONOMER (ORF) Adding TrnH as a synonym for 11562.PRE-TRNA-HIS-1-MONOMER (ORF) Adding TrnH as a synonym for 11562.PRE-TRNA-HIS-2-MONOMER (ORF) Adding TrnL as a synonym for 11562.PRE-TRNA-LEU-1-MONOMER (ORF) Adding TrnL as a synonym for 11562.PRE-TRNA-LEU-2-MONOMER (ORF) Adding TrnL as a synonym for 11562.PRE-TRNA-LEU-3-MONOMER (ORF) Adding TrnM as a synonym for 11562.PRE-TRNA-MET-2-MONOMER (ORF) Adding TrnI as a synonym for 11562.PRE-TRNA-MET-3-MONOMER (ORF) Adding TrnF as a synonym for 11562.PRE-TRNA-PHE-1-MONOMER (ORF) Adding TrnP as a synonym for 11562.PRE-TRNA-PRO-1-MONOMER (ORF) Adding TrnS as a synonym for 11562.PRE-TRNA-SER-1-MONOMER (ORF) Adding TrnS as a synonym for 11562.PRE-TRNA-SER-2-MONOMER (ORF) Adding TrnS as a synonym for 11562.PRE-TRNA-SER-3-MONOMER (ORF) Adding TrnT as a synonym for 11562.PRE-TRNA-THR-1-MONOMER (ORF) Adding TrnT as a synonym for 11562.PRE-TRNA-THR-2-MONOMER (ORF) Adding TrnW as a synonym for 11562.PRE-TRNA-TRP-1-MONOMER (ORF) Adding TrnY as a synonym for 11562.PRE-TRNA-TYR-1-MONOMER (ORF) Adding TrnV as a synonym for 11562.PRE-TRNA-VAL-1-MONOMER (ORF) Adding TrnV as a synonym for 11562.PRE-TRNA-VAL-2-MONOMER (ORF) Adding TrnR as a synonym for 11706.PRE-TRNA-ARG-1-MONOMER (ORF) Adding TrnC as a synonym for 11706.PRE-TRNA-CYS-2-MONOMER (triplet codon-amino acid adaptor activity) Adding TrnQ as a synonym for 11706.PRE-TRNA-GLN-1-MONOMER (triplet codon-amino acid adaptor activity) Adding TrnE as a synonym for 11706.PRE-TRNA-GLU-1-MONOMER (triplet codon-amino acid adaptor activity) Adding TrnH as a synonym for 11706.PRE-TRNA-HIS-1-MONOMER (triplet codon-amino acid adaptor activity) Adding TrnM as a synonym for 11706.PRE-TRNA-MET-1-MONOMER (triplet codon-amino acid adaptor activity) Adding TrnM as a synonym for 11706.PRE-TRNA-MET-2-MONOMER (triplet codon-amino acid adaptor activity) Adding TrnP as a synonym for 11706.PRE-TRNA-PHE-1-MONOMER (triplet codon-amino acid adaptor activity) Adding TrnP as a synonym for 11706.PRE-TRNA-PRO-1-MONOMER (triplet codon-amino acid adaptor activity) Adding TrnS as a synonym for 11706.PRE-TRNA-SER-1-MONOMER (triplet codon-amino acid adaptor activity) Adding TrnS as a synonym for 11706.PRE-TRNA-SER-2-MONOMER (triplet codon-amino acid adaptor activity) Adding TrnS as a synonym for 11706.PRE-TRNA-SER-3-MONOMER (triplet codon-amino acid adaptor activity) Adding TrnW as a synonym for 11706.PRE-TRNA-TRP-1-MONOMER (triplet codon-amino acid adaptor activity) Adding TrnY as a synonym for 11706.PRE-TRNA-TYR-1-MONOMER (triplet codon-amino acid adaptor activity) Adding Tdr as a synonym for LOC_OS02G02820.1-MONOMER (helix-loop-helix DNA-binding domain containing protein, expressed//anther development//DNA binding//transcription regulator activity//anther morphogenesis//regulation of transcription//tapetal cell differentiation) Adding Lop as a synonym for LOC_OS03G11600.1-MONOMER (YABBY domain containing protein, putative, expressed//cell differentiation//meristem determinacy//carpel development//leaf development) Adding Nsr as a synonym for LOC_OS03G11614.1-MONOMER (OsMADS1 - MADS-box family gene with MIKCc type-box, expressed//DNA binding//regulation of transcription, DNA-dependent//regulation of cell proliferation//maintenance of floral meristem identity//specification of floral organ identity//flower development//protein binding//cell fate specification//sequence-specific DNA binding//transcription factor activity//regulation of cell differentiation) Adding SodA as a synonym for LOC_OS03G22810.1-MONOMER (copper/zinc superoxide dismutase, putative, expressed//superoxide metabolic process//response to superoxide//copper, zinc superoxide dismutase) Adding Slr as a synonym for LOC_OS03G49990.1-MONOMER (GRAS family transcription factor domain containing protein, expressed//regulation of gene expression, epigenetic) Adding Kao as a synonym for LOC_OS06G02019.1-MONOMER (cytochrome P450, putative, expressed//electron transport chain//gibberellin metabolic process//monooxygenase activity//secretion by cell) Adding Nop as a synonym for LOC_OS06G40570.1-MONOMER (GRAM and C2 domains containing protein, putative, expressed//calcium-mediated signaling//phosphoinositide-mediated signaling//pollen maturation) Adding SdhA as a synonym for LOC_OS07G04240.1-MONOMER (succinate dehydrogenase flavoprotein subunit,mitochondrial precursor, putative, expressed//tricarboxylic acid cycle//disulfide oxidoreductase activity//oxidoreductase activity, acting on the CH-CH group of donors//electron transport chain//mitochondrial electron transport, succinate to ubiquinone//FAD binding//oxidoreductase activity//succinate dehydrogenase (ubiquinone)) Adding Fzp as a synonym for LOC_OS07G47330.1-MONOMER (AP2 domain containing protein, expressed//regulation of transcription, DNA-dependent//multicellular organismal development//transcription factor activity) Adding Fgr as a synonym for LOC_OS08G32870.1-MONOMER (aldehyde dehydrogenase, putative, expressed//response to stress//phenylpropanoid metabolic process//glycine betaine biosynthetic process//1-pyrroline-5-carboxylate dehydrogenase//glutamate-5-semialdehyde dehydrogenase//aldehyde dehydrogenase) Adding Scl as a synonym for LOC_OS08G32870.1-MONOMER (aldehyde dehydrogenase, putative, expressed//response to stress//phenylpropanoid metabolic process//glycine betaine biosynthetic process//1-pyrroline-5-carboxylate dehydrogenase//glutamate-5-semialdehyde dehydrogenase//aldehyde dehydrogenase) Adding SdhB as a synonym for LOC_OS09G20440.1-MONOMER (succinate dehydrogenase and fumarate reductase iron-sulfur protein//tricarboxylic acid cycle//electron carrier activity//electron transport chain//iron ion binding//oxidoreductase activity//succinate dehydrogenase) Adding Sgr as a synonym for LOC_OS09G36200.1-MONOMER (senescence-inducible chloroplast stay-green protein 1, putative, expressed//PSII associated light-harvesting complex II catabolic process//chlorophyll catabolic process) Adding Rrp as a synonym for LOC_OS09G36680.1-MONOMER (ribonuclease T2 family domain containing protein, expressed//RNA binding//secretion by cell) Adding AtpG as a synonym for LOC_OS10G17280.1-MONOMER (ATP synthase gamma chain, putative, expressed//ATP synthesis coupled proton transport//hydrogen transport) Adding CcmC as a synonym for LOC_OSM1G00200.1-MONOMER (Cytochrome c biogenesis C//heme transporter activity//cytochrome complex assembly//respiratory chain complex IV assembly//heme transport//protein complex assembly) Adding Cob as a synonym for LOC_OSM1G00480.1-MONOMER (Apocytochrome b//electron transport chain//mitochondrial electron transport, ubiquinol to cytochrome c//oxidoreductase activity) Adding CytB as a synonym for LOC_OSM1G00480.1-MONOMER (Apocytochrome b//electron transport chain//mitochondrial electron transport, ubiquinol to cytochrome c//oxidoreductase activity) Adding AtpA as a synonym for LOC_OSM1G00580.1-MONOMER (ATP synthase F0 subunit 1//ATP biosynthetic process//ATP synthesis coupled proton transport//ATP binding//hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances) Adding CcmB as a synonym for LOC_OSM1G00620.1-MONOMER (Cytochrome c biogenesis B//heme transporter activity//cytochrome complex assembly//heme transport//secretion by cell) Adding PsbA as a synonym for LOC_OSP1G00110.1-MONOMER (photosystem II protein D1//electron transport chain//photosynthesis) Adding MatK as a synonym for LOC_OSP1G00120.1-MONOMER (maturase//RNA splicing) Adding PsbK as a synonym for LOC_OSP1G00140.1-MONOMER (photosystem II protein K//secretion by cell//photosynthesis) Adding PsbI as a synonym for LOC_OSP1G00150.1-MONOMER (photosystem II protein I//secretion by cell//photosynthesis) Adding PsbD as a synonym for LOC_OSP1G00170.1-MONOMER (photosystem II protein D2//electron transport chain//photosynthesis) Adding PsbC as a synonym for LOC_OSP1G00180.1-MONOMER (photosystem II 44 kDa protein//electron transport chain) Adding PsbM as a synonym for LOC_OSP1G00220.1-MONOMER (photosystem II M protein) Adding RpoB as a synonym for LOC_OSP1G00240.1-MONOMER (RNA polymerase beta chain//DNA binding//transcription) Adding AtpI as a synonym for LOC_OSP1G00280.1-MONOMER (ATP synthase CF0 A chain) Adding AtpH as a synonym for LOC_OSP1G00290.1-MONOMER (ATP synthase CF0 C chain//ATP synthesis coupled proton transport//hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances) Adding AtpF as a synonym for LOC_OSP1G00300.1-MONOMER (ATP synthase CF0 B chain//hydrogen transport//secretion by cell) Adding AtpA as a synonym for LOC_OSP1G00310.1-MONOMER (ATP synthase CF1 alpha chain//ATP biosynthetic process//ATP binding) Adding PsaB as a synonym for LOC_OSP1G00330.1-MONOMER (photosystem I P700 apoprotein A2//photosynthesis) Adding PsaA as a synonym for LOC_OSP1G00340.1-MONOMER (photosystem I P700 apoprotein A1//photosynthesis) Adding NdhJ as a synonym for LOC_OSP1G00370.1-MONOMER (NADH dehydrogenase subunit J//mitochondrial electron transport, NADH to ubiquinone) Adding NdhK as a synonym for LOC_OSP1G00380.1-MONOMER (NADH dehydrogenase subunit K) Adding PsbG as a synonym for LOC_OSP1G00380.1-MONOMER (NADH dehydrogenase subunit K) Adding NdhC as a synonym for LOC_OSP1G00390.1-MONOMER (NADH dehydrogenase subunit 3//mitochondrial electron transport, NADH to ubiquinone//secretion by cell) Adding AtpE as a synonym for LOC_OSP1G00400.1-MONOMER (ATP synthase CF1 epsilon chain//ATP biosynthetic process//electron carrier activity) Adding AtpB as a synonym for LOC_OSP1G00410.1-MONOMER (ATP synthase CF1 beta chain//ATP biosynthetic process//ATP binding) Adding RbcL as a synonym for LOC_OSP1G00420.1-MONOMER (ribulose 1,5-bisphosphate carboxylase/oxygenase large chain//carbon utilization by fixation of carbon dioxide) Adding RbcA as a synonym for LOC_OSP1G00420.1-MONOMER (ribulose 1,5-bisphosphate carboxylase/oxygenase large chain//carbon utilization by fixation of carbon dioxide) Adding AccD as a synonym for LOC_OSP1G00440.1-MONOMER (acetyl-CoA carboxylase beta subunit) Adding PsaI as a synonym for LOC_OSP1G00450.1-MONOMER (photosystem I subunit VIII//secretion by cell//photosynthesis) Adding CemA as a synonym for LOC_OSP1G00470.1-MONOMER (ORF230//molecular_function//secretion by cell) Adding PetA as a synonym for LOC_OSP1G00480.1-MONOMER (cytochrome f//electron carrier activity//electron transport chain) Adding PsbJ as a synonym for LOC_OSP1G00490.1-MONOMER (photosystem II protein J//secretion by cell) Adding PsbL as a synonym for LOC_OSP1G00500.1-MONOMER (photosystem II protein L) Adding PsbF as a synonym for LOC_OSP1G00510.1-MONOMER (cytochrome b559 beta chain//heme binding//photosynthesis, light reaction//photosynthetic electron transport chain) Adding PsbE as a synonym for LOC_OSP1G00520.1-MONOMER (cytochrome b559 alpha chain//heme binding//photosynthesis, light reaction//photosynthetic electron transport chain) Adding PetL as a synonym for LOC_OSP1G00530.1-MONOMER (cytochrome b6/f complex subunit VI//secretion by cell) Adding PetE as a synonym for LOC_OSP1G00540.1-MONOMER (cytochrome b6/f complex subunit V//electron transport chain) Adding PetG as a synonym for LOC_OSP1G00540.1-MONOMER (cytochrome b6/f complex subunit V//electron transport chain) Adding PsaJ as a synonym for LOC_OSP1G00550.1-MONOMER (photosystem I subunit IX//secretion by cell) Adding ClpP as a synonym for LOC_OSP1G00590.1-MONOMER (ATP-dependent Clp protease proteolytic subunit//serine-type endopeptidase activity//proteolysis) Adding PsbB as a synonym for LOC_OSP1G00600.1-MONOMER (photosystem II 47 kDa protein//electron transport chain) Adding PsbT as a synonym for LOC_OSP1G00610.1-MONOMER (photosystem II protein T//photosynthesis) Adding PsbH as a synonym for LOC_OSP1G00620.1-MONOMER (photosystem II phosphoprotein) Adding PsbN as a synonym for LOC_OSP1G00630.1-MONOMER (photosystem II protein N//photosynthesis) Adding PetB as a synonym for LOC_OSP1G00640.1-MONOMER (cytochrome b6//electron transport chain) Adding PetD as a synonym for LOC_OSP1G00650.1-MONOMER (cytochrome b6/f complex subunit IV//electron transport chain) Adding RpoA as a synonym for LOC_OSP1G00660.1-MONOMER (RNA polymerase alpha chain//DNA binding//transcription) Adding SecX as a synonym for LOC_OSP1G00680.1-MONOMER (ribosomal protein L36) Adding InfA as a synonym for LOC_OSP1G00690.1-MONOMER (translation initiation factor 1//translational initiation//RNA binding//translation initiation factor activity) Adding NdhF as a synonym for LOC_OSP1G00880.1-MONOMER (NADH dehydrogenase subunit 5//mitochondrial electron transport, NADH to ubiquinone//secretion by cell) Adding CcsA as a synonym for LOC_OSP1G00900.1-MONOMER (cytochrome c biogenesis protein//respiratory chain complex IV assembly//protein complex assembly//secretion by cell) Adding NdhD as a synonym for LOC_OSP1G00910.1-MONOMER (NADH dehydrogenase subunit 4//mitochondrial electron transport, NADH to ubiquinone//secretion by cell) Adding PsaC as a synonym for LOC_OSP1G00920.1-MONOMER (photosystem I subunit VII//electron carrier activity//electron transport chain//iron ion binding) Adding FrxA as a synonym for LOC_OSP1G00920.1-MONOMER (photosystem I subunit VII//electron carrier activity//electron transport chain//iron ion binding) Adding NdhE as a synonym for LOC_OSP1G00930.1-MONOMER (NADH dehydrogenase subunit 4L//mitochondrial electron transport, NADH to ubiquinone//secretion by cell) Adding NdhG as a synonym for LOC_OSP1G00940.1-MONOMER (NADH dehydrogenase subunit 6//mitochondrial electron transport, NADH to ubiquinone//secretion by cell) Adding NdhI as a synonym for LOC_OSP1G00950.1-MONOMER (NADH dehydrogenase subunit I//electron transport chain) Adding FrxB as a synonym for LOC_OSP1G00950.1-MONOMER (NADH dehydrogenase subunit I//electron transport chain) Adding NdhA as a synonym for LOC_OSP1G00960.1-MONOMER (NADH dehydrogenase subunit 1//electron transport chain) Adding NdhH as a synonym for LOC_OSP1G00970.1-MONOMER (NADH dehydrogenase subunit 7//electron transport chain) ==Done fixing references between polypeptides and genes== The report from this consistency checker run can be found at C:\Documents and Settings\dharmawd\Application Data\ptools-local\pgdbs\user\ricecyc\2.0.1.1.3\reports\consistency-checker-report-2010-02-28_08-59-59.txt