Metabolic pathway to genes

Genes assigned in the pathway

Query pathway ID 00240
Pathway name Pyrimidine metabolism
Organism Arabidopsis_thaliana
Database KEGG PATHWAY

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

Gene ID Repr. ID Gene name Functional description O.I. H.G. Other DB
At1g01210839481DNA-directed RNA polymerase III family proteinF:in 6 functions;P:RNA elongation, regulation of transcription, DNA-dependent, transcription, regulation of transcription;C:nucleus;MOFAPO.I.H.G.
At1g07980837313NF-YC10 (NUCLEAR FACTOR Y, SUBUNIT C10)F:transcription factor activity;P:regulation of transcription;C:intracellular, chloroplast;MFPOO.I.H.G.
At1g08260837346TIL1 (TILTED 1)Similar to POL2A, DNA polymerase epsilon catalytic subunit. Essential for Arabidopsis growth. Null homozygotes are embryo lethal, partial loss of function alleles show embryo patterning defects such as root pole displacement. Delayed progression through cell cycle results in embryos with smaller numbers of larger cells.O.I.H.G.
At1g09815837513POLD4 (POLYMERASE DELTA 4)F:DNA-directed DNA polymerase activity;P:DNA replication;C:nucleus;FMPOO.I.H.G.
At1g11475837690NRPB10Non-catalytic subunit common to nuclear DNA-dependent RNA polymerases II, IV and V; homologous to budding yeast RPB10.O.I.H.G.
At1g29900839868CARB (CARBAMOYL PHOSPHATE SYNTHETASE B)carbamoyl phosphate synthetase large chain (CARB) mRNA,O.I.H.G.
At1g29940839872NRPA2Encodes a subunit of RNA polymerase 1 (aka RNA polymerase A).O.I.H.G.
At1g30820839964CTP synthase, putative / UTP--ammonia ligase, putativeF:CTP synthase activity, catalytic activity;P:pyrimidine ribonucleotide metabolic process, pyrimidine nucleotide biosynthetic process;C:unknown;OBMFAPO.I.H.G.
At1g54250841866NRPB8AOne of two highly similar proteins that can serve as non-catalytic subunits of Nuclear RNA polymerases II and V; homologous to budding yeast RPB8. Probably redundant with At3g59600.O.I.H.G.
At1g61700842467DNA-directed RNA polymerase II, putative (RPB10)Protein of unknown function that is homologous to the At1g11475 locus that encodes a non-catalytic subunit common to nuclear DNA-dependent RNA polymerases II, IV and V. Homologous to budding yeast RPB10.O.I.H.G.
At1g67320843052DNA primase, large subunit familyF:DNA primase activity;P:DNA replication, synthesis of RNA primer;C:alpha DNA polymerase:primase complex;MFOPAO.I.H.G.
At1g67630843086POLA2 (DNA POLYMERASE ALPHA 2)F:DNA binding, DNA-directed DNA polymerase activity;P:DNA replication;C:mitochondrion;MFOPO.I.H.G.
At1g72880843619acid phosphatase survival protein SurE, putativeF:hydrolase activity, acid phosphatase activity;P:biological_process unknown;C:cellular_component unknown;BOAPFO.I.H.G.
At1g78650844201POLD3Similar to DNA polymerase delta (POLD3), which in other organism was shown to be involved in the elongation of DNA replication.O.I.H.G.
At2g04630815006NRPB6BOne of two highly similar proteins that can serve as a non-catalytic subunit of nuclear DNA-dependent RNA polymerases II and V; homologous to budding yeast RPB6 and the E. coli RNA polymerase omega subunit. Probably redundant with At5g51940.O.I.H.G.
At2g15430816035NRPB3Non-catalytic subunit of nuclear DNA-dependent RNA polymerases II, IV and V; homologous to budding yeast RPB3 and the E. coli RNA polymerase alpha subunit. A closely related paralog, encoded by At2g15400, can substitute for At2g15430 in the context of Pol V.O.I.H.G.
At2g16370816134THY-1 (THYMIDYLATE SYNTHASE 1)Encodes a bifunctional dihydrofolate reductase - thymidylate synthase gene. This is unique in Arabidopsis and protozoa. Other organisms have independent genes for this function.O.I.H.G.
At2g19570816476CDA1 (CYTIDINE DEAMINASE 1)Encodes a cytidine deaminase that deaminates cytidine and deoxycytidine and is competitively inhibited by cytosine-containing compounds.O.I.H.G.
At2g21790816715RNR1 (RIBONUCLEOTIDE REDUCTASE 1)encodes large subunit of ribonucleotide reductase involved in the production of deoxyribonucleoside triphosphates (dNTPs) for DNA replication and repairO.I.H.G.
At2g27120817254TIL2 (TILTED 2)Encodes a protein with similarity to DNA polymerase epsilon catalytic subunit. Based on yeast two hybrid analysis, not predicted to be a subunit of the DNA polymerase epsilon complex. No phenotype observed in homozygous mutant embryos or plants but in combination with TIL1-1/til1-1 heterozygotes arrest earlier than til1 homozygotes suggesting TIL2 functions redundantly with TIL1.O.I.H.G.
At2g29540817503ATRPC14 (RNA POLYMERASE 14 KDA SUBUNIT)RNA polymerase I(A) and III(C) 14 kDa subunitO.I.H.G.
At2g34890818054CTP synthase, putative / UTP--ammonia ligase, putativeF:CTP synthase activity, catalytic activity;P:pyrimidine ribonucleotide metabolic process, pyrimidine nucleotide biosynthetic process;C:endomembrane system;OBMFAPO.I.H.G.
At2g42120818812POLD2 (DNA POLYMERASE DELTA SMALL SUBUNIT)F:DNA binding, DNA-directed DNA polymerase activity;P:DNA replication;C:nucleus;OMFAPO.I.H.G.
At3g03710821181RIF10 (resistant to inhibition with FSM 10)Mutants impaired in the expression of this gene have been selected through their resistance to fosmidomycin, a strong inhibitor of DXR, an enzyme of the methylerythritol-dependent IPP biosynthesis pathway. The pathway enzymes were upregulated in the mutant seedlings.O.I.H.G.
At3g07800819971thymidine kinase, putativeF:thymidine kinase activity, ATP binding;P:pyrimidine deoxyribonucleoside interconversion, anaerobic respiration;C:cellular_component unknown;BOVMPAFO.I.H.G.
At3g12670820447emb2742 (embryo defective 2742)F:CTP synthase activity, catalytic activity;P:embryonic development ending in seed dormancy, response to cadmium ion;C:endomembrane system;OBMFAPO.I.H.G.
At3g16980820954NRPB9AOne of two highly similar, non-catalytic subunits common to nuclear DNA-directed RNA polymerases II, IV and V; homologous to budding yeast RPB9. Appears to be redundant with At4g16265O.I.H.G.
At3g18090821334NRPD2bEncodes a subunit of RNA polymerase IV (aka RNA polymerase D). NRPD2b is closely related to NRPD2a, but has lower levels of transcription and does not affect endogenous siRNA when mutated.O.I.H.G.
At3g18680821399aspartate/glutamate/uridylate kinase family proteinF:uridylate kinase activity, UMP kinase activity;P:amino acid biosynthetic process, 'de novo' pyrimidine base biosynthetic process, pyrimidine nucleotide biosynthetic process;C:chloroplast;BOAPFO.I.H.G.
At3g20330821577aspartate carabmoyltransferase, chloroplast / aspartate transcarbamylase / ATCase (PYRB)encodes aspartate carbamoyltransferase catalyzing the second step in the de novo pyrimidine ribonucleotide biosynthesisO.I.H.G.
At3g22320821801NRPB5Non-catalytic subunit common to DNA-dependent RNA polymerases I, II, III and IV; homologous to budding yeast RPB5.O.I.H.G.
At3g22900821862NRPD7Non-catalytic subunit specific to DNA-directed RNA polymerase IV; homologous to budding yeast RPB7O.I.H.G.
At3g23580821937RNR2A (RIBONUCLEOTIDE REDUCTASE 2A)Encodes one of the 3 ribonucleotide reductase (RNR) small subunit genes (RNR2A). Functionally redundant with the ribonucleotide reductase TSO2. mRNA was shown to specifically accumulate during the S-phase of the cell cycle in synchronized tobacco BY2 cells. Critical for cell cycle progression, DNA damage repair and plant development.O.I.H.G.
At3g27060822324TSO2 (TSO meaning 'ugly' in Chinese)Encodes one of the 3 ribonucleotide reductase (RNR) small subunit genes. TSO2 transcription occurs predominantly at the S-phase of the cell cycle and its expression pattern is consistent with its role in dNDP biosynthesis during DNA replication in actively dividing cells. Critical for cell cycle progression, DNA damage repair and plant development.O.I.H.G.
At3g27740822396CARA (CARBAMOYL PHOSPHATE SYNTHETASE A)carbamoyl phosphate synthetase small subunit mRNA (carA),O.I.H.G.
At3g46940823847deoxyuridine 5'-triphosphate nucleotidohydrolase familyF:hydrolase activity, dUTP diphosphatase activity;P:2'-deoxyribonucleotide metabolic process, dUTP metabolic process;C:cellular_component unknown;BOVMFPAO.I.H.G.
At3g48540824013cytidine/deoxycytidylate deaminase family proteinF:hydrolase activity, zinc ion binding, catalytic activity;P:biological_process unknown;C:endomembrane system;BOMFVAPO.I.H.G.
At3g52090824372NRPB11Non-catalytic subunit common to nuclear DNA-dependent RNA polymerases II, IV and V; homologous to budding yeast RPB11 and the E. oli RNA polymerase alpha subunit.O.I.H.G.
At3g53900824557uracil phosphoribosyltransferase, putative / UMP pyrophosphorylase, putative / UPRTase, putativeF:uracil phosphoribosyltransferase activity;P:uracil salvage, nucleoside metabolic process;C:chloroplast;BOFMPAO.I.H.G.
At3g54470824612uridine 5'-monophosphate synthase / UMP synthase (PYRE-F) (UMPS)encodes the bi-functional orotate phosphoribosyltransferase/orotidine-5'-phosphate decarboxylase catalyzing the fifth and sixth step in the de novo pyrimidine ribonucleotide biosynthesisO.I.H.G.
At3g57080824875NRPE5Non-catalytic subunit unique to Nuclear DNA-dependent RNA polymerase V; homologous to budding yeast RPB5.O.I.H.G.
At3g57660824935NRPA1Encodes a subunit of RNA polymerase I (aka RNA polymerase A).O.I.H.G.
At3g59600825129NRPB8BOne of two highly similar proteins that can serve as non-catalytic subunits of Nuclear RNA polymerases II, IV and V; homologous to budding yeast RPB8. Probably redundant with At1g54250.O.I.H.G.
At4g13720827006inosine triphosphate pyrophosphatase, putative / HAM1 family proteinF:hydrolase activity, pyrophosphatase activity;P:biological_process unknown;C:unknown;BOAMFPVO.I.H.G.
At4g14660827116NRPE7Non-catalytic subunit specific to DNA-directed RNA polymerase V; homologous to budding yeast RPB7O.I.H.G.
At4g14930827151acid phosphatase survival protein SurE, putativeF:hydrolase activity, acid phosphatase activity;P:biological_process unknown;C:cellular_component unknown;BOAFPO.I.H.G.
At4g21710828259NRPB2Encodes the unique second-largest subunit of DNA-dependent RNA polymerase II; the ortholog of budding yeast RPB2 and a homolog of the E. coli RNA polymerase beta subunit.O.I.H.G.
At4g22930828392PYR4 (PYRIMIDIN 4)Encodes dihydroorotase (PYR4).O.I.H.G.
At4g23900828490nucleoside diphosphate kinase 4 (NDK4)F:nucleoside diphosphate kinase activity, ATP binding;P:UTP biosynthetic process, GTP biosynthetic process, CTP biosynthetic process;C:mitochondrion;BOMPAFVO.I.H.G.
At4g35460829698NTRB (NADPH-DEPENDENT THIOREDOXIN REDUCTASE B)NADPH-dependent thioredoxin reductase 1 (NTR1. Similar to E.coli NTR and has conserved NADPH binding domains.O.I.H.G.
At4g35800829734NRPB1 (RNA POLYMERASE II LARGE SUBUNIT)Encodes the unique largest subunit of nuclear DNA-dependent RNA polymerase II; the ortholog of budding yeast RPB1 and a homolog of the E. coli RNA polymerase beta prime subunit.O.I.H.G.
At5g09920830853NRPB4Non-catalytic subunit specific to DNA-dependent RNA polymerase II; the ortholog of budding yeast RPB4)O.I.H.G.
At5g12200831093dihydropyrimidinase / DHPase / dihydropyrimidine amidohydrolase / hydantoinase (PYD2)F:hydrolase activity, hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, dihydropyrimidinase activity;P:unknown;C:endomembrane system;OBMAFPO.I.H.G.
At5g14580831309polyribonucleotide nucleotidyltransferase, putativeF:polyribonucleotide nucleotidyltransferase activity, 3'-5'-exoribonuclease activity, RNA binding, nucleic acid binding;P:mRNA catabolic process, RNA processing;C:unknown;BOMPAFO.I.H.G.
At5g22110832272ATDPB2 (ARABIDOPSIS THALIANA DNA POLYMERASE EPSILON SUBUNIT B2)Encodes a protein with similarity to DNA polymerase epsilon subunit B an essential gene that is required for DNA replication. Homozygous mutants are embryo lethal. Expressed in meristematic , rapidly dividing regions.O.I.H.G.
At5g23070832371thymidine kinase, putativeF:thymidine kinase activity, ATP binding;P:pyrimidine deoxyribonucleoside interconversion, anaerobic respiration;C:unknown;BOVMPAFO.I.H.G.
At5g23300832394PYRD (pyrimidine d)dihydroorotate dehydrogenase, catalyses fourth step of pyrimidine biosynthesisO.I.H.G.
At5g26667832710PYR6encodes a uridine 5'-monophosphate (UMP)/cytidine 5'-monophosphate (CMP) kinase.O.I.H.G.
At5g41010834103NRPB12Non-catalytic subunit common to nuclear DNA-dependent RNA polymerases II, IV and V; homologous to budding yeast RPB12.O.I.H.G.
At5g41880834193POLA3F:DNA primase activity;P:DNA replication, synthesis of RNA primer, DNA replication;C:unknown;MFOAPO.I.H.G.
At5g45140834550NRPC2Encodes a subunit of RNA polymerase III (aka RNA polymerase C).O.I.H.G.
At5g51940835269NRPB6AOne of two highly similar proteins that can serve as a non-catalytic subunit of nuclear DNA-dependent RNA polymerases II, IV and V; homologous to budding yeast RPB6 and the E. coli RNA polymerase omega subunit. Probably redundant with At2g04630.O.I.H.G.
At5g59180836036NRPB7Non-catalytic subunit specific to DNA-directed RNA polymerase II; the ortholog of budding yeast RPB7O.I.H.G.
At5g60040836126NRPC1Encodes a subunit of RNA polymerase III (aka RNA polymerase C).O.I.H.G.
At5g63310836451NDPK2 (NUCLEOSIDE DIPHOSPHATE KINASE 2)Maintains intracellular dNTP levels except ATP. Plays a role in response to oxidative stress and UV. Involved in phytochrome-mediated light signaling. Participates in auxin-regulated processes, partly through the modulation of auxin transport. H-bonding with His-197 inside the nucleotide-binding pocket is critical for NDPK2 functioning.O.I.H.G.
At5g63960836517EMB2780 (EMBRYO DEFECTIVE 2780)F:DNA-directed DNA polymerase activity, DNA binding, nucleotide binding, nucleic acid binding;P:nucleobase, nucleoside, nucleotide and nucleic acid metabolic process, DNA replication;C:nucleus;OVBMFAPO.I.H.G.
At5g64370836558BETA-UP (beta-ureidopropionase)PYD3 encodes a beta-ureidopropionase which, when expressed in E. coli, has been shown to convert beta-ureidopropionate into beta-alanine.O.I.H.G.
At5g67100836845ICU2 (INCURVATA2)Encodes the putative catalytic subunit of the DNA polymerase alpha. Interacts with genes involved in chromatin-mediated cellular memory. ICU2 genetically interacts with TERMINAL FLOWER2, the ortholog of HETEROCHROMATIN PROTEIN1 of animals and yeasts, and with the Polycomb group (PcG) gene CURLY LEAF. A number of regulatory genes were derepressed in the icu2-1 mutant, including genes associated with flowering time, floral meristem, and floral organ identity. Mutant has curled, involute leaves and causes early flowering.O.I.H.G.
Arthcp012O.I.H.G.
Arthcp013O.I.H.G.
Arthcp014O.I.H.G.
Arthcp055O.I.H.G.

Comparison with co-expressed genes



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