Metabolic pathway to genes

Genes assigned in the pathway

Query pathway ID 03018
Pathway name RNA degradation
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
At1g02080839244transcriptional regulator-relatedF:transcription regulator activity;P:unknown;C:membrane;MOFBPO.I.H.G.
At1g03330839526small nuclear ribonucleoprotein D, putative / snRNP core SM-like protein, putative / U6 snRNA-associated Sm-like protein, putativeF:molecular_function unknown;P:unknown;C:small nucleolar ribonucleoprotein complex, nucleus;MFOPAO.I.H.G.
At1g03360839521ATRRP4 (ARABIDOPSIS THALIANA RIBOSOMAL RNA PROCESSING 4)F:RNA binding, exonuclease activity;P:unknown;C:mitochondrion;OMAFPO.I.H.G.
At1g03905839376ABC transporter family proteinF:nucleoside-triphosphatase activity, ATPase activity, nucleotide binding, ATP binding;P:unknown;C:unknown;BOAMFPVO.I.H.G.
At1g07705837284transcription regulatorF:transcription regulator activity;P:regulation of transcription;C:nucleus, chloroplast;MOBFPVO.I.H.G.
At1g17980838378nucleotidyltransferase family proteinF:protein binding, nucleotidyltransferase activity;P:RNA polyadenylation;C:nucleus;MFOPBO.I.H.G.
At1g21190838714small nuclear ribonucleoprotein, putative / snRNP, putative / Sm protein, putativeF:molecular_function unknown;P:biological_process unknown;C:small nucleolar ribonucleoprotein complex, nucleus;MAOFPO.I.H.G.
At1g59760842269ATP-dependent RNA helicase, putativeF:hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, helicase activity, ATP binding, ATP-dependent helicase activity, nucleic acid binding;P:N-terminal protein myristoylation;C:unknown;OBMFAPVO.I.H.G.
At1g600808423033' exoribonuclease family domain 1-containing proteinF:3'-5'-exoribonuclease activity, RNA binding;P:RNA processing;C:cellular_component unknown;MAOFPBO.I.H.G.
At1g65700842881small nuclear ribonucleoprotein, putative / snRNP, putative / Sm protein, putativeF:molecular_function unknown;P:biological_process unknown;C:small nucleolar ribonucleoprotein complex, nucleus;MFOPO.I.H.G.
At1g74030843741enolase, putativeF:phosphopyruvate hydratase activity;P:in 12 processes;C:phosphopyruvate hydratase complex, chloroplast;OBMFAPO.I.H.G.
At1g75660843900XRN3Encodes a protein with similarity to yeast 5'-3'exonucleases and can functionally complement the yeast mutations. In Arabidopsis XRN3 acts as a suppressor of posttranscriptional gene silencing. Mutants accumulate excised miRNA products suggesting that XRN3 is involved in degradation of these products.O.I.H.G.
At1g76630843996tetratricopeptide repeat (TPR)-containing proteinF:binding;P:biological_process unknown;C:cellular_component unknown;BOMAFPO.I.H.G.
At1g76860844021small nuclear ribonucleoprotein, putative / snRNP, putative / Sm protein, putativeF:molecular_function unknown;P:biological_process unknown;C:small nucleolar ribonucleoprotein complex, nucleus;MAOFPO.I.H.G.
At1g79090844250unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPOBO.I.H.G.
At1g80780844417CCR4-NOT transcription complex protein, putativeF:ribonuclease activity, nucleic acid binding;P:RNA modification;C:nucleus;PMOFO.I.H.G.
At2g03870814913small nuclear ribonucleoprotein, putative / snRNP, putative / Sm protein, putativeF:molecular_function unknown;P:unknown;C:small nucleolar ribonucleoprotein complex, nucleus;MFAOPO.I.H.G.
At2g17510816257EMB2763 (EMBRYO DEFECTIVE 2763)F:ribonuclease activity, RNA binding;P:unknown;C:unknown;BOMFPAVO.I.H.G.
At2g25355817074exonuclease-relatedF:RNA binding;P:N-terminal protein myristoylation;C:cellular_component unknown;MFOPAO.I.H.G.
At2g33210817883HSP60-2 (HEAT SHOCK PROTEIN 60-2)F:ATP binding;P:response to salt stress, inflammatory response;C:mitochondrion, plasma membrane, chloroplast;BOMFPAVO.I.H.G.
At2g36530818226LOS2Involved in light-dependent cold tolerance and encodes an enolase. Protein is tyrosine-phosphorylated and its phosphorylation state is modulated in response to ABA in Arabidopsis thaliana seeds.O.I.H.G.
At2g43810818985small nuclear ribonucleoprotein F, putative / U6 snRNA-associated Sm-like protein, putative / Sm protein F, putativeF:molecular_function unknown;P:unknown;C:small nucleolar ribonucleoprotein complex, nucleus;MAFOPO.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.
At3g077508199663' exoribonuclease family domain 1-containing proteinF:3'-5'-exoribonuclease activity, RNA binding;P:RNA processing;C:cellular_component unknown;MOFAPBO.I.H.G.
At3g13300820530VCS (VARICOSE)Encodes VCS (VARICOSE). Involved in mRNA decapping. VCS forms a mRNA decapping complex with DCP1 (At1g08370) and DCP2 (At5g13570). Unlike DCP2, VCS itself does not have mRNA decapping activity in vitro. DCP1, DCP2 and VCS colocalize in cytoplasmic loci, which are putative Arabidopsis mRNA processing bodies. Null mutants of DCP1, DCP2, and VCS accumulate capped mRNAs with a reduced degradation rate. These mutants also share a similar lethal phenotype at the seedling cotyledon stage, with disorganized veins, swollen root hairs, and altered epidermal cell morphology. VCS is also required for leaf development.O.I.H.G.
At3g14080820624small nuclear ribonucleoprotein, putative / snRNP, putative / Sm protein, putativeF:molecular_function unknown;P:unknown;C:small nucleolar ribonucleoprotein complex, nucleus;MFPOAO.I.H.G.
At3g20800821628rcd1-like cell differentiation protein, putativeF:molecular_function unknown;P:multicellular organismal development;C:cellular_component unknown;MFOPO.I.H.G.
At3g23990821983HSP60 (HEAT SHOCK PROTEIN 60)mitochondrial chaperonin HSP. assist in rapid assembly of the oligomeric protein structures in the mitochondria.O.I.H.G.
At3g45630823705RNA recognition motif (RRM)-containing proteinF:protein binding, RNA binding, zinc ion binding, nucleotide binding, nucleic acid binding;P:unknown;C:unknown;OBMFPVO.I.H.G.
At3g462108237663' exoribonuclease family domain 1-containing proteinF:3'-5'-exoribonuclease activity, RNA binding;P:RNA processing;C:cellular_component unknown;BOMAFPO.I.H.G.
At3g46960823849ATP binding / ATP-dependent helicase/ helicase/ hydrolase, acting on acid anhydrides, in phosphorus-containing anhydrides / nucleic acid bindingF:hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, helicase activity, ATP-dependent helicase activity, ATP binding, nucleic acid binding;P:biological_process unknown;C:vacuole;OBMFAPVO.I.H.G.
At3g58560825025endonuclease/exonuclease/phosphatase family proteinF:hydrolase activity;P:biological_process unknown;C:cellular_component unknown;MPOFBO.I.H.G.
At3g59810825150small nuclear ribonucleoprotein F, putative / U6 snRNA-associated Sm-like protein, putative / Sm protein F, putativeF:molecular_function unknown;P:unknown;C:small nucleolar ribonucleoprotein complex, nucleus;AMFOPO.I.H.G.
At3g61240825296DEAD/DEAH box helicase, putative (RH12)F:helicase activity, ATP-dependent helicase activity, ATP binding, nucleic acid binding;P:unknown;C:unknown;OBMFPAVO.I.H.G.
At3g61620825335RRP41exonuclease RRP41 (RRP41)O.I.H.G.
At4g14990827158unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOFO.I.H.G.
At4g29830829105VIP3 (vernalization independence 3)The protein is composed of repeats of WD motif which is involved in protein complex formation. The gene is involved in flower timing and flower development. This gene is predicted to encode a protein with a DWD motif. It can bind to DDB1a in Y2H assays, and DDB1b in co-IP assays, and may be involved in the formation of a CUL4-based E3 ubiquitin ligase. Loss of gene function leads to a redistribution of H3K4me3 and K3K36me2 modifications within genes but not a change in the overall abundance of these modifications within chromatin.O.I.H.G.
At4g37910829947mtHsc70-1 (mitochondrial heat shock protein 70-1)F:ATP binding;P:protein folding, response to cadmium ion, response to salt stress, response to heat;C:mitochondrion, cell wall, plasma membrane, mitochondrial matrix;OBMFPVAO.I.H.G.
At5g10960830963CCR4-NOT transcription complex protein, putativeF:ribonuclease activity, nucleic acid binding;P:RNA modification;C:nucleus;PMOFO.I.H.G.
At5g13570831201DCP2 (DECAPPING 2)Encodes DCP2 with mRNA decapping activity. DCP2 forms a mRNA decapping complex with DCP1 (At1g08370) and VCS (VARICOSE) (At3g13300). Recombinant DCP2 is enzymatically active in vitro, generating from capped mRNAs m7GDP, and 5’-phosphorylated mRNAs. DCP1, DCP2 and VCS colocalize in cytoplasmic loci, which are putative Arabidopsis mRNA processing bodies. Null mutants of DCP1, DCP2, and VCS accumulate capped mRNAs with a reduced degradation rate. These mutants also share a similar lethal phenotype at the seedling cotyledon stage, with disorganized veins, swollen root hairs, and altered epidermal cell morphology. The protein was shown by immunoprecipitation not to interact with DCP1.O.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.
At5g18230831941transcription regulator NOT2/NOT3/NOT5 family proteinF:transcription regulator activity;P:negative regulation of transcription, regulation of transcription;C:nucleus;MOFBPVAO.I.H.G.
At5g27720832834emb1644 (embryo defective 1644)F:molecular_function unknown;P:embryonic development ending in seed dormancy;C:small nucleolar ribonucleoprotein complex, nucleus;MFOPBVO.I.H.G.
At5g35430833507bindingF:binding;P:biological_process unknown;C:cellular_component unknown;MPOBFO.I.H.G.
At5g359108335773'-5' exonuclease domain-containing protein / helicase and RNase D C-terminal domain-containing protein / HRDC domain-containing proteinF:3'-5' exonuclease activity, nucleic acid binding;P:nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;C:intracellular;BOMFPO.I.H.G.
At5g38890833880exoribonuclease-relatedF:RNA binding;P:biological_process unknown;C:cellular_component unknown;FMAOPO.I.H.G.
At5g48870834945SAD1 (SUPERSENSITIVE TO ABA AND DROUGHT 1)SAD1 encodes a polypeptide similar to multifunctional Sm-like snRNP proteins that are required for mRNA splicing, export, and degradation. Mutation in this gene increases plant sensitivity to drought stress and ABA in seed germination, root growth, and the expression of some stress-responsive genes.O.I.H.G.
At5g59460836065scarecrow-like transcription factor 11 (SCL11)F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPO.I.H.G.

Comparison with co-expressed genes



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