Basic Information
Gene Structure
Domain
Regulation&
Interaction
Annotation
Orthologus Group
Expresssion
Pathway
Basic Information
Gene ID
JreChr09G10047
View in Genome Browser
Position
chr9:10430829-10447768 (-)
16939bp
Gene Type
gene
Gene Description (Protein Product)
Cleavage and polyadenylation specificity factor
Organism
Juglans regia
Also AS AT1G30460

Gene Structure

upstream:
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Domain
Database EntryID E-Value Start end InterPro ID Description

Regulation&Interaction
Protein-protein interaction (PPI)
JreChr12G11608 cleavage stimulation factor
JreChr16G11120 Cleavage stimulation factor subunit
JreChr10G12015 pcf11p-similar protein 4

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Annotation

Orthologous Group
Orthologous ID Species Number All hits in PereRegDB Hits of this species Orthologous Detail

Expression Profile
DataSet Number of Samples expressed(TPM>1) Mean Min Max Standard deviation(SD) Coeffcient variation(CV)


Pathway
Go Pathway KEGG Pathway
GO Term Description GO Category
GO:0002682 regulation of immune system process BP
GO:0002684 positive regulation of immune system process BP
GO:0003674 molecular_function MF
GO:0003676 nucleic acid binding MF
GO:0003723 RNA binding MF
GO:0003729 mRNA binding MF
GO:0003824 catalytic activity MF
GO:0004518 nuclease activity MF
GO:0004519 endonuclease activity MF
GO:0004521 RNA endonuclease activity MF
GO:0004540 ribonuclease activity MF
GO:0005488 binding MF
GO:0005515 protein binding MF
GO:0005516 calmodulin binding MF
GO:0005575 cellular_component CC
GO:0005622 intracellular anatomical structure CC
GO:0005623 obsolete cell CC
GO:0005634 nucleus CC
GO:0005654 nucleoplasm CC
GO:0005737 cytoplasm CC
GO:0005847 mRNA cleavage and polyadenylation specificity factor complex CC
GO:0005849 mRNA cleavage factor complex CC
GO:0006139 nucleobase-containing compound metabolic process BP
GO:0006378 mRNA polyadenylation BP
GO:0006396 RNA processing BP
GO:0006397 mRNA processing BP
GO:0006725 cellular aromatic compound metabolic process BP
GO:0006807 nitrogen compound metabolic process BP
GO:0006950 response to stress BP
GO:0006979 response to oxidative stress BP
GO:0008150 biological_process BP
GO:0008152 metabolic process BP
GO:0009966 regulation of signal transduction BP
GO:0009987 cellular process BP
GO:0010363 regulation of plant-type hypersensitive response BP
GO:0010467 gene expression BP
GO:0010468 regulation of gene expression BP
GO:0010646 regulation of cell communication BP
GO:0010941 regulation of cell death BP
GO:0010942 positive regulation of cell death BP
GO:0016070 RNA metabolic process BP
GO:0016071 mRNA metabolic process BP
GO:0016787 hydrolase activity MF
GO:0016788 hydrolase activity, acting on ester bonds MF
GO:0019219 regulation of nucleobase-containing compound metabolic process BP
GO:0019222 regulation of metabolic process BP
GO:0023051 regulation of signaling BP
GO:0031123 RNA 3'-end processing BP
GO:0031124 mRNA 3'-end processing BP
GO:0031323 regulation of cellular metabolic process BP
GO:0031347 regulation of defense response BP
GO:0031349 positive regulation of defense response BP
GO:0031440 regulation of mRNA 3'-end processing BP
GO:0031974 membrane-enclosed lumen CC
GO:0031981 nuclear lumen CC
GO:0032991 protein-containing complex CC
GO:0034052 positive regulation of plant-type hypersensitive response BP
GO:0034641 cellular nitrogen compound metabolic process BP
GO:0043067 regulation of programmed cell death BP
GO:0043068 positive regulation of programmed cell death BP
GO:0043170 macromolecule metabolic process BP
GO:0043226 organelle CC
GO:0043227 membrane-bounded organelle CC
GO:0043229 intracellular organelle CC
GO:0043231 intracellular membrane-bounded organelle CC
GO:0043233 organelle lumen CC
GO:0043631 RNA polyadenylation BP
GO:0044237 cellular metabolic process BP
GO:0044238 primary metabolic process BP
GO:0044422 obsolete organelle part CC
GO:0044424 obsolete intracellular part CC
GO:0044428 obsolete nuclear part CC
GO:0044446 obsolete intracellular organelle part CC
GO:0044451 obsolete nucleoplasm part CC
GO:0044464 obsolete cell part CC
GO:0045088 regulation of innate immune response BP
GO:0045089 positive regulation of innate immune response BP
GO:0046483 heterocycle metabolic process BP
GO:0048518 positive regulation of biological process BP
GO:0048522 positive regulation of cellular process BP
GO:0048583 regulation of response to stimulus BP
GO:0048584 positive regulation of response to stimulus BP
GO:0050684 regulation of mRNA processing BP
GO:0050776 regulation of immune response BP
GO:0050778 positive regulation of immune response BP
GO:0050789 regulation of biological process BP
GO:0050794 regulation of cellular process BP
GO:0050896 response to stimulus BP
GO:0051171 regulation of nitrogen compound metabolic process BP
GO:0051252 regulation of RNA metabolic process BP
GO:0060255 regulation of macromolecule metabolic process BP
GO:0065007 biological regulation BP
GO:0070013 intracellular organelle lumen CC
GO:0071704 organic substance metabolic process BP
GO:0080090 regulation of primary metabolic process BP
GO:0080134 regulation of response to stress BP
GO:0080135 regulation of cellular response to stress BP
GO:0090304 nucleic acid metabolic process BP
GO:0090305 nucleic acid phosphodiester bond hydrolysis BP
GO:0090501 RNA phosphodiester bond hydrolysis BP
GO:0090502 RNA phosphodiester bond hydrolysis, endonucleolytic BP
GO:0097159 organic cyclic compound binding MF
GO:0140098 catalytic activity, acting on RNA MF
GO:1900363 regulation of mRNA polyadenylation BP
GO:1901360 organic cyclic compound metabolic process BP
GO:1901363 heterocyclic compound binding MF
GO:1903311 regulation of mRNA metabolic process BP
GO:2000031 regulation of salicylic acid mediated signaling pathway BP
GO:2001023 regulation of response to drug BP
GO:2001038 regulation of cellular response to drug BP
KEGG Term Name Description
map03015 mRNA surveillance pathway The mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go decay (NGD). NMD is a mechanism that eliminates mRNAs containing premature translation-termination codons (PTCs). In vertebrates, PTCs trigger efficient NMD when located upstream of an exon junction complex (EJC). Upf3, together with Upf1 and Upf2, may signal the presence of the PTC to the 5'end of the transcript, resulting in decapping and rapid exonucleolytic digestion of the mRNA. In the NSD pathway, which targets mRNAs lacking termination codons, the ribosome is believed to translate through the 3' untranslated region and stall at the end of the poly(A) tail. NSD involves an eRF3-like protein, Ski7p, which is hypothesized to bind the empty A site of the ribosome and recruit the exosome to degrade the mRNA from the 3' end. NGD targets mRNAs with stalls in translation elongation for endonucleolytic cleavage in a process involving the Dom34 and Hbs1 proteins.