Basic Information
Gene Structure
Domain
Regulation&
Interaction
Annotation
Orthologus Group
Expresssion
Pathway
Basic Information
Gene ID
PtXG40710
View in Genome Browser
Position
chr10:1255122575-1255185855 (+)
63280bp
Gene Type
gene
Gene Description (Protein Product)
cleavage and polyadenylation specificity factor subunit
Organism
Pinus tabuliformis
Also AS AT4G25550

Gene Structure

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

Regulation&Interaction
Protein-protein interaction (PPI)
PtXG50600 heterogeneous nuclear ribonucleoprotein
PtXG50670 heterogeneous nuclear ribonucleoprotein
PtXG42290 -
Regulatory gene
Pt0G01630 dof zinc finger protein
Pt0G07980 dof zinc finger protein
Pt1G66310 Dof domain, zinc finger

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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:0003682 chromatin binding MF
GO:0003723 RNA binding MF
GO:0003729 mRNA binding MF
GO:0005488 binding MF
GO:0005515 protein 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:0005849 mRNA cleavage factor complex CC
GO:0006139 nucleobase-containing compound metabolic process 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:0008150 biological_process BP
GO:0008152 metabolic process BP
GO:0009893 positive regulation of metabolic process BP
GO:0009987 cellular process BP
GO:0010467 gene expression BP
GO:0010468 regulation of gene expression BP
GO:0010604 positive regulation of macromolecule metabolic process BP
GO:0010608 post-transcriptional regulation of gene expression BP
GO:0010628 positive regulation of gene expression BP
GO:0016043 cellular component organization BP
GO:0016070 RNA metabolic process BP
GO:0016071 mRNA metabolic process BP
GO:0016604 nuclear body CC
GO:0017091 mRNA 3'-UTR AU-rich region binding MF
GO:0019219 regulation of nucleobase-containing compound metabolic process BP
GO:0019222 regulation of metabolic process BP
GO:0022607 cellular component assembly BP
GO:0022613 ribonucleoprotein complex biogenesis BP
GO:0022618 ribonucleoprotein complex assembly BP
GO:0031323 regulation of cellular metabolic process BP
GO:0031325 positive regulation of cellular metabolic process BP
GO:0031437 regulation of mRNA cleavage BP
GO:0031439 positive regulation of mRNA cleavage BP
GO:0031440 regulation of mRNA 3'-end processing BP
GO:0031442 positive 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:0034622 protein-containing complex assembly BP
GO:0034641 cellular nitrogen compound metabolic process BP
GO:0042382 paraspeckles CC
GO:0042802 identical protein binding MF
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:0043933 protein-containing complex organization BP
GO:0044085 cellular component biogenesis 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:0045595 regulation of cell differentiation BP
GO:0045597 positive regulation of cell differentiation BP
GO:0045935 positive regulation of nucleobase-containing compound metabolic process BP
GO:0046483 heterocycle metabolic process BP
GO:0048518 positive regulation of biological process BP
GO:0048522 positive regulation of cellular process BP
GO:0050684 regulation of mRNA processing BP
GO:0050685 positive regulation of mRNA processing BP
GO:0050789 regulation of biological process BP
GO:0050793 regulation of developmental process BP
GO:0050794 regulation of cellular process BP
GO:0051094 positive regulation of developmental process BP
GO:0051171 regulation of nitrogen compound metabolic process BP
GO:0051173 positive regulation of nitrogen compound metabolic process BP
GO:0051239 regulation of multicellular organismal process BP
GO:0051240 positive regulation of multicellular organismal process BP
GO:0051252 regulation of RNA metabolic process BP
GO:0051254 positive regulation of RNA metabolic process BP
GO:0051259 protein complex oligomerization BP
GO:0051262 protein tetramerization BP
GO:0051290 protein heterotetramerization BP
GO:0051291 protein heterooligomerization BP
GO:0060255 regulation of macromolecule metabolic process BP
GO:0065003 protein-containing complex assembly BP
GO:0065007 biological regulation BP
GO:0070013 intracellular organelle lumen CC
GO:0071704 organic substance metabolic process BP
GO:0071826 ribonucleoprotein complex subunit organization BP
GO:0071840 cellular component organization or biogenesis BP
GO:0080090 regulation of primary metabolic process BP
GO:0090304 nucleic acid metabolic process BP
GO:0097159 organic cyclic compound binding MF
GO:0110104 mRNA alternative polyadenylation BP
GO:1900363 regulation of mRNA polyadenylation BP
GO:1900365 positive regulation of mRNA polyadenylation BP
GO:1901360 organic cyclic compound metabolic process BP
GO:1901363 heterocyclic compound binding MF
GO:1901532 regulation of hematopoietic progenitor cell differentiation BP
GO:1901534 positive regulation of hematopoietic progenitor cell differentiation BP
GO:1903311 regulation of mRNA metabolic process BP
GO:1903313 positive regulation of mRNA metabolic process BP
GO:1903706 regulation of hemopoiesis BP
GO:1903708 positive regulation of hemopoiesis BP
GO:1905456 regulation of lymphoid progenitor cell differentiation BP
GO:1905458 positive regulation of lymphoid progenitor cell differentiation BP
GO:1990120 messenger ribonucleoprotein complex assembly BP
GO:2000026 regulation of multicellular organismal development BP
GO:2000736 regulation of stem cell differentiation BP
GO:2000738 positive regulation of stem cell differentiation BP
GO:2000973 regulation of pro-B cell differentiation BP
GO:2000975 positive regulation of pro-B cell differentiation 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.