PPGR - Gene Detail

Basic Information

Gene Structure

Domain

Regulation&
Interaction

Annotation

Orthologus Group

Expresssion

Pathway

Basic Information

Gene ID	gene-LOC107433910 View in Genome Browser
Position	NC_063287.1:41749997-41754999 (-) 5002bp
Gene Type	gene
Gene Description (Protein Product)	cleavage and polyadenylation specificity factor subunit
Organism	Ziziphus jujuba
Also AS	AT5G55670

upstream:

Domain

Database	EntryID	E-Value	Start	end	InterPro ID	Description

Regulation&Interaction

Protein-protein interaction (PPI)	gene-LOC125421379 Flowering time control protein gene-LOC125423547 Splicing factor 3B subunit
Regulatory gene	gene-LOC107403899 dof zinc finger protein gene-LOC107404240 Dof zinc finger protein gene-LOC107405930 transcription factor

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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)

Select Expression

Pathway

GO Term	Description	GO Category
GO:0000228	nuclear chromosome	CC
GO:0000381	regulation of alternative mRNA splicing, via spliceosome	BP
GO:0000785	chromatin	CC
GO:0000790	chromatin	CC
GO:0000791	euchromatin	CC
GO:0000976	transcription cis-regulatory region binding	MF
GO:0000977	RNA polymerase II transcription regulatory region sequence-specific DNA binding	MF
GO:0000978	RNA polymerase II cis-regulatory region sequence-specific DNA binding	MF
GO:0000987	cis-regulatory region sequence-specific DNA binding	MF
GO:0001012	RNA polymerase II transcription regulatory region sequence-specific DNA binding	MF
GO:0001067	transcription regulatory region nucleic acid binding	MF
GO:0003674	molecular_function	MF
GO:0003676	nucleic acid binding	MF
GO:0003677	DNA binding	MF
GO:0003682	chromatin binding	MF
GO:0003690	double-stranded DNA binding	MF
GO:0003723	RNA binding	MF
GO:0003729	mRNA binding	MF
GO:0005488	binding	MF
GO:0005575	cellular_component	CC
GO:0005576	extracellular region	CC
GO:0005615	extracellular space	CC
GO:0005622	intracellular anatomical structure	CC
GO:0005623	obsolete cell	CC
GO:0005634	nucleus	CC
GO:0005681	spliceosomal complex	CC
GO:0005694	chromosome	CC
GO:0005719	euchromatin	CC
GO:0006139	nucleobase-containing compound metabolic process	BP
GO:0006351	DNA-templated transcription	BP
GO:0006355	regulation of DNA-templated transcription	BP
GO:0006357	regulation of transcription by RNA polymerase II	BP
GO:0006366	transcription by RNA polymerase II	BP
GO:0006508	proteolysis	BP
GO:0006509	membrane protein ectodomain proteolysis	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:0009058	biosynthetic process	BP
GO:0009059	macromolecule biosynthetic process	BP
GO:0009889	regulation of biosynthetic process	BP
GO:0009891	positive regulation of biosynthetic process	BP
GO:0009892	negative regulation of metabolic process	BP
GO:0009893	positive regulation of metabolic process	BP
GO:0009987	cellular process	BP
GO:0010033	response to organic substance	BP
GO:0010467	gene expression	BP
GO:0010468	regulation of gene expression	BP
GO:0010556	regulation of macromolecule biosynthetic process	BP
GO:0010557	positive regulation of macromolecule biosynthetic process	BP
GO:0010604	positive regulation of macromolecule metabolic process	BP
GO:0010605	negative regulation of macromolecule metabolic process	BP
GO:0010628	positive regulation of gene expression	BP
GO:0010629	negative regulation of gene expression	BP
GO:0016043	cellular component organization	BP
GO:0016070	RNA metabolic process	BP
GO:0018130	heterocycle biosynthetic process	BP
GO:0019219	regulation of nucleobase-containing compound metabolic process	BP
GO:0019222	regulation of metabolic process	BP
GO:0019438	aromatic compound biosynthetic process	BP
GO:0019538	protein metabolic process	BP
GO:0022607	cellular component assembly	BP
GO:0031323	regulation of cellular metabolic process	BP
GO:0031324	negative regulation of cellular metabolic process	BP
GO:0031325	positive regulation of cellular metabolic process	BP
GO:0031326	regulation of cellular biosynthetic process	BP
GO:0031328	positive regulation of cellular biosynthetic process	BP
GO:0031974	membrane-enclosed lumen	CC
GO:0031981	nuclear lumen	CC
GO:0031982	vesicle	CC
GO:0032774	RNA biosynthetic process	BP
GO:0032991	protein-containing complex	CC
GO:0033119	negative regulation of RNA splicing	BP
GO:0033120	positive regulation of RNA splicing	BP
GO:0033619	membrane protein proteolysis	BP
GO:0034097	response to cytokine	BP
GO:0034641	cellular nitrogen compound metabolic process	BP
GO:0034645	cellular macromolecule biosynthetic process	BP
GO:0034654	nucleobase-containing compound biosynthetic process	BP
GO:0042221	response to chemical	BP
GO:0043170	macromolecule metabolic process	BP
GO:0043226	organelle	CC
GO:0043227	membrane-bounded organelle	CC
GO:0043228	non-membrane-bounded organelle	CC
GO:0043229	intracellular organelle	CC
GO:0043230	extracellular organelle	CC
GO:0043231	intracellular membrane-bounded organelle	CC
GO:0043232	intracellular non-membrane-bounded organelle	CC
GO:0043233	organelle lumen	CC
GO:0043484	regulation of RNA splicing	BP
GO:0043565	sequence-specific DNA binding	MF
GO:0043933	protein-containing complex organization	BP
GO:0044085	cellular component biogenesis	BP
GO:0044212	transcription cis-regulatory region binding	MF
GO:0044237	cellular metabolic process	BP
GO:0044238	primary metabolic process	BP
GO:0044249	cellular biosynthetic process	BP
GO:0044260	cellular macromolecule metabolic process	BP
GO:0044271	cellular nitrogen compound biosynthetic process	BP
GO:0044421	obsolete extracellular region part	CC
GO:0044422	obsolete organelle part	CC
GO:0044424	obsolete intracellular part	CC
GO:0044427	obsolete chromosomal part	CC
GO:0044428	obsolete nuclear part	CC
GO:0044446	obsolete intracellular organelle part	CC
GO:0044454	obsolete nuclear chromosome part	CC
GO:0044464	obsolete cell part	CC
GO:0044530	supraspliceosomal complex	CC
GO:0045893	positive regulation of DNA-templated transcription	BP
GO:0045934	negative regulation of nucleobase-containing compound metabolic process	BP
GO:0045935	positive regulation of nucleobase-containing compound metabolic process	BP
GO:0045944	positive regulation of transcription by RNA polymerase II	BP
GO:0046483	heterocycle metabolic process	BP
GO:0048024	regulation of mRNA splicing, via spliceosome	BP
GO:0048025	negative regulation of mRNA splicing, via spliceosome	BP
GO:0048026	positive regulation of mRNA splicing, via spliceosome	BP
GO:0048518	positive regulation of biological process	BP
GO:0048519	negative regulation of biological process	BP
GO:0048522	positive regulation of cellular process	BP
GO:0048523	negative regulation of cellular process	BP
GO:0050684	regulation of mRNA processing	BP
GO:0050685	positive regulation of mRNA processing	BP
GO:0050686	negative regulation of mRNA processing	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:0051172	negative regulation of nitrogen compound metabolic process	BP
GO:0051173	positive regulation of nitrogen compound metabolic process	BP
GO:0051252	regulation of RNA metabolic process	BP
GO:0051253	negative regulation of RNA metabolic process	BP
GO:0051254	positive regulation of RNA metabolic process	BP
GO:0051259	protein complex oligomerization	BP
GO:0051260	protein homooligomerization	BP
GO:0051716	cellular response to stimulus	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:0070062	extracellular exosome	CC
GO:0070555	response to interleukin-1	BP
GO:0070887	cellular response to chemical stimulus	BP
GO:0071013	catalytic step 2 spliceosome	CC
GO:0071310	cellular response to organic substance	BP
GO:0071345	cellular response to cytokine stimulus	BP
GO:0071347	cellular response to interleukin-1	BP
GO:0071704	organic substance metabolic process	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:0097659	nucleic acid-templated transcription	BP
GO:1901360	organic cyclic compound metabolic process	BP
GO:1901362	organic cyclic compound biosynthetic process	BP
GO:1901363	heterocyclic compound binding	MF
GO:1901564	organonitrogen compound metabolic process	BP
GO:1901576	organic substance biosynthetic process	BP
GO:1902494	catalytic complex	CC
GO:1902680	positive regulation of RNA biosynthetic process	BP
GO:1903311	regulation of mRNA metabolic process	BP
GO:1903312	negative regulation of mRNA metabolic process	BP
GO:1903313	positive regulation of mRNA metabolic process	BP
GO:1903506	regulation of nucleic acid-templated transcription	BP
GO:1903508	positive regulation of nucleic acid-templated transcription	BP
GO:1903561	extracellular vesicle	CC
GO:1990837	sequence-specific double-stranded DNA binding	MF
GO:1990904	ribonucleoprotein complex	CC
GO:2000112	regulation of cellular macromolecule biosynthetic process	BP
GO:2001141	regulation of RNA biosynthetic process	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.