PPGR - Gene Detail

Basic Information

Gene Structure

Domain

Regulation&
Interaction

Annotation

Orthologus Group

Expresssion

Pathway

Basic Information

Gene ID	gene-LOC105140301 View in Genome Browser
Position	NW_011499990.1:66318-71342 (+) 5024bp
Gene Type	gene
Gene Description (Protein Product)	Nuclear cap-binding protein subunit
Organism	Populus euphratica
Also AS	Potri.009G049200AT2G13540Potri.009G049200.v4.1

upstream:

Domain

Database	EntryID	E-Value	Start	end	InterPro ID	Description

Regulation&Interaction

Protein-protein interaction (PPI)	gene-LOC105141963 Nuclear cap-binding protein subunit gene-LOC105142060 gene-LOC105142060 Belongs to the DEAD box helicase family
Regulatory gene	gene-LOC105107546 Dof zinc finger protein gene-LOC105107883 Dof zinc finger protein gene-LOC105108058 GATA 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:0000003	reproduction	BP
GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	BP
GO:0000339	RNA cap binding	MF
GO:0000375	RNA splicing, via transesterification reactions	BP
GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	BP
GO:0000394	RNA splicing, via endonucleolytic cleavage and ligation	BP
GO:0000398	mRNA splicing, via spliceosome	BP
GO:0000956	nuclear-transcribed mRNA catabolic process	BP
GO:0001101	response to acid chemical	BP
GO:0003006	developmental process involved in reproduction	BP
GO:0003674	molecular_function	MF
GO:0003676	nucleic acid binding	MF
GO:0003723	RNA binding	MF
GO:0003729	mRNA binding	MF
GO:0005488	binding	MF
GO:0005575	cellular_component	CC
GO:0005622	intracellular anatomical structure	CC
GO:0005623	obsolete cell	CC
GO:0005634	nucleus	CC
GO:0005845	mRNA cap binding complex	CC
GO:0005846	nuclear cap binding complex	CC
GO:0006139	nucleobase-containing compound metabolic process	BP
GO:0006396	RNA processing	BP
GO:0006397	mRNA processing	BP
GO:0006401	RNA catabolic process	BP
GO:0006402	mRNA catabolic process	BP
GO:0006403	RNA localization	BP
GO:0006405	RNA export from nucleus	BP
GO:0006406	mRNA export from nucleus	BP
GO:0006611	protein export from nucleus	BP
GO:0006725	cellular aromatic compound metabolic process	BP
GO:0006807	nitrogen compound metabolic process	BP
GO:0006810	transport	BP
GO:0006886	intracellular protein transport	BP
GO:0006913	nucleocytoplasmic transport	BP
GO:0007275	multicellular organism development	BP
GO:0008104	protein localization	BP
GO:0008150	biological_process	BP
GO:0008152	metabolic process	BP
GO:0008380	RNA splicing	BP
GO:0009056	catabolic process	BP
GO:0009057	macromolecule catabolic process	BP
GO:0009314	response to radiation	BP
GO:0009416	response to light stimulus	BP
GO:0009628	response to abiotic stimulus	BP
GO:0009648	photoperiodism	BP
GO:0009719	response to endogenous stimulus	BP
GO:0009725	response to hormone	BP
GO:0009737	response to abscisic acid	BP
GO:0009791	post-embryonic development	BP
GO:0009892	negative regulation of metabolic process	BP
GO:0009987	cellular process	BP
GO:0010033	response to organic substance	BP
GO:0010228	vegetative to reproductive phase transition of meristem	BP
GO:0010467	gene expression	BP
GO:0010468	regulation of gene expression	BP
GO:0010605	negative regulation of macromolecule metabolic process	BP
GO:0010608	post-transcriptional regulation of gene expression	BP
GO:0010629	negative regulation of gene expression	BP
GO:0014070	response to organic cyclic compound	BP
GO:0015031	protein transport	BP
GO:0015833	peptide transport	BP
GO:0015931	nucleobase-containing compound transport	BP
GO:0016070	RNA metabolic process	BP
GO:0016071	mRNA metabolic process	BP
GO:0016441	post-transcriptional gene silencing	BP
GO:0016458	obsolete gene silencing	BP
GO:0019222	regulation of metabolic process	BP
GO:0019439	aromatic compound catabolic process	BP
GO:0022414	reproductive process	BP
GO:0031047	RNA-mediated gene silencing	BP
GO:0031050	ncRNA processing	BP
GO:0031053	primary miRNA processing	BP
GO:0031503	protein-containing complex localization	BP
GO:0032501	multicellular organismal process	BP
GO:0032502	developmental process	BP
GO:0032991	protein-containing complex	CC
GO:0033036	macromolecule localization	BP
GO:0033993	response to lipid	BP
GO:0034470	ncRNA processing	BP
GO:0034518	RNA cap binding complex	CC
GO:0034613	protein localization	BP
GO:0034641	cellular nitrogen compound metabolic process	BP
GO:0034655	nucleobase-containing compound catabolic process	BP
GO:0034660	ncRNA metabolic process	BP
GO:0035194	RNA-mediated post-transcriptional gene silencing	BP
GO:0035195	miRNA-mediated gene silencing	BP
GO:0035196	miRNA processing	BP
GO:0040029	epigenetic regulation of gene expression	BP
GO:0042221	response to chemical	BP
GO:0042886	amide transport	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:0043331	response to dsRNA	BP
GO:0044237	cellular metabolic process	BP
GO:0044238	primary metabolic process	BP
GO:0044248	cellular catabolic process	BP
GO:0044260	cellular macromolecule metabolic process	BP
GO:0044265	cellular macromolecule catabolic process	BP
GO:0044270	cellular nitrogen compound catabolic process	BP
GO:0044424	obsolete intracellular part	CC
GO:0044464	obsolete cell part	CC
GO:0045184	establishment of protein localization	BP
GO:0046483	heterocycle metabolic process	BP
GO:0046700	heterocycle catabolic process	BP
GO:0046907	intracellular transport	BP
GO:0048519	negative regulation of biological process	BP
GO:0048571	long-day photoperiodism	BP
GO:0048573	photoperiodism, flowering	BP
GO:0048574	long-day photoperiodism, flowering	BP
GO:0048608	reproductive structure development	BP
GO:0048731	system development	BP
GO:0048856	anatomical structure development	BP
GO:0050657	nucleic acid transport	BP
GO:0050658	RNA transport	BP
GO:0050789	regulation of biological process	BP
GO:0050896	response to stimulus	BP
GO:0051028	mRNA transport	BP
GO:0051168	nuclear export	BP
GO:0051169	nuclear transport	BP
GO:0051179	localization	BP
GO:0051234	establishment of localization	BP
GO:0051236	establishment of RNA localization	BP
GO:0051641	cellular localization	BP
GO:0051649	establishment of localization in cell	BP
GO:0051716	cellular response to stimulus	BP
GO:0060255	regulation of macromolecule metabolic process	BP
GO:0061458	reproductive system development	BP
GO:0065007	biological regulation	BP
GO:0070727	cellular macromolecule localization	BP
GO:0070887	cellular response to chemical stimulus	BP
GO:0070918	regulatory ncRNA processing	BP
GO:0071166	ribonucleoprotein complex localization	BP
GO:0071310	cellular response to organic substance	BP
GO:0071359	cellular response to dsRNA	BP
GO:0071407	cellular response to organic cyclic compound	BP
GO:0071426	obsolete ribonucleoprotein complex export from nucleus	BP
GO:0071427	obsolete mRNA-containing ribonucleoprotein complex export from nucleus	BP
GO:0071702	organic substance transport	BP
GO:0071704	organic substance metabolic process	BP
GO:0071705	nitrogen compound transport	BP
GO:0090304	nucleic acid metabolic process	BP
GO:0097159	organic cyclic compound binding	MF
GO:0097305	response to alcohol	BP
GO:1901360	organic cyclic compound metabolic process	BP
GO:1901361	organic cyclic compound catabolic process	BP
GO:1901363	heterocyclic compound binding	MF
GO:1901575	organic substance catabolic process	BP
GO:1901698	response to nitrogen compound	BP
GO:1901699	cellular response to nitrogen compound	BP
GO:1901700	response to oxygen-containing compound	BP

KEGG Term	Name	Description
map03040	Spliceosome	After transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, the spliceosome. The standard spliceosome is made up of five small nuclear ribonucleoproteins (snRNPs), U1, U2, U4, U5, and U6 snRNPs, and several spliceosome-associated proteins (SAPs). Spliceosomes are not a simple stable complex, but a dynamic family of particles that assemble on the mRNA precursor and help fold it into a conformation that allows transesterification to proceed. Various spliceosome forms (e.g. A-, B- and C-complexes) have been identified.
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.
map03013	RNA transport	RNA transport from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes (NPCs) via mobile export receptors. The majority of RNAs, such as tRNAs, rRNAs, and U snRNAs, are transported by specific export receptors, which belong to the karyopherin-beta family proteins. A feature of karyopherins is their regulation by the small GTPase Ran. However, general mRNA export is mechanistically different. Nuclear export of mRNAs is functionally coupled to different steps in gene expression processes, such as transcription, splicing, 3'-end formation and even translation.