PPGR - Gene Detail

Basic Information

Gene Structure

Domain

Regulation&
Interaction

Annotation

Orthologus Group

Pathway

Basic Information

Gene ID	JhiChr14G11693.g View in Genome Browser
Position	chr14:22573033-22577093 (-) 4060bp
Gene Type	gene
Gene Description (Protein Product)	Ribonuclease H protein
Organism	Juglans hindsii
Also AS	AT3G25270

upstream:

Domain

Database	EntryID	E-Value	Start	end	InterPro ID	Description

Regulation&Interaction

Protein-protein interaction (PPI)	JhiChr16G10541.g Cleavage stimulation factor subunit JhiChr16G10072.g Cleavage stimulation factor JhiChr16G10533.g Cleavage stimulation factor
Regulatory gene	JhiChr01G10060.g zinc finger CCCH domain-containing protein JhiChr01G10116.g zinc finger CCCH domain-containing protein JhiChr01G10471.g Zinc finger protein

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Annotation

Orthologous Group

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

Pathway

GO Term	Description	GO Category
GO:0000003	reproduction	BP
GO:0000018	regulation of DNA recombination	BP
GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	BP
GO:0000226	microtubule cytoskeleton organization	BP
GO:0000335	negative regulation of transposition, DNA-mediated	BP
GO:0000337	regulation of transposition, DNA-mediated	BP
GO:0000375	RNA splicing, via transesterification reactions	BP
GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	BP
GO:0000381	regulation of alternative mRNA splicing, via spliceosome	BP
GO:0000398	mRNA splicing, via spliceosome	BP
GO:0000578	embryonic axis specification	BP
GO:0000956	nuclear-transcribed mRNA catabolic process	BP
GO:0001709	cell fate determination	BP
GO:0003002	regionalization	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: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:0005681	spliceosomal complex	CC
GO:0005730	nucleolus	CC
GO:0005737	cytoplasm	CC
GO:0005829	cytosol	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:0006996	organelle organization	BP
GO:0007010	cytoskeleton organization	BP
GO:0007017	microtubule-based process	BP
GO:0007028	cytoplasm organization	BP
GO:0007154	cell communication	BP
GO:0007165	signal transduction	BP
GO:0007166	cell surface receptor signaling pathway	BP
GO:0007167	enzyme-linked receptor protein signaling pathway	BP
GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	BP
GO:0007173	epidermal growth factor receptor signaling pathway	BP
GO:0007275	multicellular organism development	BP
GO:0007276	gamete generation	BP
GO:0007281	germ cell development	BP
GO:0007292	female gamete generation	BP
GO:0007293	germarium-derived egg chamber formation	BP
GO:0007294	germarium-derived oocyte fate determination	BP
GO:0007308	oocyte construction	BP
GO:0007309	oocyte axis specification	BP
GO:0007310	oocyte dorsal/ventral axis specification	BP
GO:0007314	oocyte anterior/posterior axis specification	BP
GO:0007315	pole plasm assembly	BP
GO:0007316	pole plasm RNA localization	BP
GO:0007317	regulation of pole plasm oskar mRNA localization	BP
GO:0007350	blastoderm segmentation	BP
GO:0007351	tripartite regional subdivision	BP
GO:0007389	pattern specification process	BP
GO:0008104	protein localization	BP
GO:0008150	biological_process	BP
GO:0008152	metabolic process	BP
GO:0008298	intracellular mRNA localization	BP
GO:0008358	maternal determination of anterior/posterior axis, embryo	BP
GO:0008380	RNA splicing	BP
GO:0008595	anterior/posterior axis specification, embryo	BP
GO:0009056	catabolic process	BP
GO:0009057	macromolecule catabolic process	BP
GO:0009653	anatomical structure morphogenesis	BP
GO:0009790	embryo development	BP
GO:0009798	axis specification	BP
GO:0009880	embryonic pattern specification	BP
GO:0009892	negative regulation of metabolic process	BP
GO:0009893	positive regulation of metabolic process	BP
GO:0009948	anterior/posterior axis specification	BP
GO:0009950	dorsal/ventral axis specification	BP
GO:0009952	anterior/posterior pattern specification	BP
GO:0009953	dorsal/ventral pattern formation	BP
GO:0009987	cellular process	BP
GO:0009994	oocyte differentiation	BP
GO:0010467	gene expression	BP
GO:0010468	regulation of gene expression	BP
GO:0010528	regulation of transposition	BP
GO:0010529	negative regulation of transposition	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:0015031	protein transport	BP
GO:0015833	peptide transport	BP
GO:0015931	nucleobase-containing compound transport	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:0016607	nuclear speck	CC
GO:0019094	pole plasm mRNA localization	BP
GO:0019219	regulation of nucleobase-containing compound metabolic process	BP
GO:0019222	regulation of metabolic process	BP
GO:0019439	aromatic compound catabolic process	BP
GO:0019953	sexual reproduction	BP
GO:0021700	developmental maturation	BP
GO:0022412	cellular process involved in reproduction in multicellular organism	BP
GO:0022414	reproductive process	BP
GO:0022607	cellular component assembly	BP
GO:0023052	signaling	BP
GO:0030154	cell differentiation	BP
GO:0030425	dendrite	CC
GO:0030706	germarium-derived oocyte differentiation	BP
GO:0030716	oocyte fate determination	BP
GO:0031123	RNA 3'-end processing	BP
GO:0031124	mRNA 3'-end processing	BP
GO:0031323	regulation of cellular metabolic process	BP
GO:0031324	negative regulation of cellular metabolic process	BP
GO:0031503	protein-containing complex localization	BP
GO:0031974	membrane-enclosed lumen	CC
GO:0031981	nuclear lumen	CC
GO:0032501	multicellular organismal process	BP
GO:0032502	developmental process	BP
GO:0032504	multicellular organism reproduction	BP
GO:0032879	regulation of localization	BP
GO:0032991	protein-containing complex	CC
GO:0033036	macromolecule localization	BP
GO:0034613	protein localization	BP
GO:0034641	cellular nitrogen compound metabolic process	BP
GO:0034655	nucleobase-containing compound catabolic process	BP
GO:0035145	exon-exon junction complex	CC
GO:0035282	segmentation	BP
GO:0036477	somatodendritic compartment	CC
GO:0038127	ERBB signaling pathway	BP
GO:0042886	amide transport	BP
GO:0042995	cell projection	CC
GO:0043005	neuron projection	CC
GO:0043025	neuronal cell body	CC
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: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:0043900	obsolete regulation of multi-organism process	BP
GO:0044085	cellular component biogenesis	BP
GO:0044087	regulation of cellular component biogenesis	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:0044297	cell body	CC
GO:0044422	obsolete organelle part	CC
GO:0044424	obsolete intracellular part	CC
GO:0044428	obsolete nuclear part	CC
GO:0044444	obsolete cytoplasmic part	CC
GO:0044446	obsolete intracellular organelle part	CC
GO:0044451	obsolete nucleoplasm part	CC
GO:0044463	obsolete cell projection part	CC
GO:0044464	obsolete cell part	CC
GO:0044703	multi-organism reproductive process	BP
GO:0045165	cell fate commitment	BP
GO:0045184	establishment of protein localization	BP
GO:0045292	mRNA cis splicing, via spliceosome	BP
GO:0045451	pole plasm oskar mRNA localization	BP
GO:0045595	regulation of cell differentiation	BP
GO:0045910	negative regulation of DNA recombination	BP
GO:0045934	negative regulation of nucleobase-containing compound metabolic process	BP
GO:0045995	regulation of embryonic development	BP
GO:0046483	heterocycle metabolic process	BP
GO:0046595	establishment of pole plasm mRNA localization	BP
GO:0046700	heterocycle catabolic process	BP
GO:0046907	intracellular transport	BP
GO:0048024	regulation of mRNA splicing, via spliceosome	BP
GO:0048468	cell development	BP
GO:0048469	cell maturation	BP
GO:0048477	oogenesis	BP
GO:0048518	positive regulation of biological process	BP
GO:0048519	negative regulation of biological process	BP
GO:0048523	negative regulation of cellular process	BP
GO:0048599	oocyte development	BP
GO:0048609	multicellular organismal reproductive process	BP
GO:0048646	anatomical structure formation involved in morphogenesis	BP
GO:0048856	anatomical structure development	BP
GO:0048869	cellular developmental process	BP
GO:0050657	nucleic acid transport	BP
GO:0050658	RNA transport	BP
GO:0050684	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:0050896	response to stimulus	BP
GO:0051028	mRNA transport	BP
GO:0051052	regulation of DNA metabolic process	BP
GO:0051053	negative regulation of DNA metabolic process	BP
GO:0051128	regulation of cellular component organization	BP
GO:0051168	nuclear export	BP
GO:0051169	nuclear transport	BP
GO:0051171	regulation of nitrogen compound metabolic process	BP
GO:0051172	negative regulation of nitrogen compound metabolic process	BP
GO:0051179	localization	BP
GO:0051234	establishment of localization	BP
GO:0051236	establishment of RNA localization	BP
GO:0051239	regulation of multicellular organismal process	BP
GO:0051252	regulation of RNA metabolic process	BP
GO:0051640	organelle localization	BP
GO:0051641	cellular localization	BP
GO:0051647	nucleus localization	BP
GO:0051649	establishment of localization in cell	BP
GO:0051663	oocyte nucleus localization involved in oocyte dorsal/ventral axis specification	BP
GO:0051704	obsolete multi-organism process	BP
GO:0051716	cellular response to stimulus	BP
GO:0060255	regulation of macromolecule metabolic process	BP
GO:0060281	regulation of oocyte development	BP
GO:0060284	regulation of cell development	BP
GO:0060341	regulation of cellular localization	BP
GO:0060810	intracellular mRNA localization involved in pattern specification process	BP
GO:0060811	intracellular mRNA localization involved in anterior/posterior axis specification	BP
GO:0065007	biological regulation	BP
GO:0070013	intracellular organelle lumen	CC
GO:0070727	cellular macromolecule localization	BP
GO:0071013	catalytic step 2 spliceosome	CC
GO:0071166	ribonucleoprotein complex localization	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: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:0097447	dendritic tree	CC
GO:0097458	obsolete neuron part	CC
GO:0120025	plasma membrane bounded cell projection	CC
GO:0120038	obsolete plasma membrane bounded cell projection part	CC
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:1902494	catalytic complex	CC
GO:1902875	regulation of embryonic pattern specification	BP
GO:1903311	regulation of mRNA metabolic process	BP
GO:1903429	regulation of cell maturation	BP
GO:1904580	regulation of intracellular mRNA localization	BP
GO:1905879	regulation of oogenesis	BP
GO:1990904	ribonucleoprotein complex	CC
GO:2000026	regulation of multicellular organismal development	BP
GO:2000241	regulation of reproductive process	BP

KEGG Term	Name	Description
map04075	Plant hormone signal transduction	-
map03050	Proteasome	The proteasome is a protein-destroying apparatus involved in many essential cellular functions, such as regulation of cell cycle, cell differentiation, signal transduction pathways, antigen processing for appropriate immune responses, stress signaling, inflammatory responses, and apoptosis. It is capable of degrading a variety of cellular proteins in a rapid and timely fashion and most substrate proteins are modified by ubiquitin before their degradation by the proteasome. The proteasome is a large protein complex consisting of a proteolytic core called the 20S particle and ancillary factors that regulate its activity in various ways. The most common form is the 26S proteasome containing one 20S core particle and two 19S regulatory particles that enable the proteasome to degrade ubiquitinated proteins by an ATP-dependent mechanism. Another form is the immunoproteasome containing two 11S regulatory particles, PA28 alpha and PA28 beta, which are induced by interferon gamma under the conditions of intensified immune response. Other regulatory particles include PA28 gamma and PA200. Although PA28 gamma also belongs to a family of activators of the 20S proteasome, it is localized within the nucleus and forms a homoheptamer. PA28 gamma has been implicated in the regulation of cell cycle progression and apoptosis. PA200 has been identified as a large nuclear protein that stimulates proteasomal hydrolysis of peptides.
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.