PPGR - Gene Detail

Basic Information

Gene Structure

Domain

Regulation&
Interaction

Annotation

Orthologus Group

Expresssion

Pathway

Basic Information

Gene ID	Pt5G10340 View in Genome Browser
Position	chr5:353308374-353309071 (-) 697bp
Gene Type	gene
Gene Description (Protein Product)	"Component of the replication protein A complex (RPA) required for DNA recombination
Organism	Pinus tabuliformis
Also AS	AT5G08020

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Domain

Database	EntryID	E-Value	Start	end	InterPro ID	Description

Regulation&Interaction

Protein-protein interaction (PPI)	Pt7G48260 DNA polymerase delta subunit Pt5G33560 Belongs to the eukaryotic-type primase small subunit family Pt5G26310 Replication protein A 14 kDa subunit
Regulatory gene	Pt1G50980 Floral homeotic protein APETALA Pt1G72280 transcription, DNA-templated Pt2G51500 B3 domain-containing protein

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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:0000228	nuclear chromosome	CC
GO:0000278	mitotic cell cycle	BP
GO:0000723	telomere maintenance	BP
GO:0000724	double-strand break repair via homologous recombination	BP
GO:0000725	recombinational repair	BP
GO:0000781	chromosome, telomeric region	CC
GO:0000784	chromosome, telomeric region	CC
GO:0000785	chromatin	CC
GO:0000790	chromatin	CC
GO:0003674	molecular_function	MF
GO:0003676	nucleic acid binding	MF
GO:0003677	DNA binding	MF
GO:0003697	single-stranded DNA binding	MF
GO:0003723	RNA 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:0005657	replication fork	CC
GO:0005662	DNA replication factor A complex	CC
GO:0005694	chromosome	CC
GO:0006139	nucleobase-containing compound metabolic process	BP
GO:0006259	DNA metabolic process	BP
GO:0006260	DNA replication	BP
GO:0006261	DNA-templated DNA replication	BP
GO:0006268	DNA unwinding involved in DNA replication	BP
GO:0006278	RNA-templated DNA biosynthetic process	BP
GO:0006279	premeiotic DNA replication	BP
GO:0006281	DNA repair	BP
GO:0006302	double-strand break repair	BP
GO:0006310	DNA recombination	BP
GO:0006725	cellular aromatic compound metabolic process	BP
GO:0006807	nitrogen compound metabolic process	BP
GO:0006950	response to stress	BP
GO:0006974	cellular response to DNA damage stimulus	BP
GO:0006996	organelle organization	BP
GO:0007004	telomere maintenance via telomerase	BP
GO:0007049	cell cycle	BP
GO:0007063	regulation of sister chromatid cohesion	BP
GO:0007088	regulation of mitotic nuclear division	BP
GO:0007346	regulation of mitotic cell cycle	BP
GO:0008150	biological_process	BP
GO:0008152	metabolic process	BP
GO:0009058	biosynthetic process	BP
GO:0009059	macromolecule biosynthetic process	BP
GO:0009314	response to radiation	BP
GO:0009411	response to UV	BP
GO:0009416	response to light stimulus	BP
GO:0009628	response to abiotic stimulus	BP
GO:0009889	regulation of biosynthetic process	BP
GO:0009891	positive regulation of biosynthetic process	BP
GO:0009893	positive regulation of metabolic process	BP
GO:0009987	cellular process	BP
GO:0010224	response to UV-B	BP
GO:0010556	regulation of macromolecule biosynthetic process	BP
GO:0010557	positive regulation of macromolecule biosynthetic process	BP
GO:0010564	regulation of cell cycle process	BP
GO:0010604	positive regulation of macromolecule metabolic process	BP
GO:0010638	positive regulation of organelle organization	BP
GO:0010639	negative regulation of organelle organization	BP
GO:0010833	telomere maintenance via telomere lengthening	BP
GO:0010948	negative regulation of cell cycle process	BP
GO:0016043	cellular component organization	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:0022402	cell cycle process	BP
GO:0022414	reproductive process	BP
GO:0030894	replisome	CC
GO:0031323	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:0032200	telomere organization	BP
GO:0032204	regulation of telomere maintenance	BP
GO:0032206	positive regulation of telomere maintenance	BP
GO:0032210	regulation of telomere maintenance via telomerase	BP
GO:0032212	positive regulation of telomere maintenance via telomerase	BP
GO:0032392	DNA geometric change	BP
GO:0032508	DNA duplex unwinding	BP
GO:0032879	regulation of localization	BP
GO:0032880	regulation of protein localization	BP
GO:0032991	protein-containing complex	CC
GO:0032993	protein-DNA complex	CC
GO:0033043	regulation of organelle organization	BP
GO:0033044	regulation of chromosome organization	BP
GO:0033045	regulation of sister chromatid segregation	BP
GO:0033046	negative regulation of sister chromatid segregation	BP
GO:0033047	regulation of mitotic sister chromatid segregation	BP
GO:0033048	negative regulation of mitotic sister chromatid segregation	BP
GO:0033260	nuclear DNA replication	BP
GO:0033554	cellular response to stress	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:0035861	site of double-strand break	CC
GO:0042162	telomeric DNA binding	MF
GO:0042592	homeostatic process	BP
GO:0043047	single-stranded telomeric DNA binding	MF
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:0043565	sequence-specific DNA binding	MF
GO:0043596	nuclear replication fork	CC
GO:0043601	nuclear replisome	CC
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: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:0044786	cell cycle DNA replication	BP
GO:0045786	negative regulation of cell cycle	BP
GO:0045839	negative regulation of mitotic nuclear division	BP
GO:0045875	negative regulation of sister chromatid cohesion	BP
GO:0045930	negative regulation of mitotic cell cycle	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:0048519	negative regulation of biological process	BP
GO:0048522	positive regulation of cellular process	BP
GO:0048523	negative regulation of cellular process	BP
GO:0050789	regulation of biological process	BP
GO:0050794	regulation of cellular process	BP
GO:0050896	response to stimulus	BP
GO:0051052	regulation of DNA metabolic process	BP
GO:0051054	positive regulation of DNA metabolic process	BP
GO:0051098	regulation of binding	BP
GO:0051101	regulation of DNA binding	BP
GO:0051128	regulation of cellular component organization	BP
GO:0051129	negative regulation of cellular component organization	BP
GO:0051130	positive regulation of cellular component organization	BP
GO:0051171	regulation of nitrogen compound metabolic process	BP
GO:0051173	positive regulation of nitrogen compound metabolic process	BP
GO:0051276	chromosome organization	BP
GO:0051321	meiotic cell cycle	BP
GO:0051716	cellular response to stimulus	BP
GO:0051726	regulation of cell cycle	BP
GO:0051783	regulation of nuclear division	BP
GO:0051784	negative regulation of nuclear division	BP
GO:0051983	regulation of chromosome segregation	BP
GO:0051985	negative regulation of chromosome segregation	BP
GO:0060249	anatomical structure homeostasis	BP
GO:0060255	regulation of macromolecule metabolic process	BP
GO:0060341	regulation of cellular localization	BP
GO:0065007	biological regulation	BP
GO:0065008	regulation of biological quality	BP
GO:0065009	regulation of molecular function	BP
GO:0070013	intracellular organelle lumen	CC
GO:0070034	telomerase RNA binding	MF
GO:0071103	DNA conformation change	BP
GO:0071704	organic substance metabolic process	BP
GO:0071840	cellular component organization or biogenesis	BP
GO:0071897	DNA biosynthetic process	BP
GO:0071922	regulation of cohesin loading	BP
GO:0071923	negative regulation of cohesin loading	BP
GO:0080090	regulation of primary metabolic process	BP
GO:0090304	nucleic acid metabolic process	BP
GO:0090734	site of DNA damage	CC
GO:0097159	organic cyclic compound binding	MF
GO:0098687	chromosomal region	CC
GO:0098847	sequence-specific single stranded DNA binding	MF
GO:0106111	regulation of mitotic cohesin ssDNA (lagging strand) loading	BP
GO:0106112	negative regulation of mitotic cohesin ssDNA (lagging strand) loading	BP
GO:1901360	organic cyclic compound metabolic process	BP
GO:1901362	organic cyclic compound biosynthetic process	BP
GO:1901363	heterocyclic compound binding	MF
GO:1901576	organic substance biosynthetic process	BP
GO:1902969	mitotic DNA replication	BP
GO:1903046	meiotic cell cycle process	BP
GO:1903047	mitotic cell cycle process	BP
GO:1903827	regulation of protein localization	BP
GO:1903828	negative regulation of protein localization	BP
GO:1904356	regulation of telomere maintenance via telomere lengthening	BP
GO:1904358	positive regulation of telomere maintenance via telomere lengthening	BP
GO:1905405	regulation of mitotic cohesin loading	BP
GO:1905412	negative regulation of mitotic cohesin loading	BP
GO:1905634	regulation of protein localization to chromatin	BP
GO:2000112	regulation of cellular macromolecule biosynthetic process	BP
GO:2000278	regulation of DNA biosynthetic process	BP
GO:2000573	positive regulation of DNA biosynthetic process	BP
GO:2001251	negative regulation of chromosome organization	BP
GO:2001252	positive regulation of chromosome organization	BP

KEGG Term	Name	Description
map03440	Homologous recombination	Homologous recombination (HR) is essential for the accurate repair of DNA double-strand breaks (DSBs), potentially lethal lesions. HR takes place in the late S-G2 phase of the cell cycle and involves the generation of a single-stranded region of DNA, followed by strand invasion, formation of a Holliday junction, DNA synthesis using the intact strand as a template, branch migration and resolution. It is investigated that RecA/Rad51 family proteins play a central role. The breast cancer susceptibility protein Brca2 and the RecQ helicase BLM (Bloom syndrome mutated) are tumor suppressors that maintain genome integrity, at least in part, through HR.
map03430	Mismatch repair	DNA mismatch repair (MMR) is a highly conserved biological pathway that plays a key role in maintaining genomic stability. MMR corrects DNA mismatches generated during DNA replication, thereby preventing mutations from becoming permanent in dividing cells. MMR also suppresses homologous recombination and was recently shown to play a role in DNA damage signaling. Defects in MMR are associated with genome-wide instability, predisposition to certain types of cancer including HNPCC, resistance to certain chemotherapeutic agents, and abnormalities in meiosis and sterility in mammalian systems.
map03420	Nucleotide excision repair	Nucleotide excision repair (NER) is a mechanism to recognize and repair bulky DNA damage caused by compounds, environmental carcinogens, and exposure to UV-light. In humans hereditary defects in the NER pathway are linked to at least three diseases: xeroderma pigmentosum (XP), Cockayne syndrome (CS), and trichothiodystrophy (TTD). The repair of damaged DNA involves at least 30 polypeptides within two different sub-pathways of NER known as transcription-coupled repair (TCR-NER) and global genome repair (GGR-NER). TCR refers to the expedited repair of lesions located in the actively transcribed strand of genes by RNA polymerase II (RNAP II). In GGR-NER the first step of damage recognition involves XPC-hHR23B complex together with XPE complex (in prokaryotes, uvrAB complex). The following steps of GGR-NER and TCR-NER are similar.
map03030	DNA replication	A complex network of interacting proteins and enzymes is required for DNA replication. Generally, DNA replication follows a multistep enzymatic pathway. At the DNA replication fork, a DNA helicase (DnaB or MCM complex) precedes the DNA synthetic machinery and unwinds the duplex parental DNA in cooperation with the SSB or RPA. On the leading strand, replication occurs continuously in a 5 to 3 direction, whereas on the lagging strand, DNA replication occurs discontinuously by synthesis and joining of short Okazaki fragments. In prokaryotes, the leading strand replication apparatus consists of a DNA polymerase (pol III core), a sliding clamp (beta), and a clamp loader (gamma delta complex). The DNA primase (DnaG) is needed to form RNA primers. Normally, during replication of the lagging-strand DNA template, an RNA primer is removed either by an RNase H or by the 5 to 3 exonuclease activity of DNA pol I, and the DNA ligase joins the Okazaki fragments. In eukaryotes, three DNA polymerases (alpha, delta, and epsilon) have been identified. DNA primase forms a permanent complex with DNA polymerase alpha. PCNA and RFC function as a clamp and a clamp loader. FEN 1 and RNase H1 remove the RNA from the Okazaki fragments and DNA ligase I joins the DNA.