PPGR - Gene Detail

Basic Information

Gene ID	gene-LOC118062154 View in Genome Browser
Position	NW_023271789.1:2168442-2174288 (+) 5846bp
Gene Type	gene
Gene Description (Protein Product)	DNA repair
Organism	Populus alba
Also AS	Potri.005G226500AT2G18760Potri.005G226500.v4.1

upstream:

Domain

Database	EntryID	E-Value	Start	end	InterPro ID	Description

Regulation&Interaction

Protein-protein interaction (PPI)

gene-LOC118063537 nucleotide-excision repair, DNA gap filling

gene-LOC118062990 Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked

gene-LOC118062472 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates

Regulatory gene

gene-LOC118027806 Cyclic dof factor

gene-LOC118027982 B3 DNA binding domain

gene-LOC118027984 B3 DNA binding domain

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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:0001207	obsolete histone displacement	BP
GO:0001208	obsolete histone H2A-H2B dimer displacement	BP
GO:0003674	molecular_function	MF
GO:0003824	catalytic activity	MF
GO:0006139	nucleobase-containing compound metabolic process	BP
GO:0006259	DNA metabolic process	BP
GO:0006281	DNA repair	BP
GO:0006283	transcription-coupled nucleotide-excision repair	BP
GO:0006289	nucleotide-excision repair	BP
GO:0006325	chromatin organization	BP
GO:0006355	regulation of DNA-templated transcription	BP
GO:0006357	regulation of transcription by RNA polymerase II	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:0008094	ATP-dependent activity, acting on DNA	MF
GO:0008150	biological_process	BP
GO:0008152	metabolic 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:0009987	cellular process	BP
GO:0010212	response to ionizing radiation	BP
GO:0010332	response to gamma radiation	BP
GO:0010468	regulation of gene expression	BP
GO:0010556	regulation of macromolecule biosynthetic process	BP
GO:0010767	regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage	BP
GO:0016043	cellular component organization	BP
GO:0016462	pyrophosphatase activity	MF
GO:0016787	hydrolase activity	MF
GO:0016817	hydrolase activity, acting on acid anhydrides	MF
GO:0016818	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	MF
GO:0016887	ATP hydrolysis activity	MF
GO:0017111	ribonucleoside triphosphate phosphatase activity	MF
GO:0019219	regulation of nucleobase-containing compound metabolic process	BP
GO:0019222	regulation of metabolic process	BP
GO:0031323	regulation of cellular metabolic process	BP
GO:0031326	regulation of cellular biosynthetic process	BP
GO:0033554	cellular response to stress	BP
GO:0034641	cellular nitrogen compound metabolic process	BP
GO:0034644	cellular response to UV	BP
GO:0034728	nucleosome organization	BP
GO:0042623	ATP hydrolysis activity	MF
GO:0043170	macromolecule metabolic process	BP
GO:0043618	regulation of transcription from RNA polymerase II promoter in response to stress	BP
GO:0043620	regulation of DNA-templated transcription in response to stress	BP
GO:0043933	protein-containing complex organization	BP
GO:0044237	cellular metabolic process	BP
GO:0044238	primary metabolic process	BP
GO:0044260	cellular macromolecule metabolic process	BP
GO:0046483	heterocycle metabolic process	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:0051252	regulation of RNA metabolic process	BP
GO:0051276	chromosome organization	BP
GO:0051716	cellular response to stimulus	BP
GO:0060255	regulation of macromolecule metabolic process	BP
GO:0065007	biological regulation	BP
GO:0071214	cellular response to abiotic stimulus	BP
GO:0071478	cellular response to radiation	BP
GO:0071482	cellular response to light stimulus	BP
GO:0071704	organic substance metabolic process	BP
GO:0071824	protein-DNA 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:0104004	cellular response to environmental stimulus	BP
GO:1901360	organic cyclic compound metabolic process	BP
GO:1903506	regulation of nucleic acid-templated transcription	BP
GO:2000112	regulation of cellular macromolecule biosynthetic process	BP
GO:2001141	regulation of RNA biosynthetic process	BP

KEGG Term	Name	Description
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.