PPGR - Gene Detail

Basic Information

Gene Structure

Domain

Regulation&
Interaction

Annotation

Orthologus Group

Expresssion

Pathway

Basic Information

Gene ID	Lchi25002.g View in Genome Browser
Position	Scaffold197:2838039-2856780 (+) 18741bp
Gene Type	gene
Gene Description (Protein Product)	Rad4 beta-hairpin domain 3
Organism	Liriodendron chinense
Also AS	AT5G16630

upstream:

Domain

Database	EntryID	E-Value	Start	end	InterPro ID	Description

Regulation&Interaction

Protein-protein interaction (PPI)	Lchi28640.g DNA repair helicase Lchi31285.g DNA repair protein Lchi27049.g repair protein
Regulatory gene	Lchi00886.g (NAC) domain-containing protein Lchi00930.g Transcriptional activator that specifically binds 5'- GATA-3' or 5'-GAT-3' motifs within gene promoters Lchi01101.g beta-amylase

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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:0000109	nucleotide-excision repair complex	CC
GO:0000111	nucleotide-excision repair factor 2 complex	CC
GO:0000217	DNA secondary structure binding	MF
GO:0000404	heteroduplex DNA loop binding	MF
GO:0000405	bubble DNA binding	MF
GO:0000715	nucleotide-excision repair, DNA damage recognition	BP
GO:0003674	molecular_function	MF
GO:0003676	nucleic acid binding	MF
GO:0003677	DNA binding	MF
GO:0003684	damaged DNA binding	MF
GO:0003690	double-stranded DNA binding	MF
GO:0003697	single-stranded DNA 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:0005654	nucleoplasm	CC
GO:0005730	nucleolus	CC
GO:0005737	cytoplasm	CC
GO:0005739	mitochondrion	CC
GO:0005886	plasma membrane	CC
GO:0006139	nucleobase-containing compound metabolic process	BP
GO:0006259	DNA metabolic process	BP
GO:0006281	DNA repair	BP
GO:0006289	nucleotide-excision repair	BP
GO:0006294	nucleotide-excision repair, preincision complex assembly	BP
GO:0006298	mismatch repair	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:0007346	regulation of mitotic cell cycle	BP
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:0009507	chloroplast	CC
GO:0009536	plastid	CC
GO:0009628	response to abiotic stimulus	BP
GO:0009987	cellular process	BP
GO:0010564	regulation of cell cycle process	BP
GO:0016020	membrane	CC
GO:0016043	cellular component organization	BP
GO:0022607	cellular component assembly	BP
GO:0030983	mismatched DNA binding	MF
GO:0031974	membrane-enclosed lumen	CC
GO:0031981	nuclear lumen	CC
GO:0032135	DNA insertion or deletion binding	MF
GO:0032991	protein-containing complex	CC
GO:0033554	cellular response to stress	BP
GO:0034622	protein-containing complex assembly	BP
GO:0034641	cellular nitrogen compound metabolic process	BP
GO:0034644	cellular response to UV	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:0043231	intracellular membrane-bounded organelle	CC
GO:0043232	intracellular non-membrane-bounded organelle	CC
GO:0043233	organelle lumen	CC
GO:0043933	protein-containing complex organization	BP
GO:0044085	cellular component biogenesis	BP
GO:0044237	cellular metabolic process	BP
GO:0044238	primary metabolic process	BP
GO:0044260	cellular macromolecule metabolic process	BP
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:0044464	obsolete cell part	CC
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:0051276	chromosome organization	BP
GO:0051716	cellular response to stimulus	BP
GO:0051726	regulation of cell cycle	BP
GO:0065003	protein-containing complex assembly	BP
GO:0065004	protein-DNA complex assembly	BP
GO:0065007	biological regulation	BP
GO:0070013	intracellular organelle lumen	CC
GO:0070911	global genome nucleotide-excision repair	BP
GO:0070914	UV-damage excision repair	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:0071942	XPC complex	CC
GO:0071944	cell periphery	CC
GO:0090304	nucleic acid metabolic process	BP
GO:0097159	organic cyclic compound binding	MF
GO:0104004	cellular response to environmental stimulus	BP
GO:1901360	organic cyclic compound metabolic process	BP
GO:1901363	heterocyclic compound binding	MF
GO:1901987	regulation of cell cycle phase transition	BP
GO:1901990	regulation of mitotic cell cycle phase transition	BP
GO:1990391	DNA repair complex	CC

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.