Biological process to genes

Query process ID GO:0006281
Process name The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
Organism Oryza sativa

Click Gene ID to show a list of co-expressed genes.

ECC Gene ID Repr. ID Gene name Functional descriptionEvAGI codeArabidopsis gene name O.I. H.G. Other DB
SOs11g0146800AB079874.1-RecA bacterial DNA recombination protein familyprotein3e-49At3g22880DMC1 (DISRUPTION OF MEIOTIC CONTROL 1)O.I.H.G.
SOs12g0143800AB079873.1-Meiotic recombination protein DMC1 homolog7e-38At3g22880DMC1 (DISRUPTION OF MEIOTIC CONTROL 1)O.I.H.G.
COs10g0518900AK070764.1-DNA repair protein rad10 family protein2e-1At4g01050hydroxyproline-rich glycoprotein family proteinO.I.H.G.
COs11g0615800AB080262.1-RAD51 homolog RAD51A1e-73At5g20850ATRAD51O.I.H.G.
COs12g0497300AB080264.1-RAD51 homolog RAD51B7e-75At5g20850ATRAD51O.I.H.G.
LOs01g0180600NM_189554.1-MutS homolog 7 (Fragment)1e-10At3g24495MSH7 (MUTS HOMOLOG 7)O.I.H.G.
LOs01g0578000AK060971.1-RecA bacterial DNA recombination protein familyprotein2e-1At2g45280ATRAD51CO.I.H.G.
LOs01g0757800AK067990.1-UMUC-like DNA-repair protein family protein8e-11At5g44740POLH (Y-FAMILT DNA POLYMERASE H)O.I.H.G.
LOs01g0777300NM_191476.1-DNA repair protein (XPGC)/yeast Rad family protein1e-9At1g29630nucleaseO.I.H.G.
LOs01g0799500AU066087-Methyladenine glycosylase family protein1e-8At3g12710methyladenine glycosylase family proteinO.I.H.G.
LOs01g0801000AK101426.1-Apurinic endonuclease-redox protein (DNA-(apurinicor apyrimidinic site) lyase) (EC
LOs01g0801100AK102132.1-Apurinic endonuclease-redox protein (DNA-(apurinicor apyrimidinic site) lyase) (EC proteinO.I.H.G.
LOs01g0901200AK103365.1-RecA protein (Recombinase A)7e-14At2g19490recA family proteinO.I.H.G.
LOs01g0953500AK058479.1-C2 domain containing protein1e-2At5g55530C2 domain-containing proteinO.I.H.G.
LOs02g0125800AK121932.1-Transcription factor Tfb4 family protein3e-15At1g18340basal transcription factor complex subunit-relatedO.I.H.G.
LOs02g0469300AK063552.1-ATP-binding region, ATPase-like domain containingprotein2e-8At4g24970ATP-binding region, ATPase-like domain-containing proteinO.I.H.G.
LOs02g0497500AK106285.1-Recombination/repair protein Rad50 family protein4e-7At2g31970RAD50O.I.H.G.
LOs02g0573200AB024337.1-Cryptochrome 16e-6At4g08920CRY1 (CRYPTOCHROME 1)O.I.H.G.
LOs03g0616300AK102930.1-DNA-directed polymerase kappa2e-8At1g49980DNA-directed DNA polymerase/ damaged DNA bindingO.I.H.G.
LOs04g0452100AB073547.2-Cryptochrome 1 apoprotein (Blue lightphotoreceptor)5e-19At4g08920CRY1 (CRYPTOCHROME 1)O.I.H.G.
LOs04g0507000AK067042.1-DNA mismatch repair protein9e-18At3g24320MSH1 (MUTL PROTEIN HOMOLOG 1)O.I.H.G.
LOs04g0548300AK063594.1-ARM repeat fold domain containing protein7e-1At3g25550F-box family proteinO.I.H.G.
LOs06g0151600AB111516.1-Peptidase S16, lon protease family protein8e-8At5g50340ATP binding / damaged DNA binding / nucleoside-triphosphatase/ nucleotide bindingO.I.H.G.
LOs06g0171800AK120233.1-Zn-finger Rad18 domain containing protein3e-5At1g48360hydrolase, acting on acid anhydrides, in phosphorus-containing anhydrides / nucleic acid binding / zinc ion bindingO.I.H.G.
LOs06g0237200AB099525.1-DNA polymerase lambda1e-15At1g10520DNA polymerase lambda (POLL)O.I.H.G.
LOs06g0643600AK065376.1-Formamidopyrimidine-DNA glycolase family protein9e-4At1g52500ATMMH-1 (ARABIDOPSIS THALIANA MUTM HOMOLOG-1)O.I.H.G.
LOs07g02305009635.m01249-Excinuclease ABC, C subunit, N-terminal domaincontaining protein4e-8At2g30350endo/excinuclease amino terminal domain-containing proteinO.I.H.G.
LOs07g0492100AK067461.1-UvrD/REP helicase family protein4e-11At4g25120ATP binding / ATP-dependent DNA helicase/ DNA binding / hydrolaseO.I.H.G.
LOs08g0304900AK063295.1-AtMMH-1 protein (F6D8.28 protein)2e-2At1g52500ATMMH-1 (ARABIDOPSIS THALIANA MUTM HOMOLOG-1)O.I.H.G.
LOs08g0430700AK101681.1-Regulator of chromosomecondensation/beta-lactamase-inhibitor protein II domaincontaining protein1e-5At3g02510regulator of chromosome condensation (RCC1) family proteinO.I.H.G.
LOs08g0489300AK104597.1-DNA-3-methyladenine glycosidase I-like protein8e-1At3g25650ASK15 (ARABIDOPSIS SKP1-LIKE 15)O.I.H.G.
LOs09g0420300AK120582.1-Methyladenine glycosylase family protein1e-5At1g80850methyladenine glycosylase family proteinO.I.H.G.
LOs09g0536000AK103074.1-AP endonuclease, family 1 protein1e-3At4g36050endonuclease/exonuclease/phosphatase family proteinO.I.H.G.
LOs10g0167600AK111418.1-CPD photolyase3e-31At1g12370PHR1 (PHOTOLYASE 1)O.I.H.G.

The upper GO terms

Process ID Gene number Process name
GO:000625916The chemical reactions and pathways involving DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
GO:00349840A change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.

The lower GO terms

Process ID Gene number Process name
GO:00000120The repair of single strand breaks in DNA. Repair of such breaks is mediated by the same enzyme systems as are used in base excision repair.
GO:00007250A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA.
GO:00007260A DNA repair process in which that does not require the exchange of genetic material between the broken DNA molecule and a homologous region of DNA.
GO:00007310Synthesis of DNA that proceeds from the broken 3' single-strand DNA end uses the homologous intact duplex as the template.
GO:00062843In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
GO:000628911A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
GO:00062900The repair of UV-induced T-T, C-T and C-C dimers.
GO:000629811A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination.
GO:00063010The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication. Includes pathways that remove replication-blocking lesions in conjunction with DNA replication.
GO:00063022The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.
GO:00063070The repair of alkylation damage, e.g. the removal of the alkyl group at the O6-position of guanine by O6-alkylguanine-DNA alkyltransferase (AGT).
GO:00102130A DNA repair process that is involved in repairing UV-induced DNA damage under non-photoreactivating conditions. The mechanism by which this repair process operates has not yet been completely elucidated.
GO:00435040The process of restoring mitochondrial DNA after damage.
GO:00450040Correction of replication errors by DNA polymerase using a 3'-5' exonuclease activity.
GO:00450200DNA repair pathways that tend to increase the endogenous mutation rate.
GO:00450210DNA repair pathways that do not increase the mutation rate above spontaneous background levels, e.g. excision and recombination pathways.
GO:00467870The process of restoring viral DNA after damage or errors in replication.
GO:00511030The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase, as occurs during DNA repair.
GO:00709140A DNA repair process that is initiated by an endonuclease that introduces a single-strand incision immediately 5' of a UV-induced damage site. UV-damage excision repair acts on both cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone 6-4 photoproducts (6-4PPs).

Comparison with co-expressed genes

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