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nucleotide excision repair pathway - Ontology Report - Rat Genome Database

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PATHWAY ONTOLOGY - ANNOTATIONS

The Pathway Ontology (PW), is currently being developed at the Rat Genome Database. For more information about this vocabulary, please see Petri et al. The rat genome database pathway portal. Database (Oxford). 2011 Apr 8;2011:bar010. Print 2011 or contact us (https://rgd.mcw.edu/rgdweb/contact/contactus.html).
Term:nucleotide excision repair pathway
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Accession:PW:0000130 term browser browse the term
Definition:The nucleotide excision repair pathway is an important mechanism for the detection of helix-distorting base alterations. Unlike the base excision repair pathway that only removes the damaged bases, the NER pathway removes an entire lesion-containing segment. The single-strand gap thus introduced is filled in by DNA polymerase using the undamaged strand as a template. The pathway can be subdivided into two sub-pathways: transcription-coupled and global genome repair. They only differ in the lesion recognition step while the core repair component is shared.
Synonyms:related_synonym: NER pathway;   Nucleotide Excision Repair;   nucleotide-excision repair
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nucleotide excision repair pathway term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ccnh cyclin H IEA KEGG rno:03420 NCBI chr 2:17,570,449...17,591,078
Ensembl chr 2:15,834,833...15,855,819 		JBrowse link
G Cdk7 cyclin-dependent kinase 7 IEA KEGG rno:03420 NCBI chr 2:33,574,623...33,599,485
Ensembl chr 2:31,840,558...31,865,383 		JBrowse link
G Cetn2 centrin 2 IEA
ISO		 KEGG
RGD		 PMID:22572993 rno:03420, RGD:7246920 NCBI chr  X:155,812,212...155,817,186
Ensembl chr  X:150,769,953...150,774,919 		JBrowse link
G Cul4a cullin 4A IEA KEGG rno:03420 NCBI chr16:83,086,688...83,124,503
Ensembl chr16:76,384,546...76,422,330 		JBrowse link
G Cul4b cullin 4B IEA KEGG rno:03420 NCBI chr  X:122,154,332...122,192,299
Ensembl chr  X:117,287,484...117,326,688 		JBrowse link
G Ddb1 damage-specific DNA binding protein 1 IEA
ISO		 KEGG
RGD		 PMID:22572993 rno:03420, RGD:7246920 NCBI chr 1:216,677,810...216,703,605
Ensembl chr 1:207,252,890...207,278,676 		JBrowse link
G Ddb2 damage specific DNA binding protein 2 ISO RGD PMID:22572993 RGD:7246920 NCBI chr 3:97,640,923...97,667,617
Ensembl chr 3:77,185,109...77,207,631 		JBrowse link
G Ercc1 ERCC excision repair 1, endonuclease non-catalytic subunit IEA
ISO		 KEGG
RGD		 PMID:19154342 rno:03420, RGD:7246926 NCBI chr 1:88,099,308...88,135,966
Ensembl chr 1:78,996,390...79,007,963 		JBrowse link
G Ercc2 ERCC excision repair 2, TFIIH core complex helicase subunit IEA
ISO		 KEGG
SMPDB
RGD		 PMID:22572993 SMP:00478 rno:03420, RGD:7246920 NCBI chr 1:88,161,342...88,175,102
Ensembl chr 1:79,033,326...79,047,102 		JBrowse link
G Ercc3 ERCC excision repair 3, TFIIH core complex helicase subunit IEA
ISO		 KEGG
RGD		 PMID:22572993 rno:03420, RGD:7246920 NCBI chr18:24,157,831...24,188,543
Ensembl chr18:23,883,580...23,914,329 		JBrowse link
G Ercc4 ERCC excision repair 4, endonuclease catalytic subunit IEA
ISO		 KEGG
SMPDB
RGD		 PMID:19154342 SMP:00478 rno:03420, RGD:7246926 NCBI chr10:2,926,085...2,958,176
Ensembl chr10:2,419,038...2,448,369
Ensembl chr10:2,419,038...2,448,369 		JBrowse link
G Ercc4l1 excision repair cross-complementing rodent repair deficiency, complementation group 4-like 1 IEA KEGG rno:03420 NCBI chr10:1,462,146...1,500,409
Ensembl chr10:954,977...983,174 		JBrowse link
G Ercc5 ERCC excision repair 5, endonuclease IEA
ISO		 KEGG
SMPDB
RGD		 PMID:19154342 SMP:00478 rno:03420, RGD:7246926 NCBI chr 9:53,801,471...53,846,611
Ensembl chr 9:46,309,389...46,354,472 		JBrowse link
G Ercc6 ERCC excision repair 6, chromatin remodeling factor IEA
ISO		 KEGG
RGD		 PMID:18166977 PMID:22824526 rno:03420, RGD:7246923, RGD:7246919 NCBI chr16:7,771,311...7,841,895
Ensembl chr16:7,765,013...7,835,587 		JBrowse link
G Ercc8 ERCC excision repair 8, CSA ubiquitin ligase complex subunit IEA
ISO		 KEGG
RGD		 PMID:18166977 PMID:22824526 rno:03420, RGD:7246923, RGD:7246919 NCBI chr 2:41,380,901...41,418,294
Ensembl chr 2:39,647,452...39,684,859 		JBrowse link
G Gtf2h1 general transcription factor IIH subunit 1 IEA
ISO		 KEGG
RGD		 PMID:22572993 rno:03420, RGD:7246920 NCBI chr 1:106,457,692...106,485,729
Ensembl chr 1:97,321,394...97,349,455 		JBrowse link
G Gtf2h2 general transcription factor IIH subunit 2 IEA
ISO		 KEGG
RGD		 PMID:21763452 rno:03420, RGD:7246922 NCBI chr 2:33,358,863...33,386,726
Ensembl chr 2:31,624,678...31,652,592 		JBrowse link
G Gtf2h3 general transcription factor IIH subunit 3 IEA KEGG rno:03420 NCBI chr12:37,669,995...37,687,505
Ensembl chr12:32,009,014...32,025,497 		JBrowse link
G Gtf2h4 general transcription factor 2H subunit 4 IEA KEGG rno:03420 NCBI chr20:3,076,110...3,081,805
Ensembl chr20:3,071,328...3,076,984 		JBrowse link
G Gtf2h5 general transcription factor IIH subunit 5 IEA KEGG rno:03420 NCBI chr 1:49,061,904...49,068,612
Ensembl chr 1:46,656,859...46,664,939 		JBrowse link
G Hmgn1 high mobility group nucleosome binding domain 1 ISO RGD PMID:22824526 RGD:7246919 NCBI chr11:48,891,813...48,897,732
Ensembl chr11:35,422,328...35,428,254 		JBrowse link
G Lig1 DNA ligase 1 IEA
ISO		 KEGG
SMPDB
RGD		 PMID: PMID:21601536 SMP:00478 rno:03420, RGD:1358139, RGD:7246935 NCBI chr 1:83,243,043...83,281,707
Ensembl chr 1:74,165,842...74,204,413 		JBrowse link
G Lig3 DNA ligase 3 ISO RGD PMID:21601536 RGD:7246935 NCBI chr10:68,215,371...68,238,705
Ensembl chr10:67,717,812...67,798,414 		JBrowse link
G Mnat1 MNAT1 component of CDK activating kinase IEA KEGG rno:03420 NCBI chr 6:97,550,566...97,706,598
Ensembl chr 6:91,814,749...91,970,744 		JBrowse link
G Pcna proliferating cell nuclear antigen IEA
ISO		 KEGG
SMPDB
RGD		 PMID:17512402 PMID:23545418 SMP:00478 rno:03420, RGD:7246931, RGD:7246932 NCBI chr 3:139,951,948...139,955,820
Ensembl chr 3:119,498,810...119,502,995 		JBrowse link
G Pold1 DNA polymerase delta 1, catalytic subunit IEA
ISO		 KEGG
RGD		 PMID: PMID:21601536 rno:03420, RGD:1358139, RGD:7246935 NCBI chr 1:104,161,984...104,178,074
Ensembl chr 1:95,025,499...95,036,465 		JBrowse link
G Pold2 DNA polymerase delta 2, accessory subunit IEA
ISO		 KEGG
RGD		 PMID:21601536 rno:03420, RGD:7246935 NCBI chr14:80,748,971...80,755,188
Ensembl chr14:80,748,974...80,755,160 		JBrowse link
G Pold3 DNA polymerase delta 3, accessory subunit IEA
ISO		 KEGG
RGD		 PMID:21601536 rno:03420, RGD:7246935 NCBI chr 1:163,830,217...163,870,015
Ensembl chr 1:154,418,084...154,456,665 		JBrowse link
G Pold4 DNA polymerase delta 4, accessory subunit IEA
ISO		 KEGG
RGD		 PMID:21601536 rno:03420, RGD:7246935 NCBI chr 1:210,956,110...210,957,863
Ensembl chr 1:201,526,665...201,528,401 		JBrowse link
G Pole DNA polymerase epsilon, catalytic subunit IEA
ISO		 KEGG
SMPDB
RGD		 PMID:12806123 PMID:21601536 SMP:00478 rno:03420, RGD:7246936, RGD:7246935 NCBI chr12:52,005,155...52,053,761
Ensembl chr12:46,345,420...46,393,939 		JBrowse link
G Pole2 DNA polymerase epsilon 2, accessory subunit IEA
ISO		 KEGG
RGD		 PMID:12806123 rno:03420, RGD:7246936 NCBI chr 6:93,410,713...93,448,782
Ensembl chr 6:87,674,702...87,699,305 		JBrowse link
G Pole3 DNA polymerase epsilon 3, accessory subunit IEA
ISO		 KEGG
RGD		 PMID:12806123 rno:03420, RGD:7246936 NCBI chr 5:80,989,508...80,992,742
Ensembl chr 5:75,974,717...75,977,231
Ensembl chr 7:75,974,717...75,977,231 		JBrowse link
G Pole3-ps3 DNA polymerase epsilon 3, accessory subunit, pseudogene 3 ISO RGD PMID:12806123 RGD:7246936 NCBI chr 7:109,236,108...109,236,813
Ensembl chr 7:109,236,321...109,236,758 		JBrowse link
G Pole4 DNA polymerase epsilon 4, accessory subunit IEA
ISO		 KEGG
RGD		 PMID:12806123 rno:03420, RGD:7246936 NCBI chr 4:116,723,040...116,728,873
Ensembl chr 4:115,165,285...115,171,097 		JBrowse link
G Polk DNA polymerase kappa ISO RGD PMID:21601536 RGD:7246935 NCBI chr 2:29,556,831...29,616,960
Ensembl chr 2:27,822,679...27,882,313 		JBrowse link
G Polr1a RNA polymerase I subunit A ISO SMPDB SMP:00478 NCBI chr 4:105,508,305...105,572,272
Ensembl chr 4:103,950,051...104,014,020 		JBrowse link
G Rad23a RAD23 homolog A, nucleotide excision repair protein IEA
ISO		 KEGG
SMPDB		 SMP:00478 rno:03420 NCBI chr19:40,219,235...40,225,543
Ensembl chr19:23,314,797...23,320,695 		JBrowse link
G Rad23b RAD23 homolog B, nucleotide excision repair protein IEA
ISO		 KEGG
RGD		 PMID:22572993 rno:03420, RGD:7246920 NCBI chr 5:74,885,518...74,923,621
Ensembl chr 5:70,090,232...70,128,319 		JBrowse link
G Rbx1 ring-box 1 IEA KEGG rno:03420 NCBI chr 7:114,870,893...114,881,194
Ensembl chr 7:112,990,835...113,001,051 		JBrowse link
G Rfc1 replication factor C subunit 1 IEA
ISO		 KEGG
SMPDB
RGD		 PMID:23545418 SMP:00478 rno:03420, RGD:7246932 NCBI chr14:43,319,768...43,395,028
Ensembl chr14:42,966,324...43,041,370 		JBrowse link
G Rfc2 replication factor C subunit 2 IEA
ISO		 KEGG
RGD		 PMID:23545418 rno:03420, RGD:7246932 NCBI chr12:27,756,920...27,770,049
Ensembl chr12:22,120,010...22,133,557 		JBrowse link
G Rfc3 replication factor C subunit 3 IEA
ISO		 KEGG
RGD		 PMID:23545418 rno:03420, RGD:7246932 NCBI chr12:5,836,546...5,847,331
Ensembl chr12:1,000,994...1,011,778 		JBrowse link
G Rfc4 replication factor C subunit 4 IEA
ISO		 KEGG
RGD		 PMID:23545418 rno:03420, RGD:7246932 NCBI chr11:91,254,273...91,268,727
Ensembl chr11:77,749,638...77,764,122 		JBrowse link
G Rfc5 replication factor C subunit 5 IEA
ISO		 KEGG
RGD		 PMID:23545418 rno:03420, RGD:7246932 NCBI chr12:44,868,322...44,877,879
Ensembl chr12:39,207,484...39,217,312 		JBrowse link
G Rpa1 replication protein A1 IEA
ISO		 KEGG
RGD		 PMID:19154342 rno:03420, RGD:7246926 NCBI chr10:60,647,185...60,698,279
Ensembl chr10:60,148,793...60,199,949 		JBrowse link
G Rpa2 replication protein A2 IEA
ISO		 KEGG
RGD		 PMID:19154342 rno:03420, RGD:7246926 NCBI chr 5:150,260,668...150,271,329
Ensembl chr 5:144,976,748...144,987,350 		JBrowse link
G Rpa3 replication protein A3 IEA
ISO		 KEGG
RGD		 PMID:19154342 rno:03420, RGD:7246926 NCBI chr 4:37,270,966...37,273,997
Ensembl chr 4:36,304,651...36,307,709 		JBrowse link
G Tent4a terminal nucleotidyltransferase 4A ISO SMPDB SMP:00478 NCBI chr 1:35,594,380...35,627,836
Ensembl chr 1:33,765,672...33,799,433 		JBrowse link
G Xab2 XPA binding protein 2 ISO RGD PMID:22824526 RGD:7246919 NCBI chr12:1,667,672...1,679,702
Ensembl chr12:1,667,672...1,679,692 		JBrowse link
G Xpa XPA, DNA damage recognition and repair factor IEA
ISO		 KEGG
SMPDB
RGD		 PMID:19154342 SMP:00478 rno:03420, RGD:7246926 NCBI chr 5:65,227,281...65,275,784
Ensembl chr 5:60,431,673...60,475,726 		JBrowse link
G Xpc XPC complex subunit, DNA damage recognition and repair factor IEA
ISO		 KEGG
RGD		 PMID:21763452 PMID:22572993 rno:03420, RGD:7246922, RGD:7246920 NCBI chr 4:125,550,833...125,578,084
Ensembl chr 4:123,993,666...124,021,010 		JBrowse link
G Xrcc1 X-ray repair cross complementing 1 ISO RGD PMID:21601536 RGD:7246935 NCBI chr 1:89,268,721...89,296,619
Ensembl chr 1:80,141,207...80,168,701 		JBrowse link
altered nucleotide excision repair pathway term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ddb1 damage-specific DNA binding protein 1 ISO RGD PMID:22824526 RGD:7246919 NCBI chr 1:216,677,810...216,703,605
Ensembl chr 1:207,252,890...207,278,676 		JBrowse link
G Ercc2 ERCC excision repair 2, TFIIH core complex helicase subunit ISO RGD PMID:22824526 RGD:7246919 NCBI chr 1:88,161,342...88,175,102
Ensembl chr 1:79,033,326...79,047,102 		JBrowse link
G Ercc3 ERCC excision repair 3, TFIIH core complex helicase subunit ISO RGD PMID:22824526 RGD:7246919 NCBI chr18:24,157,831...24,188,543
Ensembl chr18:23,883,580...23,914,329 		JBrowse link
G Ercc4 ERCC excision repair 4, endonuclease catalytic subunit ISO in silico assessment of alteration of DNA-protein, protein-protein interactions and observed reduction of DNA repair capacity in the context of nucleotide excision repair pathway for SNP RGD PMID:22824526 PMID:24004570 RGD:7246919, RGD:9588971 NCBI chr10:2,926,085...2,958,176
Ensembl chr10:2,419,038...2,448,369
Ensembl chr10:2,419,038...2,448,369 		JBrowse link
G Ercc5 ERCC excision repair 5, endonuclease ISO RGD PMID:22824526 RGD:7246919 NCBI chr 9:53,801,471...53,846,611
Ensembl chr 9:46,309,389...46,354,472 		JBrowse link
G Ercc6 ERCC excision repair 6, chromatin remodeling factor ISO RGD PMID:22824526 RGD:7246919 NCBI chr16:7,771,311...7,841,895
Ensembl chr16:7,765,013...7,835,587 		JBrowse link
G Ercc8 ERCC excision repair 8, CSA ubiquitin ligase complex subunit ISO RGD PMID:22824526 RGD:7246919 NCBI chr 2:41,380,901...41,418,294
Ensembl chr 2:39,647,452...39,684,859 		JBrowse link
G Xpa XPA, DNA damage recognition and repair factor ISO RGD PMID:22824526 RGD:7246919 NCBI chr 5:65,227,281...65,275,784
Ensembl chr 5:60,431,673...60,475,726 		JBrowse link
G Xpc XPC complex subunit, DNA damage recognition and repair factor ISO RGD PMID:22824526 RGD:7246919 NCBI chr 4:125,550,833...125,578,084
Ensembl chr 4:123,993,666...124,021,010 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  pathway 6091
    regulatory pathway 3866
      pathway pertinent to DNA replication and repair, cell cycle, maintenance of genomic integrity, RNA and protein biosynthesis 1738
        DNA repair pathway 384
          single-strand DNA repair pathway 83
            nucleotide excision repair pathway 52
              altered nucleotide excision repair pathway 9
Path 2
Term Annotations click to browse term
  pathway 6091
    regulatory pathway 3866
      pathway pertinent to DNA replication and repair, cell cycle, maintenance of genomic integrity, RNA and protein biosynthesis 1738
        DNA damage response pathway 405
          DNA repair pathway 384
            single-strand DNA repair pathway 83
              nucleotide excision repair pathway 52
                altered nucleotide excision repair pathway 9
paths to the root