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ONTOLOGY REPORT - ANNOTATIONS

Term:base-excision repair
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Accession:GO:0006284 term browser browse the term
Definition:In 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.
Synonyms:exact_synonym: BER
 xref: Wikipedia:Base_excision_repair


show annotations for term's descendants           Sort by:
base-excision repair term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Apex1 apurinic/apyrimidinic endodeoxyribonuclease 1 involved_in ISO
IBA		 (PMID:8932386)
PMID:21873635		 RGD PMID:8932386 PMID:21873635 RGD:13792537 NCBI chr15:24,144,595...24,146,785
Ensembl chr15:24,144,362...24,146,785 		JBrowse link
G Apex2 apurinic/apyrimidinic endodeoxyribonuclease 2 involved_in IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr  X:19,425,684...19,508,459
Ensembl chr  X:19,487,419...19,508,439 		JBrowse link
G Dna2 DNA replication helicase/nuclease 2 involved_in IEA GO_REF:0000107 Ensembl GO_REF:0000107 NCBI chr20:25,661,652...25,690,598
Ensembl chr20:25,662,055...25,716,319 		JBrowse link
G Ercc6 ERCC excision repair 6, chromatin remodeling factor involved_in ISO (PMID:9973627) RGD PMID:9973627 NCBI chr16:7,764,983...7,835,587
Ensembl chr16:7,765,013...7,835,587 		JBrowse link
G Fen1 flap structure-specific endonuclease 1 involved_in IEA GO_REF:0000104 UniProt GO_REF:0000104 NCBI chr 1:206,845,126...206,849,821
Ensembl chr 1:206,844,884...206,850,003 		JBrowse link
G Hmga1 high mobility group AT-hook 1 involved_in ISO (PMID:19465398) RGD PMID:19465398 NCBI chr20:5,611,088...5,618,755
Ensembl chr20:5,611,694...5,618,752 		JBrowse link
G Hmga2 high mobility group AT-hook 2 involved_in ISO
ISS		 (PMID:19465398)
GO_REF:0000024		 RGD
UniProt		 PMID:19465398 GO_REF:0000024 NCBI chr 7:55,877,145...55,998,813
Ensembl chr 7:55,880,112...55,994,784 		JBrowse link
G Hmgb1 high mobility group box 1 involved_in ISO (MGI:3722031|PMID:17803946) RGD PMID:17803946 MGI:3722031 NCBI chr12:5,973,062...5,978,565
Ensembl chr12:5,901,586...5,978,565 		JBrowse link
G Huwe1 HECT, UBA and WWE domain containing E3 ubiquitin protein ligase 1 involved_in ISS
ISO		 GO_REF:0000024
(PMID:19713937)		 UniProt
RGD		 PMID:19713937 GO_REF:0000024 NCBI chr  X:20,871,278...21,001,378
Ensembl chr  X:20,873,795...21,001,262 		JBrowse link
G Lig1 DNA ligase 1 involved_in ISO
IEA		 (PMID:19589734)
GO_REF:0000107		 RGD
Ensembl		 PMID:19589734 GO_REF:0000107 NCBI chr 1:74,165,688...74,204,400
Ensembl chr 1:74,165,842...74,204,413 		JBrowse link
G LOC100362927 replication protein A3-like involved_in IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr12:45,908,653...45,909,063
Ensembl chr12:45,908,683...45,909,048 		JBrowse link
G Mpg N-methylpurine-DNA glycosylase involved_in
acts_upstream_of_or_within		 IBA
IEA
ISO		 PMID:21873635
GO_REF:0000002
MGI:2148592|MGI:2675730 (MGI:2181327|PMID:9371767), (MGI:3028824|PMID:15177041)		 InterPro
RGD		 PMID:9371767 PMID:15177041 PMID:21873635 GO_REF:0000002 MGI:2181327 MGI:3028824, RGD:13792537 NCBI chr10:15,396,246...15,402,528
Ensembl chr10:15,395,782...15,402,520 		JBrowse link
G Mutyh mutY DNA glycosylase involved_in IEA
IBA		 GO_REF:0000104
GO_REF:0000002
PMID:21873635		 UniProt
InterPro		 PMID:21873635 GO_REF:0000002 GO_REF:0000104, RGD:13792537 NCBI chr 5:130,274,034...130,286,149
Ensembl chr 5:130,274,122...130,286,146 		JBrowse link
G Neil1 nei-like DNA glycosylase 1 involved_in IBA
ISO		 PMID:21873635
(PMID:17611195)		 RGD PMID:17611195 PMID:21873635 RGD:13792537 NCBI chr 8:57,550,142...57,556,884
Ensembl chr 8:57,550,147...57,556,258 		JBrowse link
G Neil2 nei-like DNA glycosylase 2 involved_in IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr15:37,444,676...37,454,863
Ensembl chr15:37,445,381...37,454,863 		JBrowse link
G Neil3 nei-like DNA glycosylase 3 involved_in ISO
IBA		 (PMID:23755964)
(MGI:4440390|PMID:20185759)
PMID:21873635		 RGD PMID:20185759 PMID:23755964 PMID:21873635 MGI:4440390, RGD:13792537 NCBI chr16:38,359,305...38,418,528
Ensembl chr16:38,359,371...38,418,527 		JBrowse link
G Ogg1 8-oxoguanine DNA glycosylase acts_upstream_of_or_within IDA
ISO		 MGI:2386943 (MGI:1349233|PMID:10570187), (MGI:894433|PMID:9207108) RGD PMID:9207108 PMID:10570187 PMID:9801319 MGI:1349233 MGI:894433, RGD:729091 NCBI chr 4:146,474,701...146,481,959
Ensembl chr 4:146,474,750...146,484,766 		JBrowse link
G Parp1 poly (ADP-ribose) polymerase 1 acts_upstream_of_or_within ISO (MGI:2181257|PMID:11948190) RGD PMID:11948190 MGI:2181257 NCBI chr13:92,307,593...92,339,406
Ensembl chr13:92,307,586...92,339,404 		JBrowse link
G Parp2 poly (ADP-ribose) polymerase 2 acts_upstream_of_or_within ISO (MGI:2181257|PMID:11948190) RGD PMID:11948190 MGI:2181257 NCBI chr15:24,034,069...24,044,340
Ensembl chr15:24,034,106...24,044,338 		JBrowse link
G Polb DNA polymerase beta involved_in TAS
IBA
ISS
ISO		 PMID:21873635
GO_REF:0000024
(PMID:16600869), (PMID:21362556)		 UniProt
RGD		 PMID:16600869 PMID:21362556 PMID:12388548 PMID:21873635 GO_REF:0000024, RGD:633643, RGD:13792537 NCBI chr16:69,379,438...69,402,710
Ensembl chr16:69,379,400...69,404,812 		JBrowse link
G Polq DNA polymerase theta involved_in ISO (PMID:19188258) RGD PMID:19188258 NCBI chr11:63,673,796...63,775,905
Ensembl chr11:63,673,816...63,775,878 		JBrowse link
G Rpa1 replication protein A1 involved_in ISO (PMID:9765279) RGD PMID:9765279 NCBI chr10:60,148,869...60,199,999
Ensembl chr10:60,148,793...60,199,949 		JBrowse link
G Rpa2 replication protein A2 involved_in ISO
ISS		 (PMID:9765279)
GO_REF:0000024		 RGD
UniProt		 PMID:9765279 GO_REF:0000024 NCBI chr 5:144,976,789...144,989,445
Ensembl chr 5:144,976,748...144,987,350 		JBrowse link
G Rpa3 replication protein A3 involved_in IBA
ISO		 PMID:21873635
(PMID:9765279)		 RGD PMID:9765279 PMID:21873635 RGD:13792537 NCBI chr 4:36,304,649...36,307,755
Ensembl chr 4:36,304,651...36,307,709 		JBrowse link
G Rps3 ribosomal protein S3 involved_in ISO (PMID:15518571) RGD PMID:15518571 NCBI chr 1:153,778,363...153,783,663
Ensembl chr 1:153,777,472...153,783,680 		JBrowse link
G Sirt6 sirtuin 6 involved_in ISO (MGI:3663736|PMID:16439206) RGD PMID:16439206 MGI:3663736 NCBI chr 7:8,082,312...8,087,776
Ensembl chr 7:8,082,364...8,098,914 		JBrowse link
G Slc25a16 solute carrier family 25 member 16 involved_in IEA GO_REF:0000107 Ensembl GO_REF:0000107 NCBI chr20:25,661,158...25,717,558
Ensembl chr20:25,662,055...25,716,319 		JBrowse link
G Smug1 single-strand-selective monofunctional uracil-DNA glycosylase 1 involved_in ISO
IDA		 (PMID:12161446)
PMID:12718543		 RGD PMID:12161446 PMID:12718543 RGD:634191 NCBI chr 7:134,288,565...134,302,179
Ensembl chr 7:134,287,675...134,297,226 		JBrowse link
G Tdg thymine-DNA glycosylase involved_in ISO (MGI:5287540|PMID:21817016)
(PMID:21862836), (PMID:22327402), (PMID:22573813)		 RGD PMID:21817016 PMID:21862836 PMID:22327402 PMID:22573813 MGI:5287540 NCBI chr 7:21,077,853...21,097,617
Ensembl chr 7:21,077,853...21,097,567 		JBrowse link
G Ung uracil-DNA glycosylase involved_in IDA
ISO
TAS		 (PMID:12161446) RGD PMID:12161446 PMID:12167490 PMID:11292851 PMID:15297456 RGD:634481, RGD:1599704, RGD:1599703 NCBI chr12:42,485,276...42,494,217
Ensembl chr12:42,485,276...42,494,206 		JBrowse link
G Usp47 ubiquitin specific peptidase 47 involved_in ISO (PMID:21362556) RGD PMID:21362556 NCBI chr 1:166,152,104...166,235,312
Ensembl chr 1:166,152,199...166,235,312 		JBrowse link
G Wrn WRN RecQ like helicase involved_in ISO (PMID:17611195) RGD PMID:17611195 NCBI chr16:58,763,517...58,898,604
Ensembl chr16:58,763,504...58,895,450 		JBrowse link
G Xpa XPA, DNA damage recognition and repair factor involved_in IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr 5:60,431,673...60,476,438
Ensembl chr 5:60,431,673...60,475,726 		JBrowse link
G Xrcc1 X-ray repair cross complementing 1 involved_in TAS
IBA
ISO
IDA		 PMID:21873635
(PMID:34102106), (PMID:34811483)		 RGD PMID:34102106 PMID:34811483 PMID:11056294 PMID:21873635 PMID:17412650 RGD:727220, RGD:13792537, RGD:2302580 NCBI chr 1:80,140,495...80,168,705
Ensembl chr 1:80,141,207...80,168,701 		JBrowse link
base-excision repair, AP site formation term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ercc5 ERCC excision repair 5, endonuclease involved_in ISO (PMID:9927729) RGD PMID:9927729 NCBI chr 9:46,309,477...46,354,478
Ensembl chr 9:46,309,389...46,354,472 		JBrowse link
G Nthl1 nth-like DNA glycosylase 1 involved_in IBA
ISO		 PMID:21873635
(PMID:15358233), (PMID:9927729)		 RGD PMID:9927729 PMID:15358233 PMID:21873635 RGD:13792537 NCBI chr10:13,655,791...13,661,958
Ensembl chr10:13,655,785...13,661,957 		JBrowse link
G Ogg1 8-oxoguanine DNA glycosylase involved_in IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr 4:146,474,701...146,481,959
Ensembl chr 4:146,474,750...146,484,766 		JBrowse link
G Tdg thymine-DNA glycosylase involved_in IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr 7:21,077,853...21,097,617
Ensembl chr 7:21,077,853...21,097,567 		JBrowse link
base-excision repair, AP site formation via deaminated base removal term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ung uracil-DNA glycosylase involved_in ISO
IBA		 (PMID:18973764)
PMID:21873635		 RGD PMID:18973764 PMID:21873635 RGD:13792537 NCBI chr12:42,485,276...42,494,217
Ensembl chr12:42,485,276...42,494,206 		JBrowse link
base-excision repair, DNA ligation term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Lig3 DNA ligase 3 involved_in IDA
IBA
ISO		 PMID:21873635
(PMID:24674627)
(PMID:19589734)		 RGD PMID:19589734 PMID:24674627 PMID:17412650 PMID:21873635 RGD:2302580, RGD:13792537 NCBI chr10:67,717,796...67,741,141
Ensembl chr10:67,717,812...67,798,414 		JBrowse link
base-excision repair, gap-filling term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Pcna proliferating cell nuclear antigen acts_upstream_of_or_within ISO (MGI:3045901|PMID:15177179) RGD PMID:15177179 MGI:3045901 NCBI chr 3:119,499,039...119,502,911
Ensembl chr 3:119,498,810...119,502,995 		JBrowse link
G Polb DNA polymerase beta acts_upstream_of_or_within IDA
ISO		 (MGI:3045901|PMID:15177179) RGD PMID:15177179 PMID:17412650 MGI:3045901, RGD:2302580 NCBI chr16:69,379,438...69,402,710
Ensembl chr16:69,379,400...69,404,812 		JBrowse link
G Pold1 DNA polymerase delta 1, catalytic subunit involved_in
acts_upstream_of_or_within		 IBA
IEA
ISO		 PMID:21873635
GO_REF:0000107
(MGI:3045901|PMID:15177179)
(PMID:10559260), (PMID:10559261)		 Ensembl
RGD		 PMID:10559260 PMID:10559261 PMID:15177179 PMID:21873635 GO_REF:0000107 MGI:3045901, RGD:13792537 NCBI chr 1:95,025,462...95,041,559
Ensembl chr 1:95,025,499...95,036,465 		JBrowse link
G Pole DNA polymerase epsilon, catalytic subunit involved_in ISO
IBA		 (PMID:10559260)
PMID:21873635		 RGD PMID:10559260 PMID:21873635 RGD:13792537 NCBI chr12:46,345,420...46,393,984
Ensembl chr12:46,345,420...46,393,939 		JBrowse link
G Polg DNA polymerase gamma, catalytic subunit acts_upstream_of_or_within ISO (PMID:15177179) RGD PMID:15177179 NCBI chr 1:133,382,764...133,399,578
Ensembl chr 1:133,382,766...133,398,567 		JBrowse link
G Poll DNA polymerase lambda involved_in ISO
ISS		 (PMID:19806195)
GO_REF:0000024		 RGD
UniProt		 PMID:19806195 GO_REF:0000024 NCBI chr 1:244,400,202...244,408,762
Ensembl chr 1:244,400,204...244,408,662 		JBrowse link
positive regulation of base-excision repair term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Fam168a family with sequence similarity 168, member A involved_in ISO
IBA		 (PMID:25260657)
PMID:21873635		 RGD PMID:25260657 PMID:21873635 RGD:13792537 NCBI chr 1:155,057,352...155,203,439
Ensembl chr 1:155,057,352...155,201,220 		JBrowse link
G Rps3 ribosomal protein S3 involved_in ISO (PMID:18973764) RGD PMID:18973764 NCBI chr 1:153,778,363...153,783,663
Ensembl chr 1:153,777,472...153,783,680 		JBrowse link
regulation of base-excision repair term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Parp1 poly (ADP-ribose) polymerase 1 involved_in ISO (PMID:34102106) RGD PMID:34102106 NCBI chr13:92,307,593...92,339,406
Ensembl chr13:92,307,586...92,339,404 		JBrowse link
telomere maintenance via base-excision repair term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Apex1 apurinic/apyrimidinic endodeoxyribonuclease 1 involved_in ISO
IEA		 (PMID:24703901)
GO_REF:0000107		 RGD
Ensembl		 PMID:24703901 GO_REF:0000107 NCBI chr15:24,144,595...24,146,785
Ensembl chr15:24,144,362...24,146,785 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 19818
    cellular process 17392
      cellular response to stimulus 8857
        cellular response to stress 2118
          DNA damage response 825
            DNA repair 519
              base-excision repair 43
                base-excision repair, AP site formation + 5
                base-excision repair, DNA ligation 1
                base-excision repair, gap-filling 6
                negative regulation of base-excision repair 0
                positive regulation of base-excision repair 2
                regulation of base-excision repair + 3
                telomere maintenance via base-excision repair 1
Path 2
Term Annotations click to browse term
  biological_process 19818
    metabolic process 12096
      cellular metabolic process 7496
        cellular aromatic compound metabolic process 3078
          nucleobase-containing compound metabolic process 2826
            nucleic acid metabolic process 2315
              DNA metabolic process 1001
                DNA repair 519
                  base-excision repair 43
                    base-excision repair, AP site formation + 5
                    base-excision repair, DNA ligation 1
                    base-excision repair, gap-filling 6
                    negative regulation of base-excision repair 0
                    positive regulation of base-excision repair 2
                    regulation of base-excision repair + 3
                    telomere maintenance via base-excision repair 1
paths to the root