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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



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base-excision repair term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G AL451136.1 novel protein involved_in IEA InterPro GO_REF:0000002 Ensembl chr 1:45,329,262...45,491,155 JBrowse link
G APEX1 apurinic/apyrimidinic endodeoxyribonuclease 1 involved_in IBA
IDA
(PMID:21873635)
(PMID:8932386)
GO_Central
CAFA
PMID:8932386 PMID:21873635 NCBI chr14:20,455,226...20,457,767
Ensembl chr14:20,455,191...20,457,772
JBrowse link
G APEX2 apurinic/apyrimidinic endodeoxyribonuclease 2 involved_in IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr  X:55,000,363...55,009,057
Ensembl chr  X:55,000,363...55,009,057
JBrowse link
G DNA2 DNA replication helicase/nuclease 2 involved_in IDA (PMID:18995831) UniProt PMID:18995831 NCBI chr10:68,414,064...68,472,521
Ensembl chr10:68,414,064...68,472,121
JBrowse link
G ERCC6 ERCC excision repair 6, chromatin remodeling factor involved_in IMP (PMID:9973627) UniProt PMID:9973627 NCBI chr10:49,434,881...49,539,538
Ensembl chr10:49,454,168...49,539,538
JBrowse link
G HMGA1 high mobility group AT-hook 1 involved_in IDA (PMID:19465398) UniProt PMID:19465398 NCBI chr 6:34,236,873...34,246,231
Ensembl chr 6:34,236,873...34,246,231
JBrowse link
G HMGA2 high mobility group AT-hook 2 involved_in IDA (PMID:19465398) UniProt PMID:19465398 NCBI chr12:65,824,460...65,966,291
Ensembl chr12:65,824,460...65,966,291
JBrowse link
G HMGB1 high mobility group box 1 involved_in ISO (MGI:3722031|PMID:17803946) UniProt PMID:17803946 MGI:3722031 NCBI chr13:30,456,704...30,617,597
Ensembl chr13:30,456,704...30,617,597
JBrowse link
G HUWE1 HECT, UBA and WWE domain containing E3 ubiquitin protein ligase 1 involved_in IBA
IMP
(PMID:21873635)
(PMID:19713937)
GO_Central
UniProt
PMID:19713937 PMID:21873635 NCBI chr  X:53,532,096...53,686,723
Ensembl chr  X:53,532,096...53,686,728
JBrowse link
G L34079.1 novel protein involved_in IBA (PMID:21873635) GO_Central PMID:21873635 Ensembl chr19:43,554,692...43,593,036 JBrowse link
G LIG1 DNA ligase 1 involved_in IDA (PMID:19589734) BHF-UCL PMID:19589734 NCBI chr19:48,115,445...48,170,595
Ensembl chr19:48,115,445...48,170,603
JBrowse link
G MPG N-methylpurine DNA glycosylase involved_in
acts_upstream_of_or_within
IBA
ISO
IEA
(PMID:21873635)
(MGI:3028824|PMID:15177041)
(MGI:2181327|PMID:9371767)
GO_Central
MGI
InterPro
PMID:9371767 PMID:15177041 PMID:21873635 GO_REF:0000002 MGI:2181327 MGI:3028824 NCBI chr16:77,007...85,846
Ensembl chr16:77,007...85,851
JBrowse link
G MUTYH mutY DNA glycosylase involved_in IBA
IEA
(PMID:21873635) GO_Central
UniProt
InterPro
PMID:21873635 GO_REF:0000002 GO_REF:0000104 NCBI chr 1:45,329,242...45,340,447
Ensembl chr 1:45,329,163...45,340,893
JBrowse link
G NEIL1 nei like DNA glycosylase 1 involved_in IDA
IBA
IEA
(PMID:17611195)
(PMID:21873635)
UniProt
GO_Central
InterPro
PMID:17611195 PMID:21873635 GO_REF:0000002 NCBI chr15:75,346,638...75,357,115
Ensembl chr15:75,346,955...75,357,115
JBrowse link
G NEIL2 nei like DNA glycosylase 2 involved_in IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 8:11,769,710...11,787,345
Ensembl chr 8:11,769,639...11,787,345
JBrowse link
G NEIL3 nei like DNA glycosylase 3 involved_in ISS
IBA
IDA
(PMID:21873635)
(PMID:23755964)
UniProt
GO_Central
HGNC
PMID:21873635 PMID:23755964 GO_REF:0000024 NCBI chr 4:177,309,871...177,362,936
Ensembl chr 4:177,309,874...177,362,936
JBrowse link
G NTHL1 nth like DNA glycosylase 1 involved_in IEA InterPro GO_REF:0000002 NCBI chr16:2,039,820...2,047,834
Ensembl chr16:2,039,815...2,047,866
JBrowse link
G OGG1 8-oxoguanine DNA glycosylase involved_in
acts_upstream_of_or_within
IEA
ISO
TAS
(MGI:1349233|PMID:10570187)
(MGI:894433|PMID:9207108)
(PMID:9190902)
InterPro
MGI
RGD
PINC
PMID:9190902 PMID:9207108 PMID:9801319 PMID:10570187 GO_REF:0000002 MGI:1349233 MGI:894433 RGD:729091 NCBI chr 3:9,749,952...9,788,246
Ensembl chr 3:9,749,944...9,788,219
JBrowse link
G PARP1 poly(ADP-ribose) polymerase 1 acts_upstream_of_or_within ISO (MGI:2181257|PMID:11948190) MGI PMID:11948190 MGI:2181257 NCBI chr 1:226,360,691...226,408,093
Ensembl chr 1:226,360,210...226,408,154
JBrowse link
G PARP2 poly(ADP-ribose) polymerase 2 involved_in
acts_upstream_of_or_within
IEA
ISO
(MGI:2181257|PMID:11948190) Ensembl
MGI
PMID:11948190 GO_REF:0000107 MGI:2181257 NCBI chr14:20,343,041...20,357,904
Ensembl chr14:20,343,615...20,357,904
JBrowse link
G POLB DNA polymerase beta involved_in IDA
IBA
IMP
(PMID:16600869)
(PMID:21873635)
(PMID:21362556)
UniProt
GO_Central
PMID:16600869 PMID:21362556 PMID:21873635 NCBI chr 8:42,338,452...42,371,810
Ensembl chr 8:42,338,454...42,371,808
JBrowse link
G POLQ DNA polymerase theta involved_in IDA (PMID:19188258) UniProt PMID:19188258 NCBI chr 3:121,431,431...121,545,988
Ensembl chr 3:121,431,431...121,545,988
JBrowse link
G PRMT6 protein arginine methyltransferase 6 involved_in TAS (PMID:16600869) UniProt PMID:16600869 NCBI chr 1:107,056,674...107,059,294
Ensembl chr 1:107,056,674...107,067,636
JBrowse link
G RPA1 replication protein A1 involved_in IDA (PMID:9765279) UniProt PMID:9765279 NCBI chr17:1,830,005...1,900,082
Ensembl chr17:1,829,702...1,900,082
JBrowse link
G RPA2 replication protein A2 involved_in IDA (PMID:9765279) UniProt PMID:9765279 NCBI chr 1:27,891,524...27,914,797
Ensembl chr 1:27,891,524...27,914,746
JBrowse link
G RPA3 replication protein A3 involved_in IBA
IDA
(PMID:21873635)
(PMID:9765279)
GO_Central
UniProt
PMID:9765279 PMID:21873635 NCBI chr 7:7,636,518...7,718,607
Ensembl chr 7:7,636,518...7,718,607
JBrowse link
G SIRT6 sirtuin 6 involved_in IEA Ensembl GO_REF:0000107 NCBI chr19:4,174,109...4,182,563
Ensembl chr19:4,174,109...4,182,566
JBrowse link
G SMUG1 single-strand-selective monofunctional uracil-DNA glycosylase 1 involved_in IDA
IEA
(PMID:12161446) HGNC-UCL
InterPro
PMID:12161446 GO_REF:0000002 NCBI chr12:54,121,274...54,188,985
Ensembl chr12:54,121,277...54,189,008
JBrowse link
G TDG thymine DNA glycosylase involved_in IDA (PMID:21862836), (PMID:22327402) UniProt PMID:21862836 PMID:22327402 NCBI chr12:103,965,842...103,988,874
Ensembl chr12:103,965,822...103,988,874
JBrowse link
G UNG uracil DNA glycosylase involved_in IEA
ISO
TAS
IDA
(PMID:10805771)
(PMID:12161446)
InterPro
RGD
UniProt
PINC
HGNC
PMID:10805771 PMID:12161446 PMID:12167490 GO_REF:0000002 GO_REF:0000104 RGD:634481 NCBI chr12:109,097,597...109,110,992
Ensembl chr12:109,097,597...109,110,992
JBrowse link
G USP47 ubiquitin specific peptidase 47 involved_in IMP (PMID:21362556) UniProt PMID:21362556 NCBI chr11:11,841,972...11,961,887
Ensembl chr11:11,841,423...11,961,887
JBrowse link
G WRN WRN RecQ like helicase involved_in IDA (PMID:17611195) UniProt PMID:17611195 NCBI chr 8:31,033,749...31,176,138
Ensembl chr 8:31,033,788...31,176,138
JBrowse link
G XPA XPA, DNA damage recognition and repair factor involved_in IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 9:97,654,398...97,697,403
Ensembl chr 9:97,674,909...97,697,340
JBrowse link
G XRCC1 X-ray repair cross complementing 1 involved_in IBA
IEA
ISO
(PMID:21873635) GO_Central
InterPro
RGD
PMID:17412650 PMID:21873635 GO_REF:0000002 RGD:2302580 NCBI chr19:43,543,311...43,575,527
Ensembl chr19:43,543,311...43,580,473
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 IDA (PMID:9927729) UniProt PMID:9927729 NCBI chr13:102,846,032...102,875,995
Ensembl chr13:102,845,831...102,875,995
JBrowse link
G NEIL3 nei like DNA glycosylase 3 involved_in TAS Reactome Reactome:R-HSA-73929 NCBI chr 4:177,309,871...177,362,936
Ensembl chr 4:177,309,874...177,362,936
JBrowse link
G NTHL1 nth like DNA glycosylase 1 involved_in IDA
IBA
IEA
(PMID:15358233), (PMID:9927729)
(PMID:21873635)
UniProt
GO_Central
InterPro
PMID:9927729 PMID:15358233 PMID:21873635 GO_REF:0000002 NCBI chr16:2,039,820...2,047,834
Ensembl chr16:2,039,815...2,047,866
JBrowse link
G OGG1 8-oxoguanine DNA glycosylase involved_in IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 3:9,749,952...9,788,246
Ensembl chr 3:9,749,944...9,788,219
JBrowse link
G TDG thymine DNA glycosylase involved_in IEA
IMP
IBA
IDA
(PMID:18512959)
(PMID:21873635)
(PMID:11889051)
InterPro
CAFA
GO_Central
PMID:11889051 PMID:18512959 PMID:21873635 GO_REF:0000002 NCBI chr12:103,965,842...103,988,874
Ensembl chr12:103,965,822...103,988,874
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 IDA
IBA
(PMID:18973764)
(PMID:21873635)
UniProt
GO_Central
PMID:18973764 PMID:21873635 NCBI chr12:109,097,597...109,110,992
Ensembl chr12:109,097,597...109,110,992
JBrowse link
base-excision repair, base-free sugar-phosphate removal term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G POLB DNA polymerase beta involved_in TAS Reactome Reactome:R-HSA-110375 NCBI chr 8:42,338,452...42,371,810
Ensembl chr 8:42,338,454...42,371,808
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 TAS
ISO
IDA
IMP
IBA
(PMID:19589734)
(PMID:24674627)
(PMID:21873635)
Reactome
RGD
BHF-UCL
GO_Central
PMID:17412650 PMID:19589734 PMID:21873635 PMID:24674627 RGD:2302580 Reactome:R-HSA-73931 NCBI chr17:34,980,504...35,009,743
Ensembl chr17:34,980,512...35,009,743
JBrowse link
base-excision repair, gap-filling term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ADPRS ADP-ribosylserine hydrolase involved_in TAS Reactome Reactome:R-HSA-110373 NCBI chr 1:36,088,885...36,093,932
Ensembl chr 1:36,088,892...36,093,932
JBrowse link
G APEX1 apurinic/apyrimidinic endodeoxyribonuclease 1 involved_in TAS Reactome Reactome:R-HSA-73933 NCBI chr14:20,455,226...20,457,767
Ensembl chr14:20,455,191...20,457,772
JBrowse link
G BPHL biphenyl hydrolase like involved_in TAS Reactome Reactome:R-HSA-110373 NCBI chr 6:3,118,376...3,153,599
Ensembl chr 6:3,118,374...3,153,578
JBrowse link
G FEN1 flap structure-specific endonuclease 1 involved_in TAS Reactome Reactome:R-HSA-110373 NCBI chr11:61,792,911...61,797,238
Ensembl chr11:61,792,911...61,797,238
JBrowse link
G LIG1 DNA ligase 1 involved_in TAS Reactome Reactome:R-HSA-110373 NCBI chr19:48,115,445...48,170,595
Ensembl chr19:48,115,445...48,170,603
JBrowse link
G LIG3 DNA ligase 3 involved_in TAS Reactome Reactome:R-HSA-5649702 NCBI chr17:34,980,504...35,009,743
Ensembl chr17:34,980,512...35,009,743
JBrowse link
G NEIL1 nei like DNA glycosylase 1 involved_in TAS Reactome Reactome:R-HSA-5649702 NCBI chr15:75,346,638...75,357,115
Ensembl chr15:75,346,955...75,357,115
JBrowse link
G PARG poly(ADP-ribose) glycohydrolase involved_in TAS Reactome Reactome:R-HSA-110373 NCBI chr10:49,818,279...49,942,027
Ensembl chr10:49,818,279...49,970,203
JBrowse link
G PCNA proliferating cell nuclear antigen acts_upstream_of_or_within
involved_in
ISO
IEA
(MGI:3045901|PMID:15177179) MGI
Ensembl
PMID:15177179 GO_REF:0000107 MGI:3045901 NCBI chr20:5,114,953...5,126,622
Ensembl chr20:5,114,953...5,126,626
JBrowse link
G PNKP polynucleotide kinase 3'-phosphatase involved_in TAS Reactome Reactome:R-HSA-5649702 NCBI chr19:49,861,204...49,867,576
Ensembl chr19:49,859,882...49,878,351
JBrowse link
G POLB DNA polymerase beta involved_in
acts_upstream_of_or_within
TAS
ISO
(MGI:3045901|PMID:15177179) Reactome
MGI
RGD
PMID:15177179 PMID:17412650 MGI:3045901 RGD:2302580 Reactome:R-HSA-110373 Reactome:R-HSA-110381 Reactome:R-HSA-5649702 NCBI chr 8:42,338,452...42,371,810
Ensembl chr 8:42,338,454...42,371,808
JBrowse link
G POLD1 DNA polymerase delta 1, catalytic subunit involved_in
acts_upstream_of_or_within
IBA
ISO
IDA
(PMID:21873635)
(MGI:3045901|PMID:15177179)
(PMID:10559260), (PMID:10559261)
GO_Central
MGI
UniProt
PMID:10559260 PMID:10559261 PMID:15177179 PMID:21873635 MGI:3045901 NCBI chr19:50,384,291...50,418,018
Ensembl chr19:50,384,204...50,418,018
JBrowse link
G POLE DNA polymerase epsilon, catalytic subunit involved_in IDA
IBA
(PMID:10559260)
(PMID:21873635)
UniProt
GO_Central
PMID:10559260 PMID:21873635 NCBI chr12:132,623,758...132,687,519
Ensembl chr12:132,623,753...132,687,376
JBrowse link
G POLG DNA polymerase gamma, catalytic subunit acts_upstream_of_or_within IDA (PMID:15177179) MGI PMID:15177179 NCBI chr15:89,316,320...89,334,824
Ensembl chr15:89,305,198...89,334,861
JBrowse link
G POLL DNA polymerase lambda involved_in IDA (PMID:19806195) UniProt PMID:19806195 NCBI chr10:101,578,882...101,588,319
Ensembl chr10:101,578,882...101,588,270
JBrowse link
depurination term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G MPG N-methylpurine DNA glycosylase involved_in TAS Reactome Reactome:R-HSA-110331 NCBI chr16:77,007...85,846
Ensembl chr16:77,007...85,851
JBrowse link
G MUTYH mutY DNA glycosylase involved_in TAS Reactome Reactome:R-HSA-110331 NCBI chr 1:45,329,242...45,340,447
Ensembl chr 1:45,329,163...45,340,893
JBrowse link
G NEIL3 nei like DNA glycosylase 3 involved_in TAS Reactome Reactome:R-HSA-110331 NCBI chr 4:177,309,871...177,362,936
Ensembl chr 4:177,309,874...177,362,936
JBrowse link
G OGG1 8-oxoguanine DNA glycosylase involved_in TAS Reactome Reactome:R-HSA-110331 NCBI chr 3:9,749,952...9,788,246
Ensembl chr 3:9,749,944...9,788,219
JBrowse link
depyrimidination term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G MBD4 methyl-CpG binding domain 4, DNA glycosylase involved_in TAS Reactome Reactome:R-HSA-110329 NCBI chr 3:129,430,947...129,440,029
Ensembl chr 3:129,430,947...129,440,179
JBrowse link
G NEIL1 nei like DNA glycosylase 1 involved_in TAS Reactome Reactome:R-HSA-110329 NCBI chr15:75,346,638...75,357,115
Ensembl chr15:75,346,955...75,357,115
JBrowse link
G NEIL2 nei like DNA glycosylase 2 involved_in TAS Reactome Reactome:R-HSA-110329 NCBI chr 8:11,769,710...11,787,345
Ensembl chr 8:11,769,639...11,787,345
JBrowse link
G NTHL1 nth like DNA glycosylase 1 involved_in TAS Reactome Reactome:R-HSA-110329 NCBI chr16:2,039,820...2,047,834
Ensembl chr16:2,039,815...2,047,866
JBrowse link
G OGG1 8-oxoguanine DNA glycosylase involved_in TAS Reactome Reactome:R-HSA-110329 NCBI chr 3:9,749,952...9,788,246
Ensembl chr 3:9,749,944...9,788,219
JBrowse link
G SMUG1 single-strand-selective monofunctional uracil-DNA glycosylase 1 involved_in TAS Reactome Reactome:R-HSA-110329 NCBI chr12:54,121,274...54,188,985
Ensembl chr12:54,121,277...54,189,008
JBrowse link
G TDG thymine DNA glycosylase involved_in TAS Reactome Reactome:R-HSA-110329 NCBI chr12:103,965,842...103,988,874
Ensembl chr12:103,965,822...103,988,874
JBrowse link
G UNG uracil DNA glycosylase involved_in TAS Reactome Reactome:R-HSA-110329 NCBI chr12:109,097,597...109,110,992
Ensembl chr12:109,097,597...109,110,992
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 IBA
IDA
(PMID:21873635)
(PMID:25260657)
GO_Central
UniProt
PMID:21873635 PMID:25260657 NCBI chr11:73,400,487...73,598,112
Ensembl chr11:73,400,487...73,598,189
JBrowse link
G RPS3 ribosomal protein S3 involved_in IDA (PMID:18973764) UniProt PMID:18973764 NCBI chr11:75,399,518...75,422,302
Ensembl chr11:75,399,515...75,422,280
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 IDA (PMID:24703901) BHF-UCL PMID:24703901 NCBI chr14:20,455,226...20,457,767
Ensembl chr14:20,455,191...20,457,772
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 18605
    metabolic process 11952
      cellular metabolic process 10867
        cellular macromolecule metabolic process 8305
          DNA metabolic process 989
            DNA repair 560
              base-excision repair 49
                base-excision repair, AP site formation + 12
                base-excision repair, DNA ligation 1
                base-excision repair, base-free sugar-phosphate removal 1
                base-excision repair, gap-filling 15
                negative regulation of base-excision repair 0
                positive regulation of base-excision repair 2
                regulation of base-excision repair + 2
                telomere maintenance via base-excision repair 1
Path 2
Term Annotations click to browse term
  biological_process 18605
    metabolic process 11952
      cellular metabolic process 10867
        cellular aromatic compound metabolic process 6065
          nucleobase-containing compound metabolic process 5819
            nucleic acid metabolic process 5316
              DNA metabolic process 989
                DNA repair 560
                  base-excision repair 49
                    base-excision repair, AP site formation + 12
                    base-excision repair, DNA ligation 1
                    base-excision repair, base-free sugar-phosphate removal 1
                    base-excision repair, gap-filling 15
                    negative regulation of base-excision repair 0
                    positive regulation of base-excision repair 2
                    regulation of base-excision repair + 2
                    telomere maintenance via base-excision repair 1
paths to the root