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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 AABR07018191.1 involved_in IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537
G AC095390.1 involved_in IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537
G Apex1 apurinic/apyrimidinic endodeoxyribonuclease 1 involved_in IBA
ISO
PMID:21873635
(PMID:8932386)
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 ISO
IEA
(PMID:18995831)
GO_REF:0000107
RGD
Ensembl
PMID:18995831 GO_REF:0000107 NCBI chr20:25,661,652...25,690,598 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 JBrowse link
G Huwe1 HECT, UBA and WWE domain containing E3 ubiquitin protein ligase 1 involved_in ISS
IEA
IBA
ISO
GO_REF:0000024
GO_REF:0000107
PMID:21873635
(PMID:19713937)
UniProt
Ensembl
RGD
PMID:19713937 PMID:21873635 GO_REF:0000024 GO_REF:0000107, RGD:13792537 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 (PMID:19589734) RGD PMID:19589734 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
IEA
ISO
IBA
GO_REF:0000002
GO_REF:0000107
MGI:2148592|MGI:2675730 (MGI:2181327|PMID:9371767), (MGI:3028824|PMID:15177041)
PMID:21873635
InterPro
Ensembl
RGD
PMID:9371767 PMID:15177041 PMID:21873635 GO_REF:0000002 GO_REF:0000107 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
PMID:21873635
UniProt PMID:21873635 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 NAS
ISS
ISO
GO_REF:0000024
(PMID:9765279)
UniProt
RGD
PMID:9765279 PMID:9045683 GO_REF:0000024, RGD:729744 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 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 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 (PMID:21862836), (PMID:22327402)
(MGI:5287540|PMID:21817016)
RGD PMID:21817016 PMID:21862836 PMID:22327402 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:15297456 PMID:11292851 RGD:634481, RGD:1599703, RGD:1599704 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
IDA
PMID:21873635 RGD
GO_Central
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
ISO
PMID:21873635
(PMID:11889051), (PMID:18512959)
RGD PMID:11889051 PMID:18512959 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
ISO
IBA
(PMID:24674627)
(PMID:19589734)
PMID:21873635
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
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 (PMID:24703901) RGD PMID:24703901 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 19390
    metabolic process 11736
      cellular metabolic process 10656
        cellular macromolecule metabolic process 8148
          DNA metabolic process 878
            DNA repair 485
              base-excision repair 44
                base-excision repair, AP site formation + 5
                base-excision repair, DNA ligation 1
                base-excision repair, base-free sugar-phosphate removal 0
                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 + 2
                telomere maintenance via base-excision repair 1
Path 2
Term Annotations click to browse term
  biological_process 19390
    metabolic process 11736
      cellular metabolic process 10656
        cellular aromatic compound metabolic process 5581
          nucleobase-containing compound metabolic process 5360
            nucleic acid metabolic process 4874
              DNA metabolic process 878
                DNA repair 485
                  base-excision repair 44
                    base-excision repair, AP site formation + 5
                    base-excision repair, DNA ligation 1
                    base-excision repair, base-free sugar-phosphate removal 0
                    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 + 2
                    telomere maintenance via base-excision repair 1
paths to the root