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ONTOLOGY REPORT - ANNOTATIONS


Term:DNA catabolic process
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Accession:GO:0006308 term browser browse the term
Definition:The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
Synonyms:exact_synonym: DNA breakdown;   DNA catabolism;   DNA degradation


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DNA catabolic process term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G DFFB DNA fragmentation factor subunit beta IMP (PMID:19944011) CAFA PMID:19944011 NCBI chr 1:3,857,286...3,885,429
Ensembl chr 1:3,857,267...3,885,429
JBrowse link
G DNASE1 deoxyribonuclease 1 IEA
IBA
(PMID:21873635) InterPro
GO_Central
PMID:21873635 GO_REF:0000002 NCBI chr16:3,611,737...3,665,472
Ensembl chr16:3,611,728...3,680,143
JBrowse link
G DNASE1L1 deoxyribonuclease 1 like 1 IEA
IBA
(PMID:21873635) InterPro
GO_Central
PMID:21873635 GO_REF:0000002 NCBI chr  X:154,401,236...154,412,101
Ensembl chr  X:154,401,236...154,412,112
JBrowse link
G DNASE1L2 deoxyribonuclease 1 like 2 IEA
IBA
(PMID:21873635) InterPro
GO_Central
PMID:21873635 GO_REF:0000002 NCBI chr16:2,236,444...2,238,711
Ensembl chr16:2,235,816...2,238,711
JBrowse link
G DNASE1L3 deoxyribonuclease 1 like 3 IEA
IBA
(PMID:21873635) InterPro
GO_Central
PMID:21873635 GO_REF:0000002 NCBI chr 3:58,192,257...58,210,972
Ensembl chr 3:58,192,257...58,214,697
JBrowse link
G DNASE2 deoxyribonuclease 2, lysosomal ISO (MGI:3521632|PMID:15568025) MGI PMID:15568025 MGI:3521632 NCBI chr19:12,875,209...12,881,449
Ensembl chr19:12,875,209...12,881,466
JBrowse link
G TREX1 three prime repair exonuclease 1 ISO (MGI:4848004|PMID:20871604)
(MGI:3834787|PMID:18724932), (MGI:4414715|PMID:19923437), (MGI:5562498|PMID:23993650)
(MGI:5637600|PMID:25848017)
MGI PMID:18724932, PMID:19923437, PMID:20871604, PMID:23993650, PMID:25848017 MGI:3834787, MGI:4414715, MGI:4848004, MGI:5562498, MGI:5637600 NCBI chr 3:48,465,830...48,467,645
Ensembl chr 3:48,465,811...48,467,645
JBrowse link
apoptotic DNA fragmentation term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CASP3 caspase 3 TAS Reactome Reactome:R-HSA-140342 NCBI chr 4:184,627,696...184,649,447
Ensembl chr 4:184,627,696...184,649,509
JBrowse link
G CECR2 CECR2 histone acetyl-lysine reader TAS (PMID:12762840) HGNC PMID:12762840 NCBI chr22:17,359,949...17,558,151
Ensembl chr22:17,359,949...17,558,149
JBrowse link
G DFFA DNA fragmentation factor subunit alpha TAS
IEA
Reactome
InterPro
GO_REF:0000002, Reactome:R-HSA-140342 NCBI chr 1:10,456,522...10,472,529
Ensembl chr 1:10,456,522...10,472,529
JBrowse link
G DFFB DNA fragmentation factor subunit beta TAS
IEA
IBA
IDA
(PMID:21873635)
(PMID:15572351), (PMID:22253444)
Reactome
InterPro
GO_Central
MGI
PMID:15572351, PMID:21873635, PMID:22253444 GO_REF:0000002, Reactome:R-HSA-140342 NCBI chr 1:3,857,286...3,885,429
Ensembl chr 1:3,857,267...3,885,429
JBrowse link
G DICER1 dicer 1, ribonuclease III IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr14:95,086,228...95,158,263
Ensembl chr14:95,086,228...95,158,010
JBrowse link
G DNASE1L3 deoxyribonuclease 1 like 3 IDA
IBA
(PMID:23229555)
(PMID:21873635)
UniProtKB
GO_Central
PMID:21873635, PMID:23229555 NCBI chr 3:58,192,257...58,210,972
Ensembl chr 3:58,192,257...58,214,697
JBrowse link
G DNASE2 deoxyribonuclease 2, lysosomal IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr19:12,875,209...12,881,449
Ensembl chr19:12,875,209...12,881,466
JBrowse link
G DNASE2B deoxyribonuclease 2 beta IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 1:84,398,484...84,415,895
Ensembl chr 1:84,398,532...84,415,018
JBrowse link
G ENDOG endonuclease G IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 9:128,818,402...128,822,676
Ensembl chr 9:128,818,500...128,822,676
JBrowse link
G EXOG exo/endonuclease G IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 3:38,496,127...38,526,304
Ensembl chr 3:38,496,127...38,542,161
JBrowse link
G FOXL2 forkhead box L2 IMP (PMID:16153597) UniProtKB PMID:16153597 NCBI chr 3:138,944,224...138,947,137
Ensembl chr 3:138,944,224...138,947,137
JBrowse link
G H1-0 H1.0 linker histone TAS Reactome Reactome:R-HSA-140342 NCBI chr22:37,805,229...37,807,432
Ensembl chr22:37,805,093...37,807,436
JBrowse link
G HMGB1 high mobility group box 1 TAS Reactome Reactome:R-HSA-140342 NCBI chr13:30,456,704...30,617,597
Ensembl chr13:30,456,704...30,617,597
JBrowse link
G HMGB2 high mobility group box 2 TAS Reactome Reactome:R-HSA-140342 NCBI chr 4:173,331,376...173,334,358
Ensembl chr 4:173,331,376...173,334,432
JBrowse link
G KPNA1 karyopherin subunit alpha 1 TAS Reactome Reactome:R-HSA-140342 NCBI chr 3:122,421,902...122,514,939
Ensembl chr 3:122,421,902...122,514,945
JBrowse link
G KPNB1 karyopherin subunit beta 1 TAS Reactome Reactome:R-HSA-140342 NCBI chr17:47,649,919...47,685,505
Ensembl chr17:47,649,476...47,685,505
JBrowse link
DNA catabolic process, endonucleolytic term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G DNASE1 deoxyribonuclease 1 ISS
IBA
(PMID:29191910)
(PMID:21873635)
UniProtKB
GO_Central
PMID:21873635, PMID:29191910 NCBI chr16:3,611,737...3,665,472
Ensembl chr16:3,611,728...3,680,143
JBrowse link
G DNASE1L1 deoxyribonuclease 1 like 1 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr  X:154,401,236...154,412,101
Ensembl chr  X:154,401,236...154,412,112
JBrowse link
G DNASE1L2 deoxyribonuclease 1 like 2 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr16:2,236,444...2,238,711
Ensembl chr16:2,235,816...2,238,711
JBrowse link
G DNASE1L3 deoxyribonuclease 1 like 3 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 3:58,192,257...58,210,972
Ensembl chr 3:58,192,257...58,214,697
JBrowse link
G DNASE2 deoxyribonuclease 2, lysosomal ISO (MGI:3818215|PMID:18991290) MGI PMID:18991290 MGI:3818215 NCBI chr19:12,875,209...12,881,449
Ensembl chr19:12,875,209...12,881,466
JBrowse link
G ENDOG endonuclease G IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 9:128,818,402...128,822,676
Ensembl chr 9:128,818,500...128,822,676
JBrowse link
G EXOG exo/endonuclease G IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 3:38,496,127...38,526,304
Ensembl chr 3:38,496,127...38,542,161
JBrowse link
G FBH1 F-box DNA helicase 1 IMP (PMID:23361013) MGI PMID:23361013 NCBI chr10:5,889,572...5,937,593
Ensembl chr10:5,890,203...5,937,594
JBrowse link
G MUS81 MUS81 structure-specific endonuclease subunit IMP (PMID:23361013) MGI PMID:23361013 NCBI chr11:65,860,244...65,867,653
Ensembl chr11:65,857,126...65,867,653
JBrowse link
G REXO4 REX4 homolog, 3'-5' exonuclease IDA
IBA
(PMID:21602889)
(PMID:21873635)
ARUK-UCL
GO_Central
PMID:21602889, PMID:21873635 NCBI chr 9:133,406,058...133,418,172
Ensembl chr 9:133,406,059...133,418,096
JBrowse link
G SETMAR SET domain and mariner transposase fusion gene IMP
IDA
(PMID:24573677)
(PMID:20521842), (PMID:21491884)
UniProtKB PMID:20521842, PMID:21491884, PMID:24573677 NCBI chr 3:4,303,304...4,320,649
Ensembl chr 3:4,303,304...4,317,567
JBrowse link
G SPO11 SPO11 initiator of meiotic double stranded breaks IEA InterPro GO_REF:0000002 NCBI chr20:57,329,757...57,343,993
Ensembl chr20:57,329,803...57,343,994
JBrowse link
DNA catabolic process, exonucleolytic term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ERI1 exoribonuclease 1 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 8:8,892,225...9,100,262
Ensembl chr 8:9,002,147...9,116,746
JBrowse link
G ERI2 ERI1 exoribonuclease family member 2 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr16:20,780,193...20,806,472
Ensembl chr16:20,780,193...20,900,349
JBrowse link
G ERI3 ERI1 exoribonuclease family member 3 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 1:44,221,070...44,355,298
Ensembl chr 1:44,221,070...44,355,260
JBrowse link
G ISG20 interferon stimulated exonuclease gene 20 IDA
IBA
(PMID:11401564)
(PMID:21873635)
UniProtKB
GO_Central
PMID:11401564, PMID:21873635 NCBI chr15:88,635,614...88,656,483
Ensembl chr15:88,636,153...88,656,483
JBrowse link
G REXO4 REX4 homolog, 3'-5' exonuclease IDA
IBA
(PMID:21602889)
(PMID:21873635)
ARUK-UCL
GO_Central
PMID:21602889, PMID:21873635 NCBI chr 9:133,406,058...133,418,172
Ensembl chr 9:133,406,059...133,418,096
JBrowse link
G TREX1 three prime repair exonuclease 1 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 3:48,465,830...48,467,645
Ensembl chr 3:48,465,811...48,467,645
JBrowse link
G TREX2 three prime repair exonuclease 2 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr  X:153,444,720...153,446,487
Ensembl chr  X:153,444,720...153,470,587
JBrowse link
G XRN2 5'-3' exoribonuclease 2 IDA (PMID:15565158) UniProtKB PMID:15565158 NCBI chr20:21,303,313...21,389,825
Ensembl chr20:21,303,331...21,389,825
JBrowse link
negative regulation of apoptotic DNA fragmentation term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G DFFA DNA fragmentation factor subunit alpha IDA (PMID:15572351) MGI PMID:15572351 NCBI chr 1:10,456,522...10,472,529
Ensembl chr 1:10,456,522...10,472,529
JBrowse link
G NMNAT1 nicotinamide nucleotide adenylyltransferase 1 IEA Ensembl GO_REF:0000107 NCBI chr 1:9,942,923...9,996,884
Ensembl chr 1:9,943,428...9,985,501
JBrowse link
G PAM16 presequence translocase associated motor 16 IEA Ensembl GO_REF:0000107 NCBI chr16:4,340,251...4,351,321
Ensembl chr16:4,331,549...4,355,607
JBrowse link
negative regulation of DNA catabolic process term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G RGN regucalcin IEA Ensembl GO_REF:0000107 NCBI chr  X:47,078,414...47,093,313
Ensembl chr  X:47,078,355...47,093,314
JBrowse link
positive regulation of apoptotic DNA fragmentation term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G BAX BCL2 associated X, apoptosis regulator IMP (PMID:11350920) BHF-UCL PMID:11350920 NCBI chr19:48,954,825...48,961,798
Ensembl chr19:48,954,815...48,961,798
JBrowse link
G ENDOG endonuclease G IEA Ensembl GO_REF:0000107 NCBI chr 9:128,818,402...128,822,676
Ensembl chr 9:128,818,500...128,822,676
JBrowse link
G HSF1 heat shock transcription factor 1 IEA Ensembl GO_REF:0000107 NCBI chr 8:144,291,603...144,314,720
Ensembl chr 8:144,291,591...144,314,720
JBrowse link
G IGFBP3 insulin like growth factor binding protein 3 ISO RGD PMID:15125883 RGD:10402776 NCBI chr 7:45,912,245...45,921,272
Ensembl chr 7:45,912,245...45,921,874
JBrowse link
G IL6 interleukin 6 IMP (PMID:28433754) ARUK-UCL PMID:28433754 NCBI chr 7:22,725,889...22,732,002
Ensembl chr 7:22,725,884...22,732,002
JBrowse link
G ST20 suppressor of tumorigenicity 20 IDA (PMID:11857354) UniProtKB PMID:11857354 NCBI chr15:79,898,842...79,923,752
Ensembl chr15:79,898,840...79,923,702
JBrowse link
positive regulation of DNA catabolic process term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ATM ATM serine/threonine kinase IEA Ensembl GO_REF:0000107 NCBI chr11:108,222,484...108,369,102
Ensembl chr11:108,222,832...108,369,102
Ensembl chr11:108,222,832...108,369,102
JBrowse link
regulation of apoptotic DNA fragmentation term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G AIFM1 apoptosis inducing factor mitochondria associated 1 ISO (MGI:3577148|PMID:15703386) MGI PMID:15703386 MGI:3577148 NCBI chr  X:130,129,362...130,165,841
Ensembl chr  X:130,124,666...130,165,879
Ensembl chr  X:130,124,666...130,165,879
JBrowse link
G APAF1 apoptotic peptidase activating factor 1 IEA Ensembl GO_REF:0000107 NCBI chr12:98,645,141...98,735,433
Ensembl chr12:98,645,141...98,735,433
Ensembl chr12:98,645,141...98,735,433
JBrowse link
G CDKN2A cyclin dependent kinase inhibitor 2A IMP (PMID:12082630) BHF-UCL PMID:12082630 NCBI chr 9:21,967,752...21,995,324
Ensembl chr 9:21,967,753...21,995,301
JBrowse link
G CIDEA cell death inducing DFFA like effector a ISS (PMID:9564035) BHF-UCL PMID:9564035 NCBI chr18:12,254,361...12,277,595
Ensembl chr18:12,254,361...12,277,595
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 18672
    metabolic process 12302
      cellular metabolic process 11278
        cellular macromolecule metabolic process 8770
          DNA metabolic process 1026
            DNA catabolic process 44
              DNA catabolic process, endonucleolytic + 35
              DNA catabolic process, exonucleolytic 8
              mitochondrial DNA catabolic process 0
              negative regulation of DNA catabolic process + 4
              positive regulation of DNA catabolic process + 7
              regulation of DNA catabolic process + 15
Path 2
Term Annotations click to browse term
  biological_process 18672
    cellular process 17690
      cellular metabolic process 11278
        cellular aromatic compound metabolic process 6222
          nucleobase-containing compound metabolic process 5984
            nucleic acid metabolic process 5435
              DNA metabolic process 1026
                DNA catabolic process 44
                  DNA catabolic process, endonucleolytic + 35
                  DNA catabolic process, exonucleolytic 8
                  mitochondrial DNA catabolic process 0
                  negative regulation of DNA catabolic process + 4
                  positive regulation of DNA catabolic process + 7
                  regulation of DNA catabolic process + 15
paths to the root

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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.