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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 ISO (PMID:19944011) CAFA PMID:19944011 NCBI chr 6:65,310,868...65,323,816
Ensembl chr 6:65,310,863...65,323,816
JBrowse link
G DNASE1 deoxyribonuclease 1 IEA
IBA
(PMID:21873635) InterPro
GO_Central
PMID:21873635 GO_REF:0000002 NCBI chr 3:38,590,045...38,646,852
Ensembl chr 3:38,586,600...38,646,834
JBrowse link
G DNASE1L1 deoxyribonuclease 1 like 1 IEA
IBA
(PMID:21873635) InterPro
GO_Central
PMID:21873635 GO_REF:0000002 NCBI chr  X:124,931,410...124,937,569
Ensembl chr  X:124,931,408...124,939,965
JBrowse link
G DNASE1L2 deoxyribonuclease 1 like 2 ISO (MGI:5308183|PMID:21307874) MGI PMID:21307874 MGI:5308183 NCBI chr 3:39,757,725...39,761,497 JBrowse link
G DNASE1L3 deoxyribonuclease 1 like 3 IEA
IBA
(PMID:21873635) InterPro
GO_Central
PMID:21873635 GO_REF:0000002 NCBI chr13:39,958,384...39,976,114
Ensembl chr13:39,954,804...39,975,946
JBrowse link
G DNASE2 deoxyribonuclease 2, lysosomal ISO (MGI:3521632|PMID:15568025) MGI PMID:15568025 MGI:3521632 NCBI chr 2:66,150,071...66,152,857
Ensembl chr 2:66,149,862...66,152,855
JBrowse link
G TREX1 three prime repair exonuclease 1 ISO (MGI:4848004|PMID:20871604)
(MGI:5637600|PMID:25848017)
(MGI:3834787|PMID:18724932), (MGI:4414715|PMID:19923437), (MGI:5562498|PMID:23993650)
MGI PMID:18724932, PMID:19923437, PMID:20871604, PMID:23993650, PMID:25848017 MGI:3834787, MGI:4414715, MGI:4848004, MGI:5562498, MGI:5637600 NCBI chr13:31,177,604...31,180,764
Ensembl chr13:31,178,601...31,180,592
JBrowse link
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 IEA InterPro GO_REF:0000002 NCBI chr 6:70,725,403...70,736,264
Ensembl chr 6:70,724,587...70,736,236
JBrowse link
G DFFB DNA fragmentation factor subunit beta IBA
IEA
(PMID:21873635) GO_Central
InterPro
PMID:21873635 GO_REF:0000002 NCBI chr 6:65,310,868...65,323,816
Ensembl chr 6:65,310,863...65,323,816
JBrowse link
G DICER1 dicer 1, ribonuclease III IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 7:116,361,630...116,436,471
Ensembl chr 7:116,361,630...116,436,519
JBrowse link
G DNASE1L3 deoxyribonuclease 1 like 3 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr13:39,958,384...39,976,114
Ensembl chr13:39,954,804...39,975,946
JBrowse link
G DNASE2 deoxyribonuclease 2, lysosomal IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 2:66,150,071...66,152,857
Ensembl chr 2:66,149,862...66,152,855
JBrowse link
G ENDOG endonuclease G IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 1:269,153,955...269,157,789
Ensembl chr 1:269,154,090...269,157,788
JBrowse link
G EXOG exo/endonuclease G IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr13:23,278,458...23,330,540
Ensembl chr13:23,278,932...23,322,541
JBrowse link
G FOXL2 forkhead box L2 IEA Ensembl GO_REF:0000107 NCBI chr13:79,708,693...79,709,825
Ensembl chr13:79,709,013...79,709,825
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)
UniProt
GO_Central
PMID:21873635, PMID:29191910 NCBI chr 3:38,590,045...38,646,852
Ensembl chr 3:38,586,600...38,646,834
JBrowse link
G DNASE1L1 deoxyribonuclease 1 like 1 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr  X:124,931,410...124,937,569
Ensembl chr  X:124,931,408...124,939,965
JBrowse link
G DNASE1L3 deoxyribonuclease 1 like 3 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr13:39,958,384...39,976,114
Ensembl chr13:39,954,804...39,975,946
JBrowse link
G DNASE2 deoxyribonuclease 2, lysosomal ISO (MGI:3818215|PMID:18991290) MGI PMID:18991290 MGI:3818215 NCBI chr 2:66,150,071...66,152,857
Ensembl chr 2:66,149,862...66,152,855
JBrowse link
G ENDOG endonuclease G IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 1:269,153,955...269,157,789
Ensembl chr 1:269,154,090...269,157,788
JBrowse link
G EXOG exo/endonuclease G IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr13:23,278,458...23,330,540
Ensembl chr13:23,278,932...23,322,541
JBrowse link
G FBH1 F-box DNA helicase 1 IEA Ensembl GO_REF:0000107 NCBI chr10:65,060,714...65,108,975
Ensembl chr10:64,955,189...65,108,380
JBrowse link
G LOC100514009 histone-lysine N-methyltransferase SETMAR ISO (PMID:24573677)
(PMID:20521842), (PMID:21491884)
UniProtKB PMID:20521842, PMID:21491884, PMID:24573677 NCBI chr13:60,914,412...60,933,064 JBrowse link
G MUS81 MUS81 structure-specific endonuclease subunit IEA Ensembl GO_REF:0000107 NCBI chr 2:6,462,825...6,470,780
Ensembl chr 2:6,463,413...6,469,112
JBrowse link
G REXO4 REX4 homolog, 3'-5' exonuclease IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 1:273,011,736...273,021,956
Ensembl chr 1:273,011,733...273,021,940
JBrowse link
G SPO11 SPO11 initiator of meiotic double stranded breaks IEA InterPro GO_REF:0000002 NCBI chr17:57,730,676...57,745,875
Ensembl chr17:57,730,749...57,745,875
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 chr15:56,091,790...56,123,520
Ensembl chr15:56,093,581...56,123,510
JBrowse link
G ERI3 ERI1 exoribonuclease family member 3 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 6:166,957,241...167,082,631
Ensembl chr 6:166,957,316...167,082,632
JBrowse link
G ISG20 interferon stimulated exonuclease gene 20 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 1:191,155,853...191,195,601
Ensembl chr 1:191,183,374...191,195,475
JBrowse link
G REXO4 REX4 homolog, 3'-5' exonuclease IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 1:273,011,736...273,021,956
Ensembl chr 1:273,011,733...273,021,940
JBrowse link
G TREX1 three prime repair exonuclease 1 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr13:31,177,604...31,180,764
Ensembl chr13:31,178,601...31,180,592
JBrowse link
G XRN2 5'-3' exoribonuclease 2 IEA Ensembl GO_REF:0000107 NCBI chr17:29,107,641...29,193,500
Ensembl chr17:29,107,668...29,193,494
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 IEA Ensembl GO_REF:0000107 NCBI chr 6:70,725,403...70,736,264
Ensembl chr 6:70,724,587...70,736,236
JBrowse link
G LOC100513346 mitochondrial import inner membrane translocase subunit TIM16 ISO RGD PMID:24069394 RGD:13462066 NCBI chr 3:37,928,098...38,005,619
Ensembl chr 3:37,989,180...38,005,617
JBrowse link
G NMNAT1 nicotinamide nucleotide adenylyltransferase 1 ISO RGD PMID:27184051 RGD:13781945 NCBI chr 6:70,271,296...70,307,403
Ensembl chr 6:70,272,030...70,310,603
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 ISO RGD PMID:2001740 RGD:9590215 NCBI chr  X:41,725,660...41,749,736
Ensembl chr  X:41,726,526...41,749,726
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 ISO (PMID:11350920) BHF-UCL PMID:11350920 NCBI chr 6:54,222,341...54,228,150
Ensembl chr 6:54,187,260...54,228,144
JBrowse link
G ENDOG endonuclease G ISO RGD PMID:16407272 RGD:9685355 NCBI chr 1:269,153,955...269,157,789
Ensembl chr 1:269,154,090...269,157,788
JBrowse link
G HSF1 heat shock transcription factor 1 ISO RGD PMID:21192280 RGD:10403035 NCBI chr 4:463,531...486,483
Ensembl chr 4:461,559...486,473
JBrowse link
G IGFBP3 insulin like growth factor binding protein 3 ISO RGD PMID:15125883 RGD:10402776 NCBI chr18:50,002,921...50,009,425 JBrowse link
G IL6 interleukin 6 IEA Ensembl GO_REF:0000107 NCBI chr 9:91,506,421...91,510,830
Ensembl chr 9:91,506,340...91,511,263
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 ISO RGD PMID:27895165 RGD:12879393 NCBI chr 9:36,620,656...36,759,555
Ensembl chr 9:36,620,658...36,759,554
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:106,676,596...106,708,290
Ensembl chr  X:106,670,519...106,708,317
JBrowse link
G APAF1 apoptotic peptidase activating factor 1 IEA Ensembl GO_REF:0000107 NCBI chr 5:85,166,616...85,258,751
Ensembl chr 5:85,166,628...85,258,364
JBrowse link
G CIDEA cell death inducing DFFA like effector a ISO (MGI:1203887|PMID:9564035) BHF-UCL PMID:9564035 MGI:1203887 NCBI chr 6:97,253,074...97,268,355 JBrowse link
G P14ARF p14ARF protein ISO (PMID:12082630) BHF-UCL PMID:12082630 NCBI chr 1:200,774,496...200,799,149
Ensembl chr 1:200,774,496...200,798,854
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 16548
    metabolic process 10584
      cellular metabolic process 9574
        cellular macromolecule metabolic process 7423
          DNA metabolic process 821
            DNA catabolic process 33
              DNA catabolic process, endonucleolytic + 25
              DNA catabolic process, exonucleolytic 6
              mitochondrial DNA catabolic process 0
              negative regulation of DNA catabolic process + 4
              positive regulation of DNA catabolic process + 6
              regulation of DNA catabolic process + 14
Path 2
Term Annotations click to browse term
  biological_process 16548
    cellular process 15780
      cellular metabolic process 9574
        cellular aromatic compound metabolic process 5098
          nucleobase-containing compound metabolic process 4911
            nucleic acid metabolic process 4490
              DNA metabolic process 821
                DNA catabolic process 33
                  DNA catabolic process, endonucleolytic + 25
                  DNA catabolic process, exonucleolytic 6
                  mitochondrial DNA catabolic process 0
                  negative regulation of DNA catabolic process + 4
                  positive regulation of DNA catabolic process + 6
                  regulation of DNA catabolic process + 14
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.