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ONTOLOGY REPORT - ANNOTATIONS


Term:apoptotic cell clearance
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Accession:GO:0043277 term browser browse the term
Definition:The recognition and removal of an apoptotic cell by a neighboring cell or by a phagocyte.
Comment:Note that unlike mammals or Drosophila, C. elegans (and many lower organisms) do not have professional macrophages/phagocytes, instead cell corpses are engulfed by neighboring cells. Cell types that can function as engulfing cells include hypodermal cells, gonadal sheath cells, pharyngeal muscle cells, and intestinal cells.
Synonyms:exact_synonym: apoptotic cell removal;   efferocytosis;   programmed cell clearance


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apoptotic cell clearance term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ADGRB1 adhesion G protein-coupled receptor B1 ISO (PMID:24509909) UniProtKB PMID:24509909 NCBI chr 4:1,582,321...1,658,639
Ensembl chr 4:1,582,324...1,659,163
JBrowse link
G ALOX12 arachidonate 12-lipoxygenase, 12S type IEA Ensembl GO_REF:0000107 NCBI chr12:52,401,861...52,414,913
Ensembl chr12:52,286,019...52,414,907
JBrowse link
G ALOX15 arachidonate 15-lipoxygenase IEA Ensembl GO_REF:0000107 NCBI chr12:52,287,174...52,295,873
Ensembl chr12:52,286,019...52,414,907
JBrowse link
G AXL AXL receptor tyrosine kinase ISO (MGI:MGI:3841855|PMID:18804096)
(MGI:MGI:5509105|PMID:23878224)
(MGI:MGI:3836130|PMID:17442946)
(MGI:MGI:3778590|PMID:18159085)
MGI PMID:17442946, PMID:18159085, PMID:18804096, PMID:23878224 MGI:MGI:3778590, MGI:MGI:3836130, MGI:MGI:3841855, MGI:MGI:5509105 NCBI chr 6:49,245,802...49,277,917
Ensembl chr 6:49,245,673...49,277,914
JBrowse link
G CD36 CD36 molecule IEA Ensembl GO_REF:0000107 NCBI chr 9:99,685,748...99,782,296
Ensembl chr 9:99,605,181...99,782,105
JBrowse link
G GAS6 growth arrest specific 6 IEA Ensembl GO_REF:0000107 NCBI chr11:78,848,797...78,880,733
Ensembl chr11:78,848,794...78,881,272
JBrowse link
G HMGB1 high mobility group box 1 ISS UniProt GO_REF:0000024 NCBI chr11:7,195,556...7,321,071 JBrowse link
G ITGAV integrin subunit alpha V IEA Ensembl GO_REF:0000107 NCBI chr15:91,604,666...91,711,843
Ensembl chr15:91,604,676...91,711,840
JBrowse link
G ITGB3 integrin subunit beta 3 IEA Ensembl GO_REF:0000107 NCBI chr12:16,694,466...16,752,228
Ensembl chr12:16,693,505...16,752,292
JBrowse link
G JMJD6 jumonji domain containing 6, arginine demethylase and lysine hydroxylase NOT ISO (MGI:MGI:3618422|PMID:15647754)
(MGI:MGI:3042820|PMID:14715629)
(MGI:MGI:3580691|PMID:15345036)
MGI PMID:14715629, PMID:15345036, PMID:15647754 MGI:MGI:3042820, MGI:MGI:3580691, MGI:MGI:3618422 NCBI chr12:4,809,014...4,819,853
Ensembl chr12:4,808,691...4,818,062
JBrowse link
G LOC100511343 platelet glycoprotein 4-like IEA Ensembl GO_REF:0000107 NCBI chr 9:99,601,863...99,670,275
Ensembl chr 9:99,605,181...99,782,105
JBrowse link
G LRP1 LDL receptor related protein 1 ISO (MGI:MGI:3618422|PMID:15647754) MGI PMID:15647754 MGI:MGI:3618422 NCBI chr 5:22,435,636...22,519,276 JBrowse link
G MARCO macrophage receptor with collagenous structure ISO (MGI:MGI:3831958|PMID:19201851) MGI PMID:19201851 MGI:MGI:3831958 NCBI chr15:24,502,935...24,541,286
Ensembl chr15:24,503,108...24,541,353
JBrowse link
G MERTK MER proto-oncogene, tyrosine kinase ISO (MGI:MGI:3778590|PMID:18159085)
(MGI:MGI:6120635|PMID:29440417)
(MGI:MGI:3836130|PMID:17442946)
(MGI:MGI:5509105|PMID:23878224)
MGI
UniProtKB
PMID:17442946, PMID:18159085, PMID:23878224, PMID:29440417 MGI:MGI:3778590, MGI:MGI:3836130, MGI:MGI:5509105, MGI:MGI:6120635 NCBI chr 3:44,349,377...44,483,400
Ensembl chr 3:44,349,380...44,483,402
JBrowse link
G MFGE8 milk fat globule EGF and factor V/VIII domain containing IEA Ensembl GO_REF:0000107 NCBI chr 7:54,539,970...54,554,885
Ensembl chr 7:54,539,614...54,571,637
JBrowse link
G NR1H3 nuclear receptor subfamily 1 group H member 3 ISO (PMID:19628791) UniProtKB PMID:19628791 NCBI chr 2:15,315,283...15,336,785
Ensembl chr 2:15,270,789...15,334,820
JBrowse link
G RARA retinoic acid receptor alpha IEA Ensembl GO_REF:0000107 NCBI chr12:22,047,449...22,085,759
Ensembl chr12:22,047,442...22,085,674
JBrowse link
G TGM2 transglutaminase 2 IEA Ensembl GO_REF:0000107 NCBI chr17:41,186,765...41,221,686
Ensembl chr17:41,186,766...41,221,637
JBrowse link
G TIMD4 T cell immunoglobulin and mucin domain containing 4 ISO (MGI:MGI:6120635|PMID:29440417) MGI PMID:29440417 MGI:MGI:6120635 NCBI chr16:66,253,572...66,292,963
Ensembl chr16:66,253,604...66,292,961
JBrowse link
G TREM2 triggering receptor expressed on myeloid cells 2 ISO (MGI:MGI:3531054|PMID:15728241) UniProt PMID:15728241 MGI:MGI:3531054 NCBI chr 7:36,465,921...36,471,509
Ensembl chr 7:36,464,034...36,471,516
JBrowse link
G TREX1 three prime repair exonuclease 1 IEA Ensembl GO_REF:0000107 NCBI chr13:31,177,604...31,180,764
Ensembl chr13:31,178,601...31,180,592
JBrowse link
G TXNDC5 thioredoxin domain containing 5 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 7:5,210,192...5,236,857
Ensembl chr 7:5,210,049...5,236,812
JBrowse link
G TYRO3 TYRO3 protein tyrosine kinase ISS UniProt GO_REF:0000024 NCBI chr 1:129,811,540...129,829,395
Ensembl chr 1:129,811,539...129,828,991
JBrowse link
G TYROBP transmembrane immune signaling adaptor TYROBP ISS
IEA
UniProt
Ensembl
GO_REF:0000024, GO_REF:0000107 NCBI chr 6:45,309,199...45,312,562
Ensembl chr 6:45,309,197...45,312,537
JBrowse link
engulfment of apoptotic cell term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ADGRB1 adhesion G protein-coupled receptor B1 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 4:1,582,321...1,658,639
Ensembl chr 4:1,582,324...1,659,163
JBrowse link
G BECN1 beclin 1 IEA Ensembl GO_REF:0000107 NCBI chr12:20,041,914...20,054,249
Ensembl chr12:20,041,956...20,054,373
JBrowse link
G MEGF10 multiple EGF like domains 10 ISO (MGI:MGI:5775214|PMID:27170117) MGI PMID:27170117 MGI:MGI:5775214 NCBI chr 2:130,226,222...130,403,960 JBrowse link
G RAC1 Rac family small GTPase 1 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 3:4,781,776...4,803,510
Ensembl chr 3:4,781,771...4,803,687
JBrowse link
G RAC2 Rac family small GTPase 2 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 5:10,553,986...10,571,082
Ensembl chr 5:10,553,433...10,573,017
JBrowse link
G RHOBTB1 Rho related BTB domain containing 1 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr14:64,326,461...64,465,331
Ensembl chr14:64,326,453...64,465,281
JBrowse link
G RHOG ras homolog family member G IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 9:6,283,558...6,295,376 JBrowse link
G RHOH ras homolog family member H IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 8:31,321,005...31,372,366
Ensembl chr 8:31,321,113...31,372,364
JBrowse link
G THBS1 thrombospondin 1 IEA Ensembl GO_REF:0000107 NCBI chr 1:131,728,781...131,746,098
Ensembl chr 1:131,728,781...131,746,115
JBrowse link
G XKR4 XK related 4 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 4:76,056,895...76,382,976
Ensembl chr 4:76,062,403...76,382,818
JBrowse link
G XKR5 XK related 5 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr15:37,880,406...37,898,737
Ensembl chr15:37,880,101...37,898,718
JBrowse link
G XKR7 XK related 7 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr17:35,632,287...35,662,600
Ensembl chr17:35,632,158...35,658,305
JBrowse link
G XKR8 XK related 8 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 6:85,084,641...85,093,167
Ensembl chr 6:85,083,859...85,093,166
JBrowse link
G XKR9 XK related 9 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 4:64,678,734...64,727,495
Ensembl chr 4:64,679,170...64,707,710
JBrowse link
negative regulation of apoptotic cell clearance term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CD300LF CD300 molecule like family member f ISO (MGI:MGI:5819329|PMID:26768664) UniProtKB PMID:26768664 MGI:MGI:5819329 NCBI chr12:6,501,151...6,521,135 JBrowse link
G HMGB1 high mobility group box 1 ISO (PMID:20826760) BHF-UCL PMID:20826760 NCBI chr11:7,195,556...7,321,071 JBrowse link
neutrophil clearance term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ANXA1 annexin A1 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 1:226,414,200...226,431,963
Ensembl chr 1:226,414,307...226,432,287
JBrowse link
G AXL AXL receptor tyrosine kinase IEA Ensembl GO_REF:0000107 NCBI chr 6:49,245,802...49,277,917
Ensembl chr 6:49,245,673...49,277,914
JBrowse link
G CCR2 C-C motif chemokine receptor 2 IEA Ensembl GO_REF:0000107 NCBI chr13:29,368,735...29,374,564
Ensembl chr13:29,251,959...29,376,346
JBrowse link
G HMGB1 high mobility group box 1 ISS UniProt GO_REF:0000024 NCBI chr11:7,195,556...7,321,071 JBrowse link
G MERTK MER proto-oncogene, tyrosine kinase IEA Ensembl GO_REF:0000107 NCBI chr 3:44,349,377...44,483,400
Ensembl chr 3:44,349,380...44,483,402
JBrowse link
phagosome-lysosome fusion involved in apoptotic cell clearance term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G SPG11 SPG11 vesicle trafficking associated, spatacsin IEA Ensembl GO_REF:0000107 NCBI chr 1:126,890,464...126,998,014
Ensembl chr 1:126,890,892...126,998,059
JBrowse link
positive regulation of apoptotic cell clearance term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G C2 complement C2 IEA Ensembl GO_REF:0000107 NCBI chr 7:24,020,590...24,034,042
Ensembl chr 7:23,995,982...24,034,040
JBrowse link
G C3 complement C3 IEA Ensembl GO_REF:0000107 NCBI chr 2:72,431,470...72,471,622
Ensembl chr 2:72,431,499...72,528,112
JBrowse link
G C4A complement C4A (Rodgers blood group) ISO (PMID:19302245) BHF-UCL PMID:19302245 NCBI chr 7:24,068,019...24,083,060
Ensembl chr 7:24,067,995...24,083,065
JBrowse link
G CCL2 chemokine (C-C motif) ligand 2 ISO (MGI:MGI:4943793|PMID:20691665) BHF-UCL PMID:20691665 MGI:MGI:4943793 NCBI chr12:40,798,109...40,800,013
Ensembl chr12:40,798,109...40,800,028
JBrowse link
G CD300LF CD300 molecule like family member f ISO (MGI:MGI:5819329|PMID:26768664)
(MGI:MGI:5301804|PMID:21865548)
UniProtKB PMID:21865548, PMID:26768664 MGI:MGI:5301804, MGI:MGI:5819329 NCBI chr12:6,501,151...6,521,135 JBrowse link
positive regulation of engulfment of apoptotic cell term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ABCA7 ATP binding cassette subfamily A member 7 ISO (MGI:MGI:3662940|PMID:16908670) Alzheimers_University_of_Toronto PMID:16908670 MGI:MGI:3662940 NCBI chr 2:77,357,161...77,375,349
Ensembl chr 2:77,357,211...77,375,180
JBrowse link
G TREM2 triggering receptor expressed on myeloid cells 2 IEA Ensembl GO_REF:0000107 NCBI chr 7:36,465,921...36,471,509
Ensembl chr 7:36,464,034...36,471,516
JBrowse link
recognition of apoptotic cell term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G FCN1 ficolin (collagen/fibrinogen domain containing) 1 ISO (PMID:15804047) UniProtKB PMID:15804047 NCBI chr 1:274,125,666...274,132,917 JBrowse link
G FCN2 ficolin (collagen/fibrinogen domain containing lectin) 2 (hucolin) IEA Ensembl GO_REF:0000107 NCBI chr 1:274,106,276...274,111,970
Ensembl chr 1:274,103,877...274,111,970
JBrowse link
G JMJD6 jumonji domain containing 6, arginine demethylase and lysine hydroxylase IEA Ensembl GO_REF:0000107 NCBI chr12:4,809,014...4,819,853
Ensembl chr12:4,808,691...4,818,062
JBrowse link
G MEGF10 multiple EGF like domains 10 ISO (MGI:MGI:4414741|PMID:19915564) MGI PMID:19915564 MGI:MGI:4414741 NCBI chr 2:130,226,222...130,403,960 JBrowse link
G PEAR1 platelet endothelial aggregation receptor 1 IEA Ensembl GO_REF:0000107 NCBI chr 4:93,178,854...93,205,186
Ensembl chr 4:93,177,143...93,205,156
JBrowse link
G SCARB1 scavenger receptor class B member 1 IEA Ensembl GO_REF:0000107 NCBI chr14:28,301,421...28,393,568
Ensembl chr14:28,301,294...28,393,565
JBrowse link
regulation of engulfment of apoptotic cell term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ALOX12 arachidonate 12-lipoxygenase, 12S type IEA Ensembl GO_REF:0000107 NCBI chr12:52,401,861...52,414,913
Ensembl chr12:52,286,019...52,414,907
JBrowse link
G ALOX15 arachidonate 15-lipoxygenase IEA Ensembl GO_REF:0000107 NCBI chr12:52,287,174...52,295,873
Ensembl chr12:52,286,019...52,414,907
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 16545
    cellular process 15775
      vesicle-mediated transport 1447
        phagocytosis 210
          apoptotic cell clearance 50
            engulfment of apoptotic cell + 18
            negative regulation of apoptotic cell clearance + 2
            neutrophil clearance 5
            phagosome maturation involved in apoptotic cell clearance + 1
            positive regulation of apoptotic cell clearance + 7
            recognition of apoptotic cell 6
            regulation of apoptotic cell clearance + 8
Path 2
Term Annotations click to browse term
  biological_process 16545
    localization 5926
      establishment of localization 4430
        transport 4283
          vesicle-mediated transport 1447
            phagocytosis 210
              apoptotic cell clearance 50
                engulfment of apoptotic cell + 18
                negative regulation of apoptotic cell clearance + 2
                neutrophil clearance 5
                phagosome maturation involved in apoptotic cell clearance + 1
                positive regulation of apoptotic cell clearance + 7
                recognition of apoptotic cell 6
                regulation of apoptotic cell clearance + 8
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.