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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 chrNW_004936470:9,247,749...9,313,230 JBrowse link
G Alox15 arachidonate 15-lipoxygenase ISO (MGI:MGI:5436199|PMID:22503541) UniProtKB PMID:22503541 MGI:MGI:5436199 NCBI chrNW_004936677:3,232,183...3,241,307 JBrowse link
G Axl AXL receptor tyrosine kinase ISO (MGI:MGI:3841855|PMID:18804096)
(MGI:MGI:3778590|PMID:18159085)
(MGI:MGI:5509105|PMID:23878224)
(MGI:MGI:3836130|PMID:17442946)
MGI PMID:17442946, PMID:18159085, PMID:18804096, PMID:23878224 MGI:MGI:3778590, MGI:MGI:3836130, MGI:MGI:3841855, MGI:MGI:5509105 NCBI chrNW_004936661:3,658,140...3,687,290 JBrowse link
G Cd36 CD36 molecule ISO (MGI:MGI:3618422|PMID:15647754) MGI PMID:15647754 MGI:MGI:3618422 NCBI chrNW_004936810:791,823...838,303 JBrowse link
G Gas6 growth arrest specific 6 ISO (MGI:MGI:3778590|PMID:18159085)
(PMID:21501828)
MGI
UniProtKB
PMID:18159085, PMID:21501828 MGI:MGI:3778590 NCBI chrNW_004936472:27,116...57,158 JBrowse link
G Hmgb1 high mobility group box 1 ISO (PMID:18768881) UniProtKB PMID:18768881 NCBI chrNW_004936472:25,236,728...25,246,585 JBrowse link
G Itgav integrin subunit alpha V ISO (MGI:MGI:3618422|PMID:15647754)
(MGI:MGI:5285150|PMID:20826760)
(PMID:20826760)
MGI
BHF-UCL
PMID:15647754, PMID:20826760 MGI:MGI:3618422, MGI:MGI:5285150 NCBI chrNW_004936506:10,750,116...10,839,018 JBrowse link
G Itgb3 integrin subunit beta 3 ISO (PMID:20826760)
(MGI:MGI:5285150|PMID:20826760)
BHF-UCL PMID:20826760 MGI:MGI:5285150 NCBI chrNW_004936541:2,822,789...2,871,069 JBrowse link
G Jmjd6 jumonji domain containing 6, arginine demethylase and lysine hydroxylase NOT ISO (MGI:MGI:3618422|PMID:15647754)
(MGI:MGI:3580691|PMID:15345036)
(MGI:MGI:3042820|PMID:14715629)
MGI PMID:14715629, PMID:15345036, PMID:15647754 MGI:MGI:3042820, MGI:MGI:3580691, MGI:MGI:3618422 NCBI chrNW_004936594:1,760,924...1,771,022 JBrowse link
G Lrp1 LDL receptor related protein 1 ISO (MGI:MGI:3618422|PMID:15647754) MGI PMID:15647754 MGI:MGI:3618422 NCBI chrNW_004936646:1,326,900...1,407,236 JBrowse link
G Marco macrophage receptor with collagenous structure ISO (MGI:MGI:3831958|PMID:19201851) MGI PMID:19201851 MGI:MGI:3831958 NCBI chrNW_004936469:51,323,746...51,366,551 JBrowse link
G Mertk MER proto-oncogene, tyrosine kinase ISO (MGI:MGI:3778590|PMID:18159085)
(MGI:MGI:6120635|PMID:29440417)
(MGI:MGI:5509105|PMID:23878224)
(MGI:MGI:3836130|PMID:17442946)
UniProtKB
MGI
PMID:17442946, PMID:18159085, PMID:23878224, PMID:29440417 MGI:MGI:3778590, MGI:MGI:3836130, MGI:MGI:5509105, MGI:MGI:6120635 NCBI chrNW_004936783:607,425...704,879 JBrowse link
G Mfge8 milk fat globule EGF and factor V/VIII domain containing ISO (MGI:MGI:5285150|PMID:20826760) BHF-UCL PMID:20826760 MGI:MGI:5285150 NCBI chrNW_004936483:14,868,171...14,880,552 JBrowse link
G Nr1h3 nuclear receptor subfamily 1 group H member 3 ISO (PMID:19628791) UniProtKB PMID:19628791 NCBI chrNW_004936562:1,937,665...1,946,680 JBrowse link
G Rara retinoic acid receptor alpha ISO (PMID:19628791) UniProtKB PMID:19628791 NCBI chrNW_004936490:15,376,217...15,420,638 JBrowse link
G Tgm2 transglutaminase 2 ISO (PMID:19628791) UniProtKB PMID:19628791 NCBI chrNW_004936561:3,178,244...3,207,551 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 chrNW_004936515:6,106,991...6,141,027 JBrowse link
G Trem2 triggering receptor expressed on myeloid cells 2 ISO (MGI:MGI:3531054|PMID:15728241) UniProt PMID:15728241 MGI:MGI:3531054 NCBI chrNW_004936476:18,659,725...18,665,406 JBrowse link
G Trex1 three prime repair exonuclease 1 ISO (MGI:MGI:5554502|PMID:24218451) MGI PMID:24218451 MGI:MGI:5554502 NCBI chrNW_004936529:264,535...266,451 JBrowse link
G Tyro3 TYRO3 protein tyrosine kinase ISO (MGI:MGI:3836130|PMID:17442946)
(MGI:MGI:3778590|PMID:18159085)
MGI PMID:17442946, PMID:18159085 MGI:MGI:3778590, MGI:MGI:3836130 NCBI chrNW_004936471:4,893,185...4,910,779 JBrowse link
G Tyrobp transmembrane immune signaling adaptor TYROBP ISO (MGI:MGI:3531054|PMID:15728241) UniProt PMID:15728241 MGI:MGI:3531054 NCBI chrNW_004936570:457,993...460,735 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 ISO (MGI:MGI:3764740|PMID:17960134)
(PMID:24509909)
UniProtKB PMID:17960134, PMID:24509909 MGI:MGI:3764740 NCBI chrNW_004936470:9,247,749...9,313,230 JBrowse link
G Becn1 beclin 1 ISO (MGI:MGI:5619450|PMID:22393062) CACAO PMID:22393062 MGI:MGI:5619450 NCBI chrNW_004936490:17,518,100...17,531,126 JBrowse link
G Megf10 multiple EGF like domains 10 ISO (MGI:MGI:5775214|PMID:27170117) MGI PMID:27170117 MGI:MGI:5775214 NCBI chrNW_004936504:634,167...753,438 JBrowse link
G Rac1 Rac family small GTPase 1 ISO (MGI:MGI:4943793|PMID:20691665) BHF-UCL PMID:20691665 MGI:MGI:4943793 NCBI chrNW_004936750:107,689...122,679 JBrowse link
G Thbs1 thrombospondin 1 ISO (PMID:16882710) BHF-UCL PMID:16882710 NCBI chrNW_004936471:3,064,466...3,081,125 JBrowse link
G Xkr8 XK related 8 ISO (PMID:23845944) UniProtKB PMID:23845944 NCBI chrNW_004936474:12,180,741...12,187,904 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 Hmgb1 high mobility group box 1 ISO (PMID:20826760) BHF-UCL PMID:20826760 NCBI chrNW_004936472:25,236,728...25,246,585 JBrowse link
neutrophil clearance term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Anxa1 annexin A1 ISO (PMID:21957127) BHF-UCL PMID:21957127 NCBI chrNW_004936503:9,124,314...9,142,372 JBrowse link
G Axl AXL receptor tyrosine kinase ISO (MGI:MGI:5509105|PMID:23878224) MGI PMID:23878224 MGI:MGI:5509105 NCBI chrNW_004936661:3,658,140...3,687,290 JBrowse link
G Hmgb1 high mobility group box 1 ISO (PMID:18768881) UniProtKB PMID:18768881 NCBI chrNW_004936472:25,236,728...25,246,585 JBrowse link
G Mertk MER proto-oncogene, tyrosine kinase ISO (MGI:MGI:5509105|PMID:23878224) MGI PMID:23878224 MGI:MGI:5509105 NCBI chrNW_004936783:607,425...704,879 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 ISO (MGI:MGI:5749311|PMID:26284655) MGI PMID:26284655 MGI:MGI:5749311 NCBI chrNW_004936471:7,540,647...7,618,783 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 ISO (PMID:19302245) BHF-UCL PMID:19302245 NCBI chrNW_004936727:1,602,400...1,615,974 JBrowse link
G C3 complement C3 ISO (PMID:19302245) BHF-UCL PMID:19302245 NCBI chrNW_004936588:3,985,732...4,023,221 JBrowse link
G C4a complement C4A (Rodgers blood group) ISO (PMID:19302245) BHF-UCL PMID:19302245 NCBI chrNW_004936727:1,556,204...1,570,084 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 chrNW_004936588:460,308...477,382 JBrowse link
G Trem2 triggering receptor expressed on myeloid cells 2 ISO (PMID:24990881) UniProt PMID:24990881 NCBI chrNW_004936476:18,659,725...18,665,406 JBrowse link
recognition of apoptotic cell term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Fcn3 ficolin 3 ISO (PMID:15804047) UniProtKB PMID:15804047 NCBI chrNW_004936474:11,680,166...11,685,214 JBrowse link
G Jmjd6 jumonji domain containing 6, arginine demethylase and lysine hydroxylase ISO (MGI:MGI:1855743|PMID:10811223)
(MGI:MGI:2682078|PMID:14645847)
MGI PMID:10811223, PMID:14645847 MGI:MGI:1855743, MGI:MGI:2682078 NCBI chrNW_004936594:1,760,924...1,771,022 JBrowse link
G Megf10 multiple EGF like domains 10 ISO (MGI:MGI:4414741|PMID:19915564) MGI PMID:19915564 MGI:MGI:4414741 NCBI chrNW_004936504:634,167...753,438 JBrowse link
G Pear1 platelet endothelial aggregation receptor 1 ISO (MGI:MGI:4414741|PMID:19915564) MGI PMID:19915564 MGI:MGI:4414741 NCBI chrNW_004936580:6,030,426...6,052,330 JBrowse link
G Scarb1 scavenger receptor class B member 1 ISO PMID:12016218
(PMID:9211901)
BHF-UCL PMID:9211901, PMID:12016218 RGD:1304245 NCBI chrNW_004936558:530,828...555,098 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 Alox15 arachidonate 15-lipoxygenase ISO (MGI:MGI:5436199|PMID:22503541), (MGI:MGI:5508294|PMID:11278875) UniProtKB PMID:11278875, PMID:22503541 MGI:MGI:5436199, MGI:MGI:5508294 NCBI chrNW_004936677:3,232,183...3,241,307 JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 12001
    cellular process 11174
      vesicle-mediated transport 1116
        phagocytosis 173
          apoptotic cell clearance 35
            engulfment of apoptotic cell + 9
            negative regulation of apoptotic cell clearance + 1
            neutrophil clearance 4
            phagosome maturation involved in apoptotic cell clearance + 1
            positive regulation of apoptotic cell clearance + 5
            recognition of apoptotic cell 5
            regulation of apoptotic cell clearance + 6
Path 2
Term Annotations click to browse term
  biological_process 12001
    localization 4781
      establishment of localization 3430
        transport 3278
          vesicle-mediated transport 1116
            phagocytosis 173
              apoptotic cell clearance 35
                engulfment of apoptotic cell + 9
                negative regulation of apoptotic cell clearance + 1
                neutrophil clearance 4
                phagosome maturation involved in apoptotic cell clearance + 1
                positive regulation of apoptotic cell clearance + 5
                recognition of apoptotic cell 5
                regulation of apoptotic cell clearance + 6
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.