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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_004955454:1,250,261...1,313,547
Ensembl chrNW_004955454:1,237,363...1,314,127
JBrowse link
G Alox15 arachidonate 15-lipoxygenase ISO (MGI:MGI:5436199|PMID:22503541) UniProtKB PMID:22503541 MGI:MGI:5436199 NCBI chrNW_004955467:10,032,792...10,039,789 JBrowse link
G Axl AXL receptor tyrosine kinase ISO (MGI:MGI:5509105|PMID:23878224)
(MGI:MGI:3841855|PMID:18804096)
(MGI:MGI:3778590|PMID:18159085)
(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_004955555:189,445...218,509
Ensembl chrNW_004955555:189,174...218,565
JBrowse link
G Cd36 CD36 molecule ISO (MGI:MGI:3618422|PMID:15647754) MGI PMID:15647754 MGI:MGI:3618422 NCBI chrNW_004955410:5,003,720...5,120,903
Ensembl chrNW_004955410:5,003,668...5,075,313
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_004955404:276,397...303,864
Ensembl chrNW_004955404:275,946...304,809
JBrowse link
G Hmgb1 high mobility group box 1 ISO (PMID:18768881) UniProtKB PMID:18768881 NCBI chrNW_004955431:15,373,207...15,377,339 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_004955403:11,588,536...11,669,809
Ensembl chrNW_004955403:11,592,339...11,659,297
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_004955478:9,788,192...9,830,254 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 chrNW_004955506:5,577,735...5,588,307
Ensembl chrNW_004955506:5,577,437...5,588,372
JBrowse link
G Lrp1 LDL receptor related protein 1 ISO (MGI:MGI:3618422|PMID:15647754) MGI PMID:15647754 MGI:MGI:3618422 NCBI chrNW_004955458:4,861,431...4,941,939
Ensembl chrNW_004955458:4,861,431...4,941,146
JBrowse link
G Marco macrophage receptor with collagenous structure ISO (MGI:MGI:3831958|PMID:19201851) MGI PMID:19201851 MGI:MGI:3831958 NCBI chrNW_004955459:10,700,645...10,739,222
Ensembl chrNW_004955459:10,698,294...10,739,131
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)
UniProtKB
MGI
PMID:17442946, PMID:18159085, PMID:23878224, PMID:29440417 MGI:MGI:3778590, MGI:MGI:3836130, MGI:MGI:5509105, MGI:MGI:6120635 NCBI chrNW_004955470:2,065,468...2,167,909
Ensembl chrNW_004955470:2,065,411...2,167,909
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_004955416:16,092,263...16,103,097
Ensembl chrNW_004955416:16,091,684...16,103,768
JBrowse link
G Nr1h3 nuclear receptor subfamily 1 group H member 3 ISO (PMID:19628791) UniProtKB PMID:19628791 NCBI chrNW_004955422:940,310...954,170
Ensembl chrNW_004955422:940,310...949,049
JBrowse link
G Rara retinoic acid receptor alpha ISO (PMID:19628791) UniProtKB PMID:19628791 NCBI chrNW_004955451:14,876,663...14,917,134
Ensembl chrNW_004955451:14,897,726...14,917,134
JBrowse link
G Tgm2 transglutaminase 2 ISO (PMID:19628791) UniProtKB PMID:19628791 NCBI chrNW_004955445:18,544,192...18,576,576
Ensembl chrNW_004955445:18,544,183...18,576,570
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_004955408:10,969,413...10,998,042 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_004955437:7,780,886...7,785,597
Ensembl chrNW_004955437:7,780,679...7,785,697
JBrowse link
G Trex1 three prime repair exonuclease 1 ISO (MGI:MGI:5554502|PMID:24218451) MGI PMID:24218451 MGI:MGI:5554502 NCBI chrNW_004955532:533,877...535,767
Ensembl chrNW_004955532:533,877...535,767
JBrowse link
G Tyro3 TYRO3 protein tyrosine kinase ISO (MGI:MGI:3778590|PMID:18159085)
(MGI:MGI:3836130|PMID:17442946)
MGI PMID:17442946, PMID:18159085 MGI:MGI:3778590, MGI:MGI:3836130 NCBI chrNW_004955416:8,361,722...8,377,629
Ensembl chrNW_004955416:8,359,207...8,377,692
JBrowse link
G Tyrobp transmembrane immune signaling adaptor TYROBP ISO (MGI:MGI:3531054|PMID:15728241) UniProt PMID:15728241 MGI:MGI:3531054 NCBI chrNW_004955468:2,673,657...2,677,633
Ensembl chrNW_004955468:2,673,980...2,677,321
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 (PMID:24509909)
(MGI:MGI:3764740|PMID:17960134)
UniProtKB PMID:17960134, PMID:24509909 MGI:MGI:3764740 NCBI chrNW_004955454:1,250,261...1,313,547
Ensembl chrNW_004955454:1,237,363...1,314,127
JBrowse link
G Becn1 beclin 1 ISO (MGI:MGI:5619450|PMID:22393062) CACAO PMID:22393062 MGI:MGI:5619450 NCBI chrNW_004955451:16,616,595...16,625,731 JBrowse link
G Megf10 multiple EGF like domains 10 ISO (MGI:MGI:5775214|PMID:27170117) MGI PMID:27170117 MGI:MGI:5775214 NCBI chrNW_004955415:393,642...513,157
Ensembl chrNW_004955415:335,012...513,891
JBrowse link
G Rac1 Rac family small GTPase 1 ISO (MGI:MGI:4943793|PMID:20691665) BHF-UCL PMID:20691665 MGI:MGI:4943793 NCBI chrNW_004955460:13,270,159...13,295,562
Ensembl chrNW_004955460:13,270,159...13,311,351
JBrowse link
G Thbs1 thrombospondin 1 ISO (PMID:16882710) BHF-UCL PMID:16882710 NCBI chrNW_004955416:6,490,034...6,506,419
Ensembl chrNW_004955416:6,489,451...6,506,419
JBrowse link
G Xkr8 XK related 8 ISO (PMID:23845944) UniProtKB PMID:23845944 NCBI chrNW_004955452:7,141,088...7,148,571
Ensembl chrNW_004955452:7,141,201...7,146,443
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 chrNW_004955553:1,596,406...1,610,479
Ensembl chrNW_004955553:1,488,501...1,610,555
JBrowse link
G Hmgb1 high mobility group box 1 ISO (PMID:20826760) BHF-UCL PMID:20826760 NCBI chrNW_004955431:15,373,207...15,377,339 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_004955512:5,686,508...5,703,645 JBrowse link
G Axl AXL receptor tyrosine kinase ISO (MGI:MGI:5509105|PMID:23878224) MGI PMID:23878224 MGI:MGI:5509105 NCBI chrNW_004955555:189,445...218,509
Ensembl chrNW_004955555:189,174...218,565
JBrowse link
G Ccr2 C-C motif chemokine receptor 2 ISO (MGI:MGI:1100445|PMID:9342361) MGI PMID:9342361 MGI:MGI:1100445 NCBI chrNW_004955420:25,641,184...25,664,413 JBrowse link
G Hmgb1 high mobility group box 1 ISO (PMID:18768881) UniProtKB PMID:18768881 NCBI chrNW_004955431:15,373,207...15,377,339 JBrowse link
G Mertk MER proto-oncogene, tyrosine kinase ISO (MGI:MGI:5509105|PMID:23878224) MGI PMID:23878224 MGI:MGI:5509105 NCBI chrNW_004955470:2,065,468...2,167,909
Ensembl chrNW_004955470:2,065,411...2,167,909
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_004955416:11,084,448...11,168,478
Ensembl chrNW_004955416:11,086,176...11,168,332
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_004955437:449,171...460,898
Ensembl chrNW_004955437:448,672...460,519
JBrowse link
G C3 complement C3 ISO (PMID:19302245) BHF-UCL PMID:19302245 NCBI chrNW_004955495:2,796,601...2,824,233
Ensembl chrNW_004955495:2,796,663...2,824,697
JBrowse link
G Cd300lf CD300 molecule like family member f ISO (MGI:MGI:5301804|PMID:21865548)
(MGI:MGI:5819329|PMID:26768664)
UniProtKB PMID:21865548, PMID:26768664 MGI:MGI:5301804, MGI:MGI:5819329 NCBI chrNW_004955553:1,596,406...1,610,479
Ensembl chrNW_004955553:1,488,501...1,610,555
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_004955495:6,818,002...6,838,177
Ensembl chrNW_004955495:6,815,562...6,836,772
JBrowse link
G Trem2 triggering receptor expressed on myeloid cells 2 ISO (PMID:24990881) UniProt PMID:24990881 NCBI chrNW_004955437:7,780,886...7,785,597
Ensembl chrNW_004955437:7,780,679...7,785,697
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 1 ISO (PMID:15804047) UniProtKB PMID:15804047 NCBI chrNW_004955513:3,690,550...3,697,785
Ensembl chrNW_004955513:3,687,232...3,698,673
JBrowse link
G Fcn3 ficolin 3 ISO (PMID:15804047) UniProtKB PMID:15804047 NCBI chrNW_004955452:6,630,548...6,635,334
Ensembl chrNW_004955452:6,630,505...6,635,235
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_004955506:5,577,735...5,588,307
Ensembl chrNW_004955506:5,577,437...5,588,372
JBrowse link
G Megf10 multiple EGF like domains 10 ISO (MGI:MGI:4414741|PMID:19915564) MGI PMID:19915564 MGI:MGI:4414741 NCBI chrNW_004955415:393,642...513,157
Ensembl chrNW_004955415:335,012...513,891
JBrowse link
G Pear1 platelet endothelial aggregation receptor 1 ISO (MGI:MGI:4414741|PMID:19915564) MGI PMID:19915564 MGI:MGI:4414741 NCBI chrNW_004955545:2,958,334...2,977,146
Ensembl chrNW_004955545:2,961,726...2,977,146
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_004955482:4,813,502...4,836,479
Ensembl chrNW_004955482:4,813,955...4,837,392
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_004955467:10,032,792...10,039,789 JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 11892
    cellular process 11094
      vesicle-mediated transport 1113
        phagocytosis 177
          apoptotic cell clearance 37
            engulfment of apoptotic cell + 9
            negative regulation of apoptotic cell clearance + 2
            neutrophil clearance 5
            phagosome maturation involved in apoptotic cell clearance + 1
            positive regulation of apoptotic cell clearance + 5
            recognition of apoptotic cell 6
            regulation of apoptotic cell clearance + 6
Path 2
Term Annotations click to browse term
  biological_process 11892
    localization 4760
      establishment of localization 3410
        transport 3262
          vesicle-mediated transport 1113
            phagocytosis 177
              apoptotic cell clearance 37
                engulfment of apoptotic cell + 9
                negative regulation of apoptotic cell clearance + 2
                neutrophil clearance 5
                phagosome maturation involved in apoptotic cell clearance + 1
                positive regulation of apoptotic cell clearance + 5
                recognition of apoptotic cell 6
                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.