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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 MGI GO_REF:0000096, MGI:MGI:4834177 NCBI chr15:74,516,196...74,589,465
Ensembl chr15:74,516,195...74,589,465
JBrowse link
G Alox15 arachidonate 15-lipoxygenase IMP (MGI:MGI:5436199|PMID:22503541) UniProtKB PMID:22503541 MGI:MGI:5436199 NCBI chr11:70,344,147...70,390,538
Ensembl chr11:70,344,152...70,352,031
JBrowse link
G Axl AXL receptor tyrosine kinase IGI
IMP
(MGI:MGI:3836130|PMID:17442946)
(MGI:MGI:3778590|PMID:18159085)
(MGI:MGI:5509105|PMID:23878224)
(MGI:MGI:3841855|PMID:18804096)
MGI PMID:17442946, PMID:18159085, PMID:18804096, PMID:23878224 MGI:MGI:3778590, MGI:MGI:3836130, MGI:MGI:3841855, MGI:MGI:5509105 NCBI chr 7:25,756,500...25,788,924
Ensembl chr 7:25,757,273...25,788,705
JBrowse link
G Ccr2 chemokine (C-C motif) receptor 2 IC (MGI:MGI:80507|PMID:8662823) BHF-UCL PMID:8662823 MGI:MGI:80507 NCBI chr 9:124,101,918...124,109,140
Ensembl chr 9:124,101,950...124,113,557
JBrowse link
G Cd36 CD36 molecule IMP (MGI:MGI:3618422|PMID:15647754) MGI PMID:15647754 MGI:MGI:3618422 NCBI chr 5:17,781,690...17,888,959
Ensembl chr 5:17,781,690...17,888,801
JBrowse link
G Gas6 growth arrest specific 6 IDA
ISO
(MGI:MGI:3778590|PMID:18159085) MGI PMID:18159085 GO_REF:0000096, MGI:MGI:3778590, MGI:MGI:4834177 NCBI chr 8:13,465,374...13,494,535
Ensembl chr 8:13,465,374...13,494,490
JBrowse link
G Hmgb1 high mobility group box 1 ISO (PMID:18768881) UniProtKB PMID:18768881 NCBI chr 5:149,046,702...149,053,057
Ensembl chr 5:149,046,702...149,184,489
JBrowse link
G Itgav integrin alpha V IMP
ISO
IDA
IGI
(MGI:MGI:3618422|PMID:15647754)
(MGI:MGI:5285150|PMID:20826760)
MGI
BHF-UCL
PMID:15647754, PMID:20826760 GO_REF:0000096, MGI:MGI:3618422, MGI:MGI:4834177, MGI:MGI:5285150 NCBI chr 2:83,722,303...83,806,917
Ensembl chr 2:83,724,397...83,806,916
JBrowse link
G Itgb3 integrin beta 3 IGI
ISO
(MGI:MGI:5285150|PMID:20826760) BHF-UCL
MGI
PMID:20826760 GO_REF:0000096, MGI:MGI:4834177, MGI:MGI:5285150 NCBI chr11:104,608,000...104,670,476
Ensembl chr11:104,608,000...104,670,476
JBrowse link
G Jmjd6 jumonji domain containing 6 NOT IMP (MGI:MGI:3042820|PMID:14715629)
(MGI:MGI:3618422|PMID:15647754)
(MGI:MGI:3580691|PMID:15345036)
MGI PMID:14715629, PMID:15345036, PMID:15647754 MGI:MGI:3042820, MGI:MGI:3580691, MGI:MGI:3618422 NCBI chr11:116,837,432...116,843,767
Ensembl chr11:116,837,432...116,843,449
JBrowse link
G Lrp1 low density lipoprotein receptor-related protein 1 IMP (MGI:MGI:3618422|PMID:15647754) MGI PMID:15647754 MGI:MGI:3618422 NCBI chr10:127,538,157...127,621,148
Ensembl chr10:127,538,161...127,621,148
JBrowse link
G Marco macrophage receptor with collagenous structure IMP (MGI:MGI:3831958|PMID:19201851) MGI PMID:19201851 MGI:MGI:3831958 NCBI chr 1:120,474,538...120,505,024
Ensembl chr 1:120,474,538...120,505,024
JBrowse link
G Megf10 multiple EGF-like-domains 10 IBA (MGI:MGI:6201960|PMID:21873635) GO_Central PMID:21873635 MGI:MGI:6201960 NCBI chr18:57,133,090...57,297,467
Ensembl chr18:57,133,090...57,297,467
JBrowse link
G Mertk MER proto-oncogene tyrosine kinase IGI
IDA
IMP
(MGI:MGI:3778590|PMID:18159085)
(MGI:MGI:6120635|PMID:29440417)
(MGI:MGI:5509105|PMID:23878224)
(MGI:MGI:3836130|PMID:17442946)
MGI
UniProtKB
PMID:17442946, PMID:18159085, PMID:23878224, PMID:29440417 MGI:MGI:3778590, MGI:MGI:3836130, MGI:MGI:5509105, MGI:MGI:6120635 NCBI chr 2:128,698,915...128,803,162
Ensembl chr 2:128,698,956...128,802,894
JBrowse link
G Mfge8 milk fat globule-EGF factor 8 protein IDA (MGI:MGI:5285150|PMID:20826760) BHF-UCL PMID:20826760 MGI:MGI:5285150 NCBI chr 7:79,133,768...79,149,060
Ensembl chr 7:79,133,768...79,149,060
JBrowse link
G Nr1h3 nuclear receptor subfamily 1, group H, member 3 ISO MGI GO_REF:0000096, MGI:MGI:4834177 NCBI chr 2:91,184,061...91,202,829
Ensembl chr 2:91,184,061...91,202,834
JBrowse link
G Rara retinoic acid receptor, alpha ISO MGI GO_REF:0000096, MGI:MGI:4834177 NCBI chr11:98,927,800...98,974,942
Ensembl chr11:98,927,818...98,974,942
JBrowse link
G Tgm2 transglutaminase 2, C polypeptide ISO MGI GO_REF:0000096, MGI:MGI:4834177 NCBI chr 2:158,116,405...158,146,392
Ensembl chr 2:158,116,402...158,146,436
JBrowse link
G Timd4 T cell immunoglobulin and mucin domain containing 4 IDA (MGI:MGI:6120635|PMID:29440417) MGI PMID:29440417 MGI:MGI:6120635 NCBI chr11:46,810,786...46,844,333
Ensembl chr11:46,810,800...46,844,332
JBrowse link
G Trem2 triggering receptor expressed on myeloid cells 2 IMP (MGI:MGI:3531054|PMID:15728241) UniProt PMID:15728241 MGI:MGI:3531054 NCBI chr17:48,346,401...48,352,276
Ensembl chr17:48,346,401...48,354,147
JBrowse link
G Trex1 three prime repair exonuclease 1 IMP (MGI:MGI:5554502|PMID:24218451) MGI PMID:24218451 MGI:MGI:5554502 NCBI chr 9:109,057,932...109,059,723
Ensembl chr 9:109,057,933...109,059,734
JBrowse link
G Txndc5 thioredoxin domain containing 5 IBA (MGI:MGI:6201960|PMID:21873635) GO_Central PMID:21873635 MGI:MGI:6201960 NCBI chr13:38,500,266...38,528,824
Ensembl chr13:38,500,079...38,528,824
JBrowse link
G Tyro3 TYRO3 protein tyrosine kinase 3 IGI (MGI:MGI:3778590|PMID:18159085)
(MGI:MGI:3836130|PMID:17442946)
MGI PMID:17442946, PMID:18159085 MGI:MGI:3778590, MGI:MGI:3836130 NCBI chr 2:119,797,740...119,818,104
Ensembl chr 2:119,797,733...119,818,104
JBrowse link
G Tyrobp TYRO protein tyrosine kinase binding protein IMP (MGI:MGI:3531054|PMID:15728241) UniProt PMID:15728241 MGI:MGI:3531054 NCBI chr 7:30,413,782...30,417,582
Ensembl chr 7:30,413,760...30,417,585
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 IDA
IBA
ISO
(MGI:MGI:3764740|PMID:17960134)
(MGI:MGI:6201960|PMID:21873635)
UniProtKB
GO_Central
MGI
PMID:17960134, PMID:21873635 GO_REF:0000096, MGI:MGI:3764740, MGI:MGI:4834177, MGI:MGI:6201960 NCBI chr15:74,516,196...74,589,465
Ensembl chr15:74,516,195...74,589,465
JBrowse link
G Becn1 beclin 1, autophagy related IMP (MGI:MGI:5619450|PMID:22393062) CACAO PMID:22393062 MGI:MGI:5619450 NCBI chr11:101,288,258...101,302,286
Ensembl chr11:101,285,952...101,302,286
JBrowse link
G Megf10 multiple EGF-like-domains 10 IMP (MGI:MGI:5775214|PMID:27170117) MGI PMID:27170117 MGI:MGI:5775214 NCBI chr18:57,133,090...57,297,467
Ensembl chr18:57,133,090...57,297,467
JBrowse link
G Rac1 Rac family small GTPase 1 IDA
IBA
(MGI:MGI:4943793|PMID:20691665)
(MGI:MGI:6201960|PMID:21873635)
BHF-UCL
GO_Central
PMID:20691665, PMID:21873635 MGI:MGI:4943793, MGI:MGI:6201960 NCBI chr 5:143,505,481...143,528,031
Ensembl chr 5:143,503,634...143,528,036
JBrowse link
G Rac2 Rac family small GTPase 2 IBA (MGI:MGI:6201960|PMID:21873635) GO_Central PMID:21873635 MGI:MGI:6201960 NCBI chr15:78,559,169...78,572,783
Ensembl chr15:78,559,167...78,572,783
JBrowse link
G Rhobtb1 Rho-related BTB domain containing 1 IBA (MGI:MGI:6201960|PMID:21873635) GO_Central PMID:21873635 MGI:MGI:6201960 NCBI chr10:69,151,058...69,291,791
Ensembl chr10:69,151,434...69,291,791
JBrowse link
G Rhobtb2 Rho-related BTB domain containing 2 IBA (MGI:MGI:6201960|PMID:21873635) GO_Central PMID:21873635 MGI:MGI:6201960 NCBI chr14:69,784,990...69,824,847
Ensembl chr14:69,784,990...69,805,636
JBrowse link
G Rhog ras homolog family member G IBA (MGI:MGI:6201960|PMID:21873635) GO_Central PMID:21873635 MGI:MGI:6201960 NCBI chr 7:102,239,123...102,250,118
Ensembl chr 7:102,239,123...102,256,054
JBrowse link
G Rhoh ras homolog family member H IBA (MGI:MGI:6201960|PMID:21873635) GO_Central PMID:21873635 MGI:MGI:6201960 NCBI chr 5:65,860,742...65,896,700
Ensembl chr 5:65,861,213...65,896,700
JBrowse link
G Thbs1 thrombospondin 1 ISO MGI GO_REF:0000096, MGI:MGI:4834177 NCBI chr 2:118,111,876...118,127,133
Ensembl chr 2:118,111,876...118,127,133
JBrowse link
G Xkr4 X-linked Kx blood group related 4 IBA (MGI:MGI:6201960|PMID:21873635) GO_Central PMID:21873635 MGI:MGI:6201960 NCBI chr 1:3,199,733...3,671,948
Ensembl chr 1:3,205,901...3,671,498
JBrowse link
G Xkr5 X-linked Kx blood group related 5 IBA (MGI:MGI:6201960|PMID:21873635) GO_Central PMID:21873635 MGI:MGI:6201960 NCBI chr 8:18,924,152...18,951,105
Ensembl chr 8:18,932,729...18,950,975
JBrowse link
G Xkr6 X-linked Kx blood group related 6 IBA (MGI:MGI:6201960|PMID:21873635) GO_Central PMID:21873635 MGI:MGI:6201960 NCBI chr14:63,606,530...63,845,706
Ensembl chr14:63,606,503...63,820,809
JBrowse link
G Xkr7 X-linked Kx blood group related 7 IBA (MGI:MGI:6201960|PMID:21873635) GO_Central PMID:21873635 MGI:MGI:6201960 NCBI chr 2:153,031,852...153,060,294
Ensembl chr 2:153,031,852...153,055,775
JBrowse link
G Xkr8 X-linked Kx blood group related 8 ISO
IBA
(MGI:MGI:6201960|PMID:21873635) MGI
GO_Central
PMID:21873635 GO_REF:0000096, MGI:MGI:4834177, MGI:MGI:6201960 NCBI chr 4:132,724,901...132,732,614
Ensembl chr 4:132,724,897...132,732,546
JBrowse link
G Xkr9 X-linked Kx blood group related 9 IBA (MGI:MGI:6201960|PMID:21873635) GO_Central PMID:21873635 MGI:MGI:6201960 NCBI chr 1:13,668,738...13,702,230
Ensembl chr 1:13,668,771...13,701,723
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 IMP (MGI:MGI:5819329|PMID:26768664) UniProtKB PMID:26768664 MGI:MGI:5819329 NCBI chr11:115,116,214...115,135,372
Ensembl chr11:115,116,214...115,133,992
JBrowse link
G Hmgb1 high mobility group box 1 ISO (PMID:20826760) BHF-UCL PMID:20826760 NCBI chr 5:149,046,702...149,053,057
Ensembl chr 5:149,046,702...149,184,489
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
IBA
(MGI:MGI:6201960|PMID:21873635) MGI
GO_Central
PMID:21873635 GO_REF:0000096, MGI:MGI:4834177, MGI:MGI:6201960 NCBI chr19:20,373,434...20,390,671
Ensembl chr19:20,373,428...20,390,944
JBrowse link
G Axl AXL receptor tyrosine kinase IGI (MGI:MGI:5509105|PMID:23878224) MGI PMID:23878224 MGI:MGI:5509105 NCBI chr 7:25,756,500...25,788,924
Ensembl chr 7:25,757,273...25,788,705
JBrowse link
G Ccr2 chemokine (C-C motif) receptor 2 IMP (MGI:MGI:1100445|PMID:9342361) MGI PMID:9342361 MGI:MGI:1100445 NCBI chr 9:124,101,918...124,109,140
Ensembl chr 9:124,101,950...124,113,557
JBrowse link
G Hmgb1 high mobility group box 1 ISO (PMID:18768881) UniProtKB PMID:18768881 NCBI chr 5:149,046,702...149,053,057
Ensembl chr 5:149,046,702...149,184,489
JBrowse link
G Mertk MER proto-oncogene tyrosine kinase IGI (MGI:MGI:5509105|PMID:23878224) MGI PMID:23878224 MGI:MGI:5509105 NCBI chr 2:128,698,915...128,803,162
Ensembl chr 2:128,698,956...128,802,894
JBrowse link
phagolysosome assembly involved in apoptotic cell clearance term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Rab14 RAB14, member RAS oncogene family IBA (MGI:MGI:6201960|PMID:21873635) GO_Central PMID:21873635 MGI:MGI:6201960 NCBI chr 2:35,180,205...35,201,120
Ensembl chr 2:35,180,205...35,201,120
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, spatacsin vesicle trafficking associated IMP (MGI:MGI:5749311|PMID:26284655) MGI PMID:26284655 MGI:MGI:5749311 NCBI chr 2:122,053,526...122,119,434
Ensembl chr 2:122,053,520...122,118,386
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 component 2 (within H-2S) ISO MGI GO_REF:0000096, MGI:MGI:4834177 NCBI chr17:34,862,602...34,882,100
Ensembl chr17:34,862,604...34,898,265
JBrowse link
G C3 complement component 3 ISO MGI GO_REF:0000096, MGI:MGI:4834177 NCBI chr17:57,203,967...57,228,136
Ensembl chr17:57,203,970...57,228,136
JBrowse link
G C4a complement component 4A (Rodgers blood group) ISO (PMID:19302245) BHF-UCL PMID:19302245 NCBI chr17:34,809,092...34,823,460
Ensembl chr17:34,809,092...34,823,464
JBrowse link
G C4b complement component 4B (Chido blood group) ISO (PMID:19302245) BHF-UCL PMID:19302245 NCBI chr17:34,728,139...34,743,902
Ensembl chr17:34,728,380...34,743,882
JBrowse link
G Ccl2 chemokine (C-C motif) ligand 2 IDA (MGI:MGI:4943793|PMID:20691665) BHF-UCL PMID:20691665 MGI:MGI:4943793 NCBI chr11:82,035,577...82,037,452
Ensembl chr11:82,035,571...82,037,453
JBrowse link
G Cd300lf CD300 molecule like family member F IDA
IMP
(MGI:MGI:5301804|PMID:21865548)
(MGI:MGI:5819329|PMID:26768664)
UniProtKB PMID:21865548, PMID:26768664 MGI:MGI:5301804, MGI:MGI:5819329 NCBI chr11:115,116,214...115,135,372
Ensembl chr11:115,116,214...115,133,992
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, sub-family A (ABC1), member 7 IMP (MGI:MGI:3662940|PMID:16908670) Alzheimers_University_of_Toronto PMID:16908670 MGI:MGI:3662940 NCBI chr10:79,996,453...80,015,572
Ensembl chr10:79,996,494...80,015,572
JBrowse link
G Trem2 triggering receptor expressed on myeloid cells 2 ISO MGI GO_REF:0000096, MGI:MGI:4834177 NCBI chr17:48,346,401...48,352,276
Ensembl chr17:48,346,401...48,354,147
JBrowse link
recognition of apoptotic cell term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Fcna ficolin A ISO (PMID:15804047) UniProtKB PMID:15804047 NCBI chr 2:25,624,665...25,635,440
Ensembl chr 2:25,624,666...25,628,030
JBrowse link
G Fcnb ficolin B ISO MGI GO_REF:0000096, MGI:MGI:4834177 NCBI chr 2:28,076,479...28,084,910
Ensembl chr 2:28,076,378...28,084,885
JBrowse link
G Jmjd6 jumonji domain containing 6 IDA
IMP
(MGI:MGI:1855743|PMID:10811223)
(MGI:MGI:2682078|PMID:14645847)
MGI PMID:10811223, PMID:14645847 MGI:MGI:1855743, MGI:MGI:2682078 NCBI chr11:116,837,432...116,843,767
Ensembl chr11:116,837,432...116,843,449
JBrowse link
G Megf10 multiple EGF-like-domains 10 IMP
IDA
(MGI:MGI:4414741|PMID:19915564) MGI PMID:19915564 MGI:MGI:4414741 NCBI chr18:57,133,090...57,297,467
Ensembl chr18:57,133,090...57,297,467
JBrowse link
G Pear1 platelet endothelial aggregation receptor 1 IDA
IMP
(MGI:MGI:4414741|PMID:19915564) MGI PMID:19915564 MGI:MGI:4414741 NCBI chr 3:87,749,097...87,769,110
Ensembl chr 3:87,747,890...87,824,306
JBrowse link
G Scarb1 scavenger receptor class B, member 1 ISS
IBA
ISO
(MGI:MGI:894255|PMID:9211901)
(MGI:MGI:6201960|PMID:21873635)
BHF-UCL
GO_Central
RGD
MGI
PMID:9211901, PMID:21873635 GO_REF:0000096, MGI:MGI:4417868, MGI:MGI:4834177, MGI:MGI:6201960, MGI:MGI:894255 NCBI chr 5:125,277,087...125,341,094
Ensembl chr 5:125,277,087...125,341,094
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 IMP (MGI:MGI:5436199|PMID:22503541), (MGI:MGI:5508294|PMID:11278875) UniProtKB PMID:11278875, PMID:22503541 MGI:MGI:5436199, MGI:MGI:5508294 NCBI chr11:70,344,147...70,390,538
Ensembl chr11:70,344,152...70,352,031
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 23386
    cellular process 17413
      vesicle-mediated transport 1605
        phagocytosis 364
          apoptotic cell clearance 52
            engulfment of apoptotic cell + 19
            negative regulation of apoptotic cell clearance + 2
            neutrophil clearance 5
            phagosome maturation involved in apoptotic cell clearance + 2
            positive regulation of apoptotic cell clearance + 8
            recognition of apoptotic cell 6
            regulation of apoptotic cell clearance + 9
Path 2
Term Annotations click to browse term
  biological_process 23386
    localization 6243
      establishment of localization 4693
        transport 4542
          vesicle-mediated transport 1605
            phagocytosis 364
              apoptotic cell clearance 52
                engulfment of apoptotic cell + 19
                negative regulation of apoptotic cell clearance + 2
                neutrophil clearance 5
                phagosome maturation involved in apoptotic cell clearance + 2
                positive regulation of apoptotic cell clearance + 8
                recognition of apoptotic cell 6
                regulation of apoptotic cell clearance + 9
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.