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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 IMP (PMID:24509909) UniProtKB PMID:24509909 NCBI chr 8:142,449,649...142,545,009
Ensembl chr 8:142,449,430...142,545,009
JBrowse link
G ALOX15 arachidonate 15-lipoxygenase ISS UniProtKB GO_REF:0000024 NCBI chr17:4,630,919...4,641,678
Ensembl chr17:4,630,919...4,642,294
Ensembl chr17:4,630,919...4,642,294
JBrowse link
G AXL AXL receptor tyrosine kinase ISO (MGI:MGI:3841855|PMID:18804096)
(MGI:MGI:3836130|PMID:17442946)
(MGI:MGI:3778590|PMID:18159085)
(MGI:MGI:5509105|PMID:23878224)
MGI PMID:17442946, PMID:18159085, PMID:18804096, PMID:23878224 MGI:MGI:3778590, MGI:MGI:3836130, MGI:MGI:3841855, MGI:MGI:5509105 NCBI chr19:41,219,223...41,261,766
Ensembl chr19:41,219,223...41,261,766
JBrowse link
G CD36 CD36 molecule IEA Ensembl GO_REF:0000107 NCBI chr 7:80,602,207...80,679,277
Ensembl chr 7:80,369,575...80,679,277
JBrowse link
G GAS6 growth arrest specific 6 IDA (PMID:21501828) UniProtKB PMID:21501828 NCBI chr13:113,820,549...113,864,076
Ensembl chr13:113,820,549...113,864,076
JBrowse link
G HMGB1 high mobility group box 1 IDA (PMID:18768881) UniProtKB PMID:18768881 NCBI chr13:30,456,704...30,617,597
Ensembl chr13:30,456,704...30,617,597
JBrowse link
G ITGAV integrin subunit alpha V IGI
ISS
(PMID:20826760) BHF-UCL PMID:20826760 GO_REF:0000024 NCBI chr 2:186,590,056...186,680,901
Ensembl chr 2:186,590,056...186,680,901
JBrowse link
G ITGB3 integrin subunit beta 3 IGI (PMID:20826760) BHF-UCL PMID:20826760 NCBI chr17:47,253,827...47,313,743
Ensembl chr17:47,253,846...47,313,735
Ensembl chr17:47,253,846...47,313,735
Ensembl chr17:47,253,846...47,313,735
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 chr17:76,712,830...76,726,783
Ensembl chr17:76,712,832...76,726,799
JBrowse link
G LRP1 LDL receptor related protein 1 ISS BHF-UCL GO_REF:0000024 NCBI chr12:57,128,401...57,213,377
Ensembl chr12:57,128,483...57,213,361
JBrowse link
G MARCO macrophage receptor with collagenous structure IEA Ensembl GO_REF:0000107 NCBI chr 2:118,942,180...118,994,664
Ensembl chr 2:118,942,166...118,994,660
JBrowse link
G MEGF10 multiple EGF like domains 10 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 5:127,229,519...127,461,222
Ensembl chr 5:127,290,796...127,465,737
JBrowse link
G MERTK MER proto-oncogene, tyrosine kinase ISO (MGI:MGI:3836130|PMID:17442946)
(MGI:MGI:6120635|PMID:29440417)
(MGI:MGI:5509105|PMID:23878224)
(MGI:MGI:3778590|PMID:18159085)
MGI
UniProtKB
PMID:17442946, PMID:18159085, PMID:23878224, PMID:29440417 MGI:MGI:3778590, MGI:MGI:3836130, MGI:MGI:5509105, MGI:MGI:6120635 NCBI chr 2:111,898,607...112,029,561
Ensembl chr 2:111,898,607...112,029,561
JBrowse link
G MFGE8 milk fat globule EGF and factor V/VIII domain containing IEA Ensembl GO_REF:0000107 NCBI chr15:88,898,683...88,913,405
Ensembl chr15:88,898,683...88,913,381
JBrowse link
G NR1H3 nuclear receptor subfamily 1 group H member 3 IMP (PMID:19628791) UniProtKB PMID:19628791 NCBI chr11:47,248,300...47,269,033
Ensembl chr11:47,248,300...47,269,033
JBrowse link
G RARA retinoic acid receptor alpha IMP (PMID:19628791) UniProtKB PMID:19628791 NCBI chr17:40,309,180...40,357,643
Ensembl chr17:40,309,180...40,357,643
JBrowse link
G TGM2 transglutaminase 2 IDA (PMID:19628791) UniProtKB PMID:19628791 NCBI chr20:38,127,385...38,166,508
Ensembl chr20:38,127,385...38,166,578
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 chr 5:156,919,292...156,963,226
Ensembl chr 5:156,919,292...156,963,226
JBrowse link
G TREM2 triggering receptor expressed on myeloid cells 2 ISS UniProt GO_REF:0000024 NCBI chr 6:41,158,508...41,163,116
Ensembl chr 6:41,158,506...41,163,186
JBrowse link
G TREX1 three prime repair exonuclease 1 IEA Ensembl GO_REF:0000107 NCBI chr 3:48,465,830...48,467,645
Ensembl chr 3:48,465,811...48,467,645
JBrowse link
G TXNDC5 thioredoxin domain containing 5 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 6:7,881,517...7,910,788
Ensembl chr 6:7,881,517...7,910,788
JBrowse link
G TYRO3 TYRO3 protein tyrosine kinase ISS UniProtKB GO_REF:0000024 NCBI chr15:41,559,212...41,583,589
Ensembl chr15:41,557,675...41,583,589
JBrowse link
G TYROBP transmembrane immune signaling adaptor TYROBP ISS UniProt GO_REF:0000024 NCBI chr19:35,904,403...35,908,295
Ensembl chr19:35,904,401...35,908,295
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 IMP
IBA
ISS
(PMID:24509909)
(PMID:21873635)
UniProtKB
GO_Central
PMID:21873635, PMID:24509909 GO_REF:0000024 NCBI chr 8:142,449,649...142,545,009
Ensembl chr 8:142,449,430...142,545,009
JBrowse link
G BECN1 beclin 1 ISO (MGI:MGI:5619450|PMID:22393062) CACAO PMID:22393062 MGI:MGI:5619450 NCBI chr17:42,810,132...42,824,282
Ensembl chr17:42,810,134...42,833,350
JBrowse link
G MEGF10 multiple EGF like domains 10 ISS UniProtKB GO_REF:0000024 NCBI chr 5:127,229,519...127,461,222
Ensembl chr 5:127,290,796...127,465,737
JBrowse link
G RAC1 Rac family small GTPase 1 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 7:6,374,527...6,403,967
Ensembl chr 7:6,374,527...6,403,967
JBrowse link
G RAC2 Rac family small GTPase 2 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr22:37,225,270...37,244,269
Ensembl chr22:37,225,270...37,244,448
JBrowse link
G RHOBTB1 Rho related BTB domain containing 1 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr10:60,869,438...61,001,486
Ensembl chr10:60,869,438...61,001,440
JBrowse link
G RHOBTB2 Rho related BTB domain containing 2 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 8:22,987,251...23,020,199
Ensembl chr 8:22,987,417...23,020,199
JBrowse link
G RHOG ras homolog family member G IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr11:3,826,978...3,840,959
Ensembl chr11:3,826,978...3,840,959
JBrowse link
G RHOH ras homolog family member H IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 4:40,191,080...40,246,967
Ensembl chr 4:40,191,053...40,246,967
JBrowse link
G THBS1 thrombospondin 1 IDA (PMID:16882710) BHF-UCL PMID:16882710 NCBI chr15:39,581,079...39,599,466
Ensembl chr15:39,581,079...39,599,466
JBrowse link
G XKR4 XK related 4 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 8:55,102,028...55,542,054
Ensembl chr 8:55,102,028...55,542,054
JBrowse link
G XKR5 XK related 5 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 8:6,808,517...6,835,524
Ensembl chr 8:6,808,517...6,835,524
JBrowse link
G XKR6 XK related 6 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 8:10,893,764...11,201,833
Ensembl chr 8:10,896,045...11,201,833
JBrowse link
G XKR7 XK related 7 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr20:31,968,151...32,003,387
Ensembl chr20:31,968,151...32,003,387
JBrowse link
G XKR8 XK related 8 IDA
IBA
(PMID:23845944)
(PMID:21873635)
UniProtKB
GO_Central
PMID:21873635, PMID:23845944 NCBI chr 1:27,959,557...27,968,093
Ensembl chr 1:27,959,588...27,968,093
Ensembl chr 1:27,959,588...27,968,093
Ensembl chr 1:27,959,588...27,968,093
JBrowse link
G XKR9 XK related 9 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 8:70,669,339...71,066,635
Ensembl chr 8:70,669,339...70,790,371
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 ISS UniProtKB GO_REF:0000024 NCBI chr17:74,694,308...74,713,000
Ensembl chr17:74,694,311...74,712,978
JBrowse link
G HMGB1 high mobility group box 1 IDA (PMID:20826760) BHF-UCL PMID:20826760 NCBI chr13:30,456,704...30,617,597
Ensembl chr13:30,456,704...30,617,597
JBrowse link
neutrophil clearance term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ANXA1 annexin A1 IMP
IBA
(PMID:21957127)
(PMID:21873635)
BHF-UCL
GO_Central
PMID:21873635, PMID:21957127 NCBI chr 9:73,151,865...73,170,393
Ensembl chr 9:73,151,865...73,170,393
JBrowse link
G AXL AXL receptor tyrosine kinase IEA Ensembl GO_REF:0000107 NCBI chr19:41,219,223...41,261,766
Ensembl chr19:41,219,223...41,261,766
JBrowse link
G CCR2 C-C motif chemokine receptor 2 IEA Ensembl GO_REF:0000107 NCBI chr 3:46,354,111...46,360,940
Ensembl chr 3:46,353,744...46,360,940
Ensembl chr 3:46,353,744...46,360,940
JBrowse link
G HMGB1 high mobility group box 1 IDA (PMID:18768881) UniProtKB PMID:18768881 NCBI chr13:30,456,704...30,617,597
Ensembl chr13:30,456,704...30,617,597
JBrowse link
G MERTK MER proto-oncogene, tyrosine kinase IEA Ensembl GO_REF:0000107 NCBI chr 2:111,898,607...112,029,561
Ensembl chr 2:111,898,607...112,029,561
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 (PMID:21873635) GO_Central PMID:21873635 NCBI chr 9:121,178,133...121,201,869
Ensembl chr 9:121,178,133...121,223,014
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 chr15:44,562,696...44,663,678
Ensembl chr15:44,562,696...44,663,678
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 IMP (PMID:19302245) BHF-UCL PMID:19302245 NCBI chr 6:31,897,783...31,945,672
Ensembl chr 6:31,897,785...31,945,672
JBrowse link
G C3 complement C3 IMP (PMID:19302245) BHF-UCL PMID:19302245 NCBI chr19:6,677,704...6,720,650
Ensembl chr19:6,677,704...6,730,562
JBrowse link
G C4A complement C4A (Rodgers blood group) IGI (PMID:19302245) BHF-UCL PMID:19302245 NCBI chr 6:31,982,057...32,002,681
Ensembl chr 6:31,982,057...32,002,681
JBrowse link
G C4B complement C4B (Chido blood group) IGI (PMID:19302245) BHF-UCL PMID:19302245 NCBI chr 6:32,014,795...32,035,418
Ensembl chr 6:32,014,795...32,035,418
JBrowse link
G C4B_2 complement component 4B (Chido blood group), copy 2 IGI (PMID:19302245) BHF-UCL PMID:19302245
G CCL2 C-C motif chemokine ligand 2 ISS BHF-UCL GO_REF:0000024 NCBI chr17:34,255,285...34,257,203
Ensembl chr17:34,255,218...34,257,203
JBrowse link
G CD300LF CD300 molecule like family member f ISS UniProtKB GO_REF:0000024 NCBI chr17:74,694,308...74,713,000
Ensembl chr17:74,694,311...74,712,978
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 ISS Alzheimers_University_of_Toronto GO_REF:0000024 NCBI chr19:1,040,107...1,065,572
Ensembl chr19:1,039,997...1,065,572
Ensembl chr19:1,039,997...1,065,572
JBrowse link
G TREM2 triggering receptor expressed on myeloid cells 2 IMP (PMID:24990881) UniProt PMID:24990881 NCBI chr 6:41,158,508...41,163,116
Ensembl chr 6:41,158,506...41,163,186
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 IDA (PMID:15804047) UniProtKB PMID:15804047 NCBI chr 9:134,903,232...134,917,912
Ensembl chr 9:134,903,232...134,917,912
JBrowse link
G FCN2 ficolin 2 IDA (PMID:15804047) UniProtKB PMID:15804047 NCBI chr 9:134,864,062...134,890,506
Ensembl chr 9:134,880,810...134,887,523
JBrowse link
G FCN3 ficolin 3 IDA (PMID:15804047) UniProtKB PMID:15804047 NCBI chr 1:27,369,110...27,374,852
Ensembl chr 1:27,369,110...27,374,824
Ensembl chr 1:27,369,110...27,374,824
JBrowse link
G JMJD6 jumonji domain containing 6, arginine demethylase and lysine hydroxylase IEA Ensembl GO_REF:0000107 NCBI chr17:76,712,830...76,726,783
Ensembl chr17:76,712,832...76,726,799
JBrowse link
G MEGF10 multiple EGF like domains 10 IEA Ensembl GO_REF:0000107 NCBI chr 5:127,229,519...127,461,222
Ensembl chr 5:127,290,796...127,465,737
JBrowse link
G PEAR1 platelet endothelial aggregation receptor 1 ISO (MGI:MGI:4414741|PMID:19915564) MGI PMID:19915564 MGI:MGI:4414741 NCBI chr 1:156,893,697...156,916,429
Ensembl chr 1:156,893,698...156,916,434
JBrowse link
G SCARB1 scavenger receptor class B member 1 IDA (PMID:9211901) BHF-UCL PMID:9211901 NCBI chr12:124,776,856...124,863,864
Ensembl chr12:124,776,856...124,882,668
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 ISS UniProtKB GO_REF:0000024 NCBI chr17:4,630,919...4,641,678
Ensembl chr17:4,630,919...4,642,294
Ensembl chr17:4,630,919...4,642,294
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 18670
    cellular process 17686
      vesicle-mediated transport 2309
        phagocytosis 419
          apoptotic cell clearance 54
            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 + 9
            recognition of apoptotic cell 7
            regulation of apoptotic cell clearance + 10
Path 2
Term Annotations click to browse term
  biological_process 18670
    localization 7226
      establishment of localization 5679
        transport 5537
          vesicle-mediated transport 2309
            phagocytosis 419
              apoptotic cell clearance 54
                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 + 9
                recognition of apoptotic cell 7
                regulation of apoptotic cell clearance + 10
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.