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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


show annotations for term's descendants           Sort by:
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 involved_in ISO (PMID:24509909) RGD PMID:24509909 NCBI chr 7:106,404,827...106,476,902
Ensembl chr 7:106,404,958...106,476,902 		JBrowse link
G Alox15 arachidonate 15-lipoxygenase involved_in ISS
IEA
ISO		 GO_REF:0000024
GO_REF:0000107
(MGI:5436199|PMID:22503541)		 UniProt
Ensembl
RGD		 PMID:22503541 GO_REF:0000024 GO_REF:0000107 MGI:5436199 NCBI chr10:55,060,169...55,068,885
Ensembl chr10:55,060,412...55,068,874 		JBrowse link
G Axl Axl receptor tyrosine kinase acts_upstream_of_or_within ISO MGI:104294|MGI:2387750|MGI:96965 (PMID:17442946), (PMID:18159085), (PMID:18804096), (PMID:23878224) RGD PMID:17442946 PMID:18159085 PMID:18804096 PMID:23878224 NCBI chr 1:81,265,088...81,296,278
Ensembl chr 1:81,265,088...81,296,265 		JBrowse link
G Cd36 CD36 molecule involved_in
acts_upstream_of_or_within		 IEA
ISO		 GO_REF:0000107
(PMID:15647754)		 Ensembl
RGD		 PMID:15647754 GO_REF:0000107 NCBI chr 4:17,317,343...17,410,084
Ensembl chr 4:17,354,466...17,513,903 		JBrowse link
G Gas6 growth arrest specific 6 involved_in
acts_upstream_of_or_within		 ISS
ISO		 GO_REF:0000024
(PMID:18159085)
(PMID:21501828)		 UniProt
RGD		 PMID:18159085 PMID:21501828 GO_REF:0000024 NCBI chr16:76,045,430...76,075,904
Ensembl chr16:76,045,426...76,075,904 		JBrowse link
G Hmgb1 high mobility group box 1 involved_in ISO
ISS		 (PMID:18768881)
GO_REF:0000024		 RGD
UniProt		 PMID:18768881 GO_REF:0000024 NCBI chr12:5,972,950...5,979,658
Ensembl chr12:5,901,586...5,978,565
Ensembl chr16:5,901,586...5,978,565 		JBrowse link
G Itgav integrin subunit alpha V involved_in
acts_upstream_of_or_within		 ISO UniProtKB:P43406 (PMID:20826760)
(PMID:15647754)
UniProtKB:P06756 (MGI:5285150|PMID:20826760)		 RGD PMID:15647754 PMID:20826760 MGI:5285150 NCBI chr 3:68,838,514...68,926,653
Ensembl chr 3:68,838,189...68,926,639 		JBrowse link
G Itgb3 integrin subunit beta 3 involved_in ISO
IEA		 UniProtKB:O54890 (PMID:20826760)
GO_REF:0000107
UniProtKB:P05106 (MGI:5285150|PMID:20826760)		 RGD
Ensembl		 PMID:20826760 GO_REF:0000107 MGI:5285150 NCBI chr10:89,509,917...89,564,679
Ensembl chr10:89,509,989...89,564,679 		JBrowse link
G Jmjd6 jumonji domain containing 6, arginine demethylase and lysine hydroxylase acts_upstream_of_or_within
NOT|acts_upstream_of_or_within		 ISO MGI:3043930 (PMID:14715629), (PMID:15647754)
MGI:3580706 (PMID:15345036)		 RGD PMID:14715629 PMID:15345036 PMID:15647754 NCBI chr10:102,041,131...102,047,182
Ensembl chr10:102,041,120...102,047,182 		JBrowse link
G Lrp1 LDL receptor related protein 1 acts_upstream_of_or_within ISO (PMID:15647754) RGD PMID:15647754 NCBI chr 7:63,380,325...63,461,029
Ensembl chr 7:63,380,356...63,460,910 		JBrowse link
G Marco macrophage receptor with collagenous structure acts_upstream_of_or_within ISO (PMID:19201851) RGD PMID:19201851 NCBI chr13:31,616,278...31,648,521
Ensembl chr13:31,616,278...31,648,521 		JBrowse link
G Megf10 multiple EGF-like domains 10 involved_in IBA GO_REF:0000033 GO_Central GO_REF:0000033 NCBI chr18:50,605,231...50,755,441
Ensembl chr18:50,605,656...50,754,456 		JBrowse link
G Mertk MER proto-oncogene, tyrosine kinase involved_in
acts_upstream_of_or_within		 ISO (MGI:3778590|PMID:18159085)
MGI:104294|MGI:1347244|MGI:2387768 (PMID:17442946), (PMID:18159085), (PMID:23878224), (PMID:29440417)		 RGD PMID:17442946 PMID:18159085 PMID:23878224 PMID:29440417 MGI:3778590 NCBI chr 3:115,939,351...116,045,141
Ensembl chr 3:115,939,351...116,046,554 		JBrowse link
G Mfge8 milk fat globule EGF and factor V/VIII domain containing involved_in IEA
ISO		 GO_REF:0000107
(MGI:5285150|PMID:20826760)		 Ensembl
RGD		 PMID:20826760 GO_REF:0000107 MGI:5285150 NCBI chr 1:133,064,665...133,080,069
Ensembl chr 1:133,064,665...133,080,073 		JBrowse link
G Nr1h3 nuclear receptor subfamily 1, group H, member 3 involved_in ISO (PMID:19628791) RGD PMID:19628791 NCBI chr 3:77,158,808...77,168,907
Ensembl chr 3:77,158,808...77,168,722 		JBrowse link
G Rara retinoic acid receptor, alpha involved_in ISO (PMID:19628791) RGD PMID:19628791 NCBI chr10:83,883,490...83,928,932
Ensembl chr10:83,893,384...83,928,142 		JBrowse link
G Tgm2 transglutaminase 2 involved_in ISO
IEA		 (PMID:19628791)
GO_REF:0000107		 RGD
Ensembl		 PMID:19628791 GO_REF:0000107 NCBI chr 3:146,772,684...146,801,924
Ensembl chr 3:146,772,687...146,801,981 		JBrowse link
G Timd4 T-cell immunoglobulin and mucin domain containing 4 involved_in
acts_upstream_of_or_within		 IBA
ISO		 GO_REF:0000033
(PMID:29440417)		 GO_Central
RGD		 PMID:29440417 GO_REF:0000033 NCBI chr10:31,185,751...31,221,843
Ensembl chr10:31,185,731...31,220,966 		JBrowse link
G Trem2 triggering receptor expressed on myeloid cells 2 involved_in ISO (MGI:3531054|PMID:15728241) RGD PMID:15728241 MGI:3531054 NCBI chr 9:12,647,605...12,654,190
Ensembl chr 9:12,647,259...12,654,170 		JBrowse link
G Trex1 three prime repair exonuclease 1 acts_upstream_of_or_within ISO MGI:3052754 (PMID:24218451) RGD PMID:24218451 NCBI chr 8:109,706,613...109,707,913
Ensembl chr 8:109,706,613...109,708,796 		JBrowse link
G Tyro3 TYRO3 protein tyrosine kinase involved_in
acts_upstream_of_or_within		 ISS
ISO
IEA		 GO_REF:0000024
MGI:1347244|MGI:96965 (PMID:17442946), (PMID:18159085)
GO_REF:0000107		 UniProt
RGD
Ensembl		 PMID:17442946 PMID:18159085 GO_REF:0000024 GO_REF:0000107 NCBI chr 3:106,777,686...106,797,154
Ensembl chr 3:106,777,635...106,797,142 		JBrowse link
G Tyrobp transmembrane immune signaling adaptor Tyrobp involved_in ISS
ISO		 GO_REF:0000024
(MGI:3531054|PMID:15728241)		 UniProt
RGD		 PMID:15728241 GO_REF:0000024 MGI:3531054 NCBI chr 1:85,672,931...85,676,856
Ensembl chr 1:85,672,994...85,676,848 		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 involved_in ISO
IBA
IEA		 (PMID:24509909)
GO_REF:0000033
GO_REF:0000107
(MGI:3764740|PMID:17960134)		 RGD
GO_Central
Ensembl		 PMID:17960134 PMID:24509909 GO_REF:0000033 GO_REF:0000107 MGI:3764740 NCBI chr 7:106,404,827...106,476,902
Ensembl chr 7:106,404,958...106,476,902 		JBrowse link
G Becn1 beclin 1 involved_in ISO (MGI:5619450|PMID:22393062) RGD PMID:22393062 MGI:5619450 NCBI chr10:86,231,387...86,246,742
Ensembl chr10:86,231,388...86,246,742 		JBrowse link
G Megf10 multiple EGF-like domains 10 acts_upstream_of_or_within ISO MGI:4454190 (PMID:27170117) RGD PMID:27170117 NCBI chr18:50,605,231...50,755,441
Ensembl chr18:50,605,656...50,754,456 		JBrowse link
G Rac1 Rac family small GTPase 1 involved_in ISO
IBA		 (MGI:4943793|PMID:20691665)
GO_REF:0000033		 RGD
GO_Central		 PMID:20691665 GO_REF:0000033 MGI:4943793 NCBI chr12:11,037,028...11,057,251
Ensembl chr12:11,036,698...11,057,251 		JBrowse link
G Rac3 Rac family small GTPase 3 involved_in IBA GO_REF:0000033 GO_Central GO_REF:0000033 NCBI chr10:106,002,808...106,005,243
Ensembl chr10:105,993,087...106,005,260 		JBrowse link
G Thbs1 thrombospondin 1 involved_in ISO (PMID:16882710) RGD PMID:16882710 NCBI chr 3:105,056,293...105,071,445
Ensembl chr 3:105,056,292...105,071,440 		JBrowse link
G Xkr4 XK related 4 involved_in IBA GO_REF:0000033 GO_Central GO_REF:0000033 NCBI chr 5:15,896,818...16,297,733
Ensembl chr 5:15,895,863...16,282,962 		JBrowse link
G Xkr6 XK related 6 involved_in IBA GO_REF:0000033 GO_Central GO_REF:0000033 NCBI chr15:37,857,096...38,059,699
Ensembl chr15:37,857,096...38,059,682 		JBrowse link
G Xkr7 XK related 7 involved_in IBA GO_REF:0000033 GO_Central GO_REF:0000033 NCBI chr 3:141,500,908...141,525,062
Ensembl chr 3:141,501,284...141,525,062 		JBrowse link
G Xkr8 XK related 8 involved_in ISO
IBA		 (PMID:23845944)
GO_REF:0000033
(MGI:6120635|PMID:29440417), (MGI:6435898|PMID:31712393)		 RGD
GO_Central		 PMID:23845944 PMID:29440417 PMID:31712393 GO_REF:0000033 MGI:6120635 MGI:6435898 NCBI chr 5:144,938,061...144,945,195
Ensembl chr 5:144,938,064...144,945,195 		JBrowse link
G Xkr9 XK related 9 involved_in IBA GO_REF:0000033 GO_Central GO_REF:0000033 NCBI chr 5:5,530,384...5,562,168
Ensembl chr 5:5,533,416...5,562,168 		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 involved_in ISS
ISO		 GO_REF:0000024
(MGI:5819329|PMID:26768664)		 UniProt
RGD		 PMID:26768664 GO_REF:0000024 MGI:5819329 NCBI chr10:100,359,942...100,376,130
Ensembl chr10:100,359,943...100,376,041 		JBrowse link
G Hmgb1 high mobility group box 1 involved_in ISO (PMID:20826760) RGD PMID:20826760 NCBI chr12:5,972,950...5,979,658
Ensembl chr12:5,901,586...5,978,565
Ensembl chr16:5,901,586...5,978,565 		JBrowse link
neutrophil clearance term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Anxa1 annexin A1 involved_in ISO
IEA		 (PMID:21957127)
GO_REF:0000107		 RGD
Ensembl		 PMID:21957127 GO_REF:0000107 NCBI chr 1:217,861,175...217,877,205
Ensembl chr 1:217,861,175...217,877,343 		JBrowse link
G Axl Axl receptor tyrosine kinase acts_upstream_of_or_within ISO MGI:96965 (PMID:23878224) RGD PMID:23878224 NCBI chr 1:81,265,088...81,296,278
Ensembl chr 1:81,265,088...81,296,265 		JBrowse link
G Ccr2 C-C motif chemokine receptor 2 acts_upstream_of_or_within ISO MGI:2158345 (PMID:9342361) RGD PMID:9342361 NCBI chr 8:123,734,465...123,742,483
Ensembl chr 8:123,734,430...123,742,100 		JBrowse link
G Hmgb1 high mobility group box 1 involved_in ISO
ISS		 (PMID:18768881)
GO_REF:0000024		 RGD
UniProt		 PMID:18768881 GO_REF:0000024 NCBI chr12:5,972,950...5,979,658
Ensembl chr12:5,901,586...5,978,565
Ensembl chr16:5,901,586...5,978,565 		JBrowse link
G Mertk MER proto-oncogene, tyrosine kinase acts_upstream_of_or_within ISO MGI:1347244 (PMID:23878224) RGD PMID:23878224 NCBI chr 3:115,939,351...116,045,141
Ensembl chr 3:115,939,351...116,046,554 		JBrowse link
G Xkr8 XK related 8 involved_in ISO (MGI:6120635|PMID:29440417) RGD PMID:29440417 MGI:6120635 NCBI chr 5:144,938,061...144,945,195
Ensembl chr 5:144,938,064...144,945,195 		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 involved_in IBA GO_REF:0000033 GO_Central GO_REF:0000033 NCBI chr 3:18,501,953...18,523,253
Ensembl chr 3:18,501,963...18,523,172 		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 acts_upstream_of_or_within ISO MGI:4377985 (PMID:26284655) RGD PMID:26284655 NCBI chr 3:109,007,658...109,072,904
Ensembl chr 3:109,008,135...109,072,911 		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 involved_in ISO (PMID:19302245) RGD PMID:19302245 NCBI chr20:3,951,474...3,970,376
Ensembl chr20:3,951,474...3,976,505 		JBrowse link
G C3 complement C3 involved_in ISO
IEA		 (PMID:19302245)
GO_REF:0000107		 RGD
Ensembl		 PMID:19302245 GO_REF:0000107 NCBI chr 9:2,087,437...2,114,366
Ensembl chr 9:2,087,437...2,114,429 		JBrowse link
G C4a complement C4A involved_in ISO UniProtKB:P0C0L5 (PMID:19302245) RGD PMID:19302245 NCBI chr20:4,005,731...4,020,083
Ensembl chr20:4,005,731...4,020,080 		JBrowse link
G C4b complement C4B involved_in ISO UniProtKB:P0C0L4|UniProtKB:P0C0L5 (PMID:19302245) RGD PMID:19302245 NCBI chr20:4,197,371...4,211,684
Ensembl chr20:4,197,366...4,211,681 		JBrowse link
G Ccl2 C-C motif chemokine ligand 2 involved_in ISO (MGI:4943793|PMID:20691665) RGD PMID:20691665 MGI:4943793 NCBI chr10:67,005,424...67,007,222
Ensembl chr10:67,005,424...67,007,226 		JBrowse link
G Cd300lf Cd300 molecule-like family member F involved_in ISS
ISO		 GO_REF:0000024
(MGI:5301804|PMID:21865548), (MGI:5819329|PMID:26768664)		 UniProt
RGD		 PMID:21865548 PMID:26768664 GO_REF:0000024 MGI:5301804 MGI:5819329 NCBI chr10:100,359,942...100,376,130
Ensembl chr10:100,359,943...100,376,041 		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 involved_in ISS
ISO		 GO_REF:0000024
(MGI:3662940|PMID:16908670)		 Alzheimers_University_of_Toronto
RGD		 PMID:16908670 GO_REF:0000024 MGI:3662940 NCBI chr 7:9,691,452...9,711,466
Ensembl chr 7:9,691,449...9,711,425 		JBrowse link
G Trem2 triggering receptor expressed on myeloid cells 2 involved_in ISO (PMID:24990881) RGD PMID:24990881 NCBI chr 9:12,647,605...12,654,190
Ensembl chr 9:12,647,259...12,654,170 		JBrowse link
recognition of apoptotic cell term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Fcnb ficolin B involved_in ISO (PMID:15804047) RGD PMID:15804047 NCBI chr 3:11,393,713...11,402,198
Ensembl chr 3:11,393,739...11,402,151 		JBrowse link
G Jmjd6 jumonji domain containing 6, arginine demethylase and lysine hydroxylase involved_in
acts_upstream_of_or_within		 IEA
ISO		 GO_REF:0000107
MGI:2686850 (PMID:10811223), (PMID:14645847)		 Ensembl
RGD		 PMID:10811223 PMID:14645847 GO_REF:0000107 NCBI chr10:102,041,131...102,047,182
Ensembl chr10:102,041,120...102,047,182 		JBrowse link
G Megf10 multiple EGF-like domains 10 acts_upstream_of_or_within ISO (PMID:19915564) RGD PMID:19915564 NCBI chr18:50,605,231...50,755,441
Ensembl chr18:50,605,656...50,754,456 		JBrowse link
G Pear1 platelet endothelial aggregation receptor 1 acts_upstream_of_or_within ISO (PMID:19915564) RGD PMID:19915564 NCBI chr 2:173,206,298...173,234,106
Ensembl chr 2:173,207,664...173,227,440 		JBrowse link
G Scarb1 scavenger receptor class B, member 1 involved_in ISO
IBA
IEA
IDA
ISS		 (PMID:9211901)
GO_REF:0000033
GO_REF:0000107
PMID:12016218
GO_REF:0000024		 RGD
GO_Central
Ensembl
BHF-UCL		 PMID:9211901 PMID:12016218 GO_REF:0000024 GO_REF:0000033 GO_REF:0000107, RGD:1304245 NCBI chr12:31,296,143...31,362,649
Ensembl chr12:31,296,156...31,362,647 		JBrowse link
regulation of apoptotic cell clearance term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Tgm2 transglutaminase 2 involved_in ISS
IEA
ISO		 GO_REF:0000024
GO_REF:0000107
(MGI:3580951|PMID:15905580), (MGI:3629478|PMID:12810961)
(PMID:7935379)		 UniProt
Ensembl
RGD		 PMID:7935379 PMID:12810961 PMID:15905580 GO_REF:0000024 GO_REF:0000107 MGI:3580951 MGI:3629478 NCBI chr 3:146,772,684...146,801,924
Ensembl chr 3:146,772,687...146,801,981 		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 involved_in ISS
IEA
ISO		 GO_REF:0000024
GO_REF:0000107
(MGI:5436199|PMID:22503541), (MGI:5508294|PMID:11278875)		 UniProt
Ensembl
RGD		 PMID:11278875 PMID:22503541 GO_REF:0000024 GO_REF:0000107 MGI:5436199 MGI:5508294 NCBI chr10:55,060,169...55,068,885
Ensembl chr10:55,060,412...55,068,874 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 20115
    cellular process 18524
      vesicle-mediated transport 1638
        endocytosis 735
          phagocytosis 234
            apoptotic cell clearance 45
              engulfment of apoptotic cell + 14
              negative regulation of apoptotic cell clearance + 2
              neutrophil clearance 6
              phagosome maturation involved in apoptotic cell clearance + 2
              positive regulation of apoptotic cell clearance + 8
              recognition of apoptotic cell 5
              regulation of apoptotic cell clearance + 10
Path 2
Term Annotations click to browse term
  biological_process 20115
    localization 5683
      establishment of localization 4990
        transport 4684
          vesicle-mediated transport 1638
            endocytosis 735
              phagocytosis 234
                apoptotic cell clearance 45
                  engulfment of apoptotic cell + 14
                  negative regulation of apoptotic cell clearance + 2
                  neutrophil clearance 6
                  phagosome maturation involved in apoptotic cell clearance + 2
                  positive regulation of apoptotic cell clearance + 8
                  recognition of apoptotic cell 5
                  regulation of apoptotic cell clearance + 10
paths to the root