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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
IEA		 (PMID:24509909)
GO_REF:0000107		 RGD
Ensembl		 PMID:24509909 GO_REF:0000107 NCBI chr 7:108,293,681...108,365,892
Ensembl chr 7:106,404,958...106,476,902 		JBrowse link
G Alox15 arachidonate 15-lipoxygenase involved_in ISS
ISO
IEA		 GO_REF:0000024
(PMID:22503541)
GO_REF:0000107		 UniProt
RGD
Ensembl		 PMID:22503541 GO_REF:0000024 GO_REF:0000107 NCBI chr10:55,559,060...55,567,535
Ensembl chr10:55,060,412...55,068,874 		JBrowse link
G Axl Axl receptor tyrosine kinase acts_upstream_of_or_within
involved_in		 ISO MGI:104294|MGI:2387750|MGI:96965 (PMID:17442946), (PMID:18159085), (PMID:18804096), (PMID:23878224)
UniProtKB:Q60805 (PMID:18159085)		 RGD PMID:17442946 PMID:18159085 PMID:18804096 PMID:23878224 NCBI chr 1:90,392,864...90,424,123
Ensembl chr 1:81,265,088...81,296,265 		JBrowse link
G Cd36 CD36 molecule acts_upstream_of_or_within ISO (PMID:15647754) RGD PMID:15647754 NCBI chr 4:18,209,088...18,302,142
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
IEA
ISO		 GO_REF:0000024
GO_REF:0000107
(PMID:18159085)
(PMID:21501828)		 UniProt
Ensembl
RGD		 PMID:18159085 PMID:21501828 GO_REF:0000024 GO_REF:0000107 NCBI chr16:82,747,676...82,778,090
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 chr12:11,009,236...11,015,941
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
IEA		 UniProtKB:P43406 (PMID:20826760)
GO_REF:0000107
UniProtKB:P06756 (PMID:20826760)
(PMID:15647754)		 RGD
Ensembl		 PMID:15647754 PMID:20826760 GO_REF:0000107 NCBI chr 3:89,245,382...89,333,512
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)
UniProtKB:P05106 (PMID:20826760)
GO_REF:0000107		 RGD
Ensembl		 PMID:20826760 GO_REF:0000107 NCBI chr10:90,009,927...90,067,787
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
IEA		 MGI:3043930 (PMID:14715629), (PMID:15647754)
GO_REF:0000107
MGI:3580706 (PMID:15345036)		 RGD
Ensembl		 PMID:14715629 PMID:15345036 PMID:15647754 GO_REF:0000107 NCBI chr10:102,539,935...102,545,986
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 7:65,265,639...65,346,196
Ensembl chr 7:63,380,356...63,460,910 		JBrowse link
G Marco macrophage receptor with collagenous structure acts_upstream_of_or_within ISO
IEA		 (PMID:19201851)
GO_REF:0000107		 RGD
Ensembl		 PMID:19201851 GO_REF:0000107 NCBI chr13:34,169,011...34,210,340
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 chr18:52,803,292...52,953,431
Ensembl chr18:50,605,656...50,754,456 		JBrowse link
G Mertk MER proto-oncogene, tyrosine kinase acts_upstream_of_or_within
involved_in		 ISO
IEA		 MGI:104294|MGI:1347244|MGI:2387768 (PMID:17442946), (PMID:18159085), (PMID:23878224), (PMID:29440417)
GO_REF:0000107
(PMID:18159085)		 RGD
Ensembl		 PMID:17442946 PMID:18159085 PMID:23878224 PMID:29440417 GO_REF:0000107 NCBI chr 3:136,391,936...136,498,366
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 ISO
IEA		 (PMID:20826760)
GO_REF:0000107		 RGD
Ensembl		 PMID:20826760 GO_REF:0000107 NCBI chr 1:142,474,027...142,489,431
Ensembl chr 1:133,064,665...133,080,073 		JBrowse link
G Nr1h3 nuclear receptor subfamily 1, group H, member 3 involved_in ISO
IEA		 (PMID:19628791)
GO_REF:0000107		 RGD
Ensembl		 PMID:19628791 GO_REF:0000107 NCBI chr 3:97,614,616...97,632,053
Ensembl chr 3:77,158,808...77,168,722 		JBrowse link
G Rara retinoic acid receptor, alpha involved_in ISO
IEA		 (PMID:19628791)
GO_REF:0000107		 RGD
Ensembl		 PMID:19628791 GO_REF:0000107 NCBI chr10:84,379,780...84,424,371
Ensembl chr10:83,893,384...83,928,142 		JBrowse link
G Tgm2 transglutaminase 2 involved_in ISO (PMID:19628791) RGD PMID:19628791 NCBI chr 3:167,192,612...167,221,845
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 chr10:31,686,994...31,723,095
Ensembl chr10:31,185,731...31,220,966 		JBrowse link
G Trem2 triggering receptor expressed on myeloid cells 2 involved_in ISO (PMID:15728241) RGD PMID:15728241 NCBI chr 9:20,145,215...20,151,797
Ensembl chr 9:12,647,259...12,654,170 		JBrowse link
G Trex1 three prime repair exonuclease 1 acts_upstream_of_or_within ISO
IEA		 MGI:3052754 (PMID:24218451)
GO_REF:0000107		 RGD
Ensembl		 PMID:24218451 GO_REF:0000107 NCBI chr 8:118,585,082...118,586,382
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
IEA
ISO		 GO_REF:0000024
GO_REF:0000107
UniProtKB:Q60805 (PMID:18159085)
MGI:1347244|MGI:96965 (PMID:17442946), (PMID:18159085)		 UniProt
Ensembl
RGD		 PMID:17442946 PMID:18159085 GO_REF:0000024 GO_REF:0000107 NCBI chr 3:127,231,468...127,254,806
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
(PMID:15728241)		 UniProt
RGD		 PMID:15728241 GO_REF:0000024 NCBI chr 1:94,800,372...94,804,307
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
(PMID:17960134)
GO_REF:0000107		 RGD
GO_Central
Ensembl		 PMID:17960134 PMID:24509909 GO_REF:0000033 GO_REF:0000107 NCBI chr 7:108,293,681...108,365,892
Ensembl chr 7:106,404,958...106,476,902 		JBrowse link
G Becn1 beclin 1 involved_in ISO
IEA		 (PMID:22393062)
GO_REF:0000107		 RGD
Ensembl		 PMID:22393062 GO_REF:0000107 NCBI chr10:86,731,649...86,747,002
Ensembl chr10:86,231,388...86,246,742 		JBrowse link
G Megf10 multiple EGF-like domains 10 acts_upstream_of_or_within ISO
IEA		 MGI:4454190 (PMID:27170117)
GO_REF:0000107		 RGD
Ensembl		 PMID:27170117 GO_REF:0000107 NCBI chr18:52,803,292...52,953,431
Ensembl chr18:50,605,656...50,754,456 		JBrowse link
G Rac1 Rac family small GTPase 1 involved_in ISO (PMID:20691665) RGD PMID:20691665 NCBI chr12:16,150,411...16,170,864
Ensembl chr12:11,036,698...11,057,251 		JBrowse link
G Thbs1 thrombospondin 1 involved_in ISO
IEA		 (PMID:16882710)
GO_REF:0000107		 RGD
Ensembl		 PMID:16882710 GO_REF:0000107 NCBI chr 3:125,510,250...125,525,402
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 5:20,694,433...21,095,350
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
acts_upstream_of_or_within		 ISO
IEA
IBA		 (PMID:23845944)
MGI:5528895 (PMID:29440417)
GO_REF:0000107
(PMID:29440417), (PMID:31712393)
GO_REF:0000033		 RGD
Ensembl
GO_Central		 PMID:23845944 PMID:29440417 PMID:31712393 GO_REF:0000033 GO_REF:0000107 NCBI chr 5:144,938,061...144,945,195
Ensembl chr 5:144,938,064...144,945,195 		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
(PMID:26768664)		 UniProt
RGD		 PMID:26768664 GO_REF:0000024 NCBI chr10:100,858,924...100,875,111
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 chr12:11,009,236...11,015,941
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 1:227,287,713...227,306,739
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 1:90,392,864...90,424,123
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 8:132,611,883...132,619,106
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 chr12:11,009,236...11,015,941
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
IEA		 MGI:1347244 (PMID:23878224)
GO_REF:0000107		 RGD
Ensembl		 PMID:23878224 GO_REF:0000107 NCBI chr 3:136,391,936...136,498,366
Ensembl chr 3:115,939,351...116,046,554 		JBrowse link
G Xkr8 XK related 8 involved_in ISO
IEA		 (PMID:29440417)
GO_REF:0000107		 RGD
Ensembl		 PMID:29440417 GO_REF:0000107 NCBI chr 5:144,938,061...144,945,195
Ensembl chr 5:144,938,064...144,945,195 		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
IEA		 MGI:4377985 (PMID:26284655)
GO_REF:0000107		 RGD
Ensembl		 PMID:26284655 GO_REF:0000107 NCBI chr 3:129,453,118...129,526,469
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
IEA		 (PMID:19302245)
GO_REF:0000107		 RGD
Ensembl		 PMID:19302245 GO_REF:0000107 NCBI chr20:3,944,722...3,975,006
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 9:2,174,412...2,201,339
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 chr20:4,010,306...4,024,707
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 chr20:4,201,979...4,216,292
Ensembl chr20:4,197,366...4,211,681 		JBrowse link
G Ccl2 C-C motif chemokine ligand 2 involved_in ISO
IEA		 (PMID:20691665)
GO_REF:0000107		 RGD
Ensembl		 PMID:20691665 GO_REF:0000107 NCBI chr10:67,503,077...67,504,875
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
(PMID:21865548), (PMID:26768664)		 UniProt
RGD		 PMID:21865548 PMID:26768664 GO_REF:0000024 NCBI chr10:100,858,924...100,875,111
Ensembl chr10:100,359,943...100,376,041 		JBrowse link
G Cfb complement factor B involved_in IEA GO_REF:0000107 Ensembl GO_REF:0000107 NCBI chr20:3,975,271...3,981,138
Ensembl chr20:3,951,474...3,976,505 		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
(PMID:16908670)		 Alzheimers_University_of_Toronto
RGD		 PMID:16908670 GO_REF:0000024 NCBI chr 7:10,342,092...10,362,094
Ensembl chr 7:9,691,449...9,711,425 		JBrowse link
G Trem2 triggering receptor expressed on myeloid cells 2 involved_in ISO
IEA		 (PMID:24990881)
GO_REF:0000107		 RGD
Ensembl		 PMID:24990881 GO_REF:0000107 NCBI chr 9:20,145,215...20,151,797
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
IEA		 (PMID:15804047)
GO_REF:0000107		 RGD
Ensembl		 PMID:15804047 GO_REF:0000107 NCBI chr 3:31,791,750...31,800,188
Ensembl chr 3:11,393,739...11,402,151 		JBrowse link
G Jmjd6 jumonji domain containing 6, arginine demethylase and lysine hydroxylase acts_upstream_of_or_within ISO
IEA		 MGI:2686850 (PMID:10811223), (PMID:14645847)
GO_REF:0000107		 RGD
Ensembl		 PMID:10811223 PMID:14645847 GO_REF:0000107 NCBI chr10:102,539,935...102,545,986
Ensembl chr10:102,041,120...102,047,182 		JBrowse link
G Megf10 multiple EGF-like domains 10 acts_upstream_of_or_within ISO
IEA		 (PMID:19915564)
GO_REF:0000107		 RGD
Ensembl		 PMID:19915564 GO_REF:0000107 NCBI chr18:52,803,292...52,953,431
Ensembl chr18:50,605,656...50,754,456 		JBrowse link
G Pear1 platelet endothelial aggregation receptor 1 acts_upstream_of_or_within ISO
IEA		 (PMID:19915564)
GO_REF:0000107		 RGD
Ensembl		 PMID:19915564 GO_REF:0000107 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 chr12:36,957,302...37,023,982
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
ISO		 GO_REF:0000024
(PMID:12810961), (PMID:15905580)
(PMID:7935379)		 UniProt
RGD		 PMID:7935379 PMID:12810961 PMID:15905580 GO_REF:0000024 NCBI chr 3:167,192,612...167,221,845
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
ISO
IEA		 GO_REF:0000024
(PMID:11278875), (PMID:22503541)
GO_REF:0000107		 UniProt
RGD
Ensembl		 PMID:11278875 PMID:22503541 GO_REF:0000024 GO_REF:0000107 NCBI chr10:55,559,060...55,567,535
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 20567
    cellular process 19557
      vesicle-mediated transport 1654
        endocytosis 728
          phagocytosis 234
            apoptotic cell clearance 43
              engulfment of apoptotic cell + 12
              negative regulation of apoptotic cell clearance + 2
              neutrophil clearance 6
              phagosome maturation involved in apoptotic cell clearance + 1
              positive regulation of apoptotic cell clearance + 9
              recognition of apoptotic cell 5
              regulation of apoptotic cell clearance + 11
Path 2
Term Annotations click to browse term
  biological_process 20567
    localization 5739
      establishment of localization 5084
        transport 4772
          vesicle-mediated transport 1654
            endocytosis 728
              phagocytosis 234
                apoptotic cell clearance 43
                  engulfment of apoptotic cell + 12
                  negative regulation of apoptotic cell clearance + 2
                  neutrophil clearance 6
                  phagosome maturation involved in apoptotic cell clearance + 1
                  positive regulation of apoptotic cell clearance + 9
                  recognition of apoptotic cell 5
                  regulation of apoptotic cell clearance + 11
paths to the root