Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   

ONTOLOGY REPORT - ANNOTATIONS


Term:apoptotic cell clearance
go back to main search page
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 7:106,404,844...106,476,902
Ensembl chr 7:106,404,958...106,476,902
JBrowse link
G Alox15 arachidonate 15-lipoxygenase involved_in ISS
ISO
GO_REF:0000024
(MGI:5436199|PMID:22503541)
UniProt
RGD
PMID:22503541 GO_REF:0000024 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 (MGI:3778590|PMID:18159085), (MGI:3836130|PMID:17442946), (MGI:3841855|PMID:18804096), (MGI:5509105|PMID:23878224) RGD PMID:17442946 PMID:18159085 PMID:18804096 PMID:23878224 MGI:3778590 MGI:3836130 MGI:3841855 MGI:5509105 NCBI chr 1:81,265,656...81,296,278
Ensembl chr 1:81,265,088...81,296,265
JBrowse link
G Cd36 CD36 molecule acts_upstream_of_or_within
involved_in
ISO
IEA
(MGI:3618422|PMID:15647754)
GO_REF:0000107
RGD
Ensembl
PMID:15647754 GO_REF:0000107 MGI:3618422 NCBI chr 4:17,317,343...17,410,084
Ensembl chr 4:17,354,466...17,513,903
JBrowse link
G Cd36-ps1 CD36 molecule, pseudogene 1 involved_in IEA GO_REF:0000107 Ensembl GO_REF:0000107 NCBI chr 4:17,487,837...17,514,900 JBrowse link
G Gas6 growth arrest specific 6 involved_in
acts_upstream_of_or_within
ISS
ISO
GO_REF:0000024
(MGI:3778590|PMID:18159085)
(PMID:21501828)
UniProt
RGD
PMID:18159085 PMID:21501828 GO_REF:0000024 MGI:3778590 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 chr12:5,973,062...5,978,565
Ensembl chr12:5,901,586...5,978,565
JBrowse link
G Itgav integrin subunit alpha V involved_in
acts_upstream_of_or_within
ISO UniProtKB:P43406 (PMID:20826760)
(MGI:3618422|PMID:15647754)
UniProtKB:P06756 (MGI:5285150|PMID:20826760)
RGD PMID:15647754 PMID:20826760 MGI:3618422 MGI:5285150 NCBI chr 3:68,838,524...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 NOT|acts_upstream_of_or_within ISO MGI:3580706 (MGI:3580691|PMID:15345036)
MGI:3043930 (MGI:3042820|PMID:14715629), (MGI:3618422|PMID:15647754)
RGD PMID:14715629 PMID:15345036 PMID:15647754 MGI:3042820 MGI:3580691 MGI:3618422 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 (MGI:3618422|PMID:15647754) RGD PMID:15647754 MGI:3618422 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 (MGI:3831958|PMID:19201851) RGD PMID:19201851 MGI:3831958 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 PMID:21873635 GO_Central PMID:21873635 RGD:13792537 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 acts_upstream_of_or_within
involved_in
ISO MGI:104294|MGI:1347244|MGI:2387768 (MGI:3778590|PMID:18159085), (MGI:3836130|PMID:17442946), (MGI:5509105|PMID:23878224), (MGI:6120635|PMID:29440417) RGD PMID:17442946 PMID:18159085 PMID:23878224 PMID:29440417 MGI:3778590 MGI:3836130 MGI:5509105 MGI:6120635 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
IEA
(PMID:19628791)
GO_REF:0000107
RGD
Ensembl
PMID:19628791 GO_REF:0000107 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 RGD1565355 similar to fatty acid translocase/CD36 involved_in IEA GO_REF:0000107 Ensembl GO_REF:0000107 NCBI chr 4:17,424,749...17,465,808
Ensembl chr 4:17,354,466...17,513,903
JBrowse link
G Tgm2 transglutaminase 2 involved_in ISO (PMID:19628791) RGD PMID:19628791 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 acts_upstream_of_or_within
involved_in
ISO
IBA
(MGI:6120635|PMID:29440417)
PMID:21873635
RGD PMID:29440417 PMID:21873635 MGI:6120635, RGD:13792537 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 (MGI:5554502|PMID:24218451) RGD PMID:24218451 MGI:5554502 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
GO_REF:0000024
MGI:1347244|MGI:96965 (MGI:3778590|PMID:18159085), (MGI:3836130|PMID:17442946)
UniProt
RGD
PMID:17442946 PMID:18159085 GO_REF:0000024 MGI:3778590 MGI:3836130 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
(PMID:24509909)
(MGI:3764740|PMID:17960134)
PMID:21873635
RGD PMID:17960134 PMID:24509909 PMID:21873635 MGI:3764740, RGD:13792537 NCBI chr 7:106,404,844...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 (MGI:5775214|PMID:27170117) RGD PMID:27170117 MGI:5775214 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 IBA
ISO
PMID:21873635
(MGI:4943793|PMID:20691665)
RGD PMID:20691665 PMID:21873635 MGI:4943793, RGD:13792537 NCBI chr12:11,037,028...11,057,251
Ensembl chr12:11,036,698...11,057,251
JBrowse link
G Rac2 Rac family small GTPase 2 involved_in IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr 7:110,101,344...110,128,718
Ensembl chr 7:110,116,260...110,128,720
JBrowse link
G Rhobtb1 Rho-related BTB domain containing 1 involved_in IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr20:19,327,142...19,456,121
Ensembl chr20:19,327,155...19,403,012
JBrowse link
G Rhobtb2 Rho-related BTB domain containing 2 involved_in IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr15:44,868,251...44,888,436
Ensembl chr15:44,870,376...44,888,651
JBrowse link
G Rhog ras homolog family member G involved_in IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr 1:156,618,713...156,630,710
Ensembl chr 1:156,615,349...156,631,257
JBrowse link
G Rhoh ras homolog family member H involved_in IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr14:42,341,135...42,371,971
Ensembl chr14:42,337,751...42,386,369
JBrowse link
G Thbs1 thrombospondin 1 involved_in ISO (PMID:16882710) RGD PMID:16882710 NCBI chr 3:105,056,286...105,071,445
Ensembl chr 3:105,056,292...105,071,440
JBrowse link
G Xkr4 XK related 4 involved_in IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr 5:15,896,188...16,297,733
Ensembl chr 5:15,895,863...16,282,962
JBrowse link
G Xkr5 XK related 5 involved_in IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr16:70,874,983...70,892,972
Ensembl chr16:70,875,093...70,892,967
JBrowse link
G Xkr6 XK related 6 involved_in IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 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 PMID:21873635 GO_Central PMID:21873635 RGD:13792537 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)
PMID:21873635
(MGI:6120635|PMID:29440417), (MGI:6435898|PMID:31712393)
RGD PMID:23845944 PMID:29440417 PMID:31712393 PMID:21873635 MGI:6120635 MGI:6435898, RGD:13792537 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 PMID:21873635 GO_Central PMID:21873635 RGD:13792537 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 chr12:5,973,062...5,978,565
Ensembl chr12:5,901,586...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 IBA
ISO
PMID:21873635
(PMID:21957127)
RGD PMID:21957127 PMID:21873635 RGD:13792537 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 (MGI:5509105|PMID:23878224) RGD PMID:23878224 MGI:5509105 NCBI chr 1:81,265,656...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 (MGI:1100445|PMID:9342361) RGD PMID:9342361 MGI:1100445 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 chr12:5,973,062...5,978,565
Ensembl chr12:5,901,586...5,978,565
JBrowse link
G Mertk MER proto-oncogene, tyrosine kinase acts_upstream_of_or_within ISO MGI:1347244 (MGI:5509105|PMID:23878224) RGD PMID:23878224 MGI:5509105 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 PMID:21873635 GO_Central PMID:21873635 RGD:13792537 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 (MGI:5749311|PMID:26284655) RGD PMID:26284655 MGI:5749311 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 (Chido blood group) 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 Fcna ficolin A involved_in ISO (PMID:15804047) RGD PMID:15804047 NCBI chr 3:8,445,904...8,449,128
Ensembl chr 3:8,445,907...8,449,105
JBrowse link
G Fcnb ficolin B involved_in ISO (PMID:15804047) RGD PMID:15804047 NCBI chr 3:11,393,771...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 acts_upstream_of_or_within ISO MGI:2686850 (MGI:1855743|PMID:10811223), (MGI:2682078|PMID:14645847) RGD PMID:10811223 PMID:14645847 MGI:1855743 MGI:2682078 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 (MGI:4414741|PMID:19915564) RGD PMID:19915564 MGI:4414741 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 (MGI:4414741|PMID:19915564) RGD PMID:19915564 MGI:4414741 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
IDA
ISS
IBA
(PMID:9211901)
PMID:12016218
GO_REF:0000024
PMID:21873635
RGD
BHF-UCL
PMID:9211901 PMID:12016218 PMID:21873635 GO_REF:0000024, RGD:1304245, RGD:13792537 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
ISO
GO_REF:0000024
(MGI:3580951|PMID:15905580), (MGI:3629478|PMID:12810961)
(PMID:7935379)
UniProt
RGD
PMID:7935379 PMID:12810961 PMID:15905580 GO_REF:0000024 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
ISO
GO_REF:0000024
(MGI:5436199|PMID:22503541), (MGI:5508294|PMID:11278875)
UniProt
RGD
PMID:11278875 PMID:22503541 GO_REF:0000024 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 20091
    localization 5663
      establishment of localization 4991
        transport 4826
          vesicle-mediated transport 1664
            phagocytosis 276
              apoptotic cell clearance 53
                engulfment of apoptotic cell + 19
                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 6
                regulation of apoptotic cell clearance + 10
paths to the root