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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 (PMID:24509909) RGD PMID:24509909 NCBI chr 7:115,766,484...115,828,514 JBrowse link
G Alox15 arachidonate 15-lipoxygenase ISO
ISS
(MGI:MGI:5436199|PMID:22503541)
GO_REF:0000024
RGD
UniProt
PMID:22503541 GO_REF:0000024, MGI:MGI:5436199 NCBI chr10:56,953,692...56,962,145
Ensembl chr10:56,953,691...56,962,161
JBrowse link
G Axl Axl receptor tyrosine kinase ISO MGI:MGI:104294|MGI:MGI:2387750|MGI:MGI:96965 (MGI:MGI:3778590|PMID:18159085), (MGI:MGI:3836130|PMID:17442946), (MGI:MGI:3841855|PMID:18804096), (MGI:MGI:5509105|PMID:23878224) RGD PMID:17442946, PMID:18159085, PMID:18804096, PMID:23878224 MGI:MGI:3778590, MGI:MGI:3836130, MGI:MGI:3841855, MGI:MGI:5509105 NCBI chr 1:82,550,892...82,580,761
Ensembl chr 1:82,549,420...82,580,761
JBrowse link
G Cd36 CD36 molecule ISO (MGI:MGI:3618422|PMID:15647754) RGD PMID:15647754 MGI:MGI:3618422 NCBI chr 4:14,150,309...14,191,498
Ensembl chr 4:14,001,761...14,249,749
JBrowse link
G Gas6 growth arrest specific 6 ISO
ISS
(MGI:MGI:3778590|PMID:18159085)
GO_REF:0000024
(PMID:21501828)
RGD
UniProt
PMID:18159085, PMID:21501828 GO_REF:0000024, MGI:MGI:3778590 NCBI chr16:81,213,364...81,243,824
Ensembl chr16:81,213,364...81,243,757
JBrowse link
G Hmgb1 high mobility group box 1 ISO
ISS
(PMID:18768881)
GO_REF:0000024
RGD
UniProt
PMID:18768881 GO_REF:0000024 NCBI chr12:7,082,529...7,090,246
Ensembl chr16:37,500,017...37,502,237
JBrowse link
G Itgav integrin subunit alpha V ISO UniProtKB:P43406 (PMID:20826760)
UniProtKB:P06756 (MGI:MGI:3618422|PMID:15647754), (MGI:MGI:5285150|PMID:20826760)
RGD PMID:15647754, PMID:20826760 MGI:MGI:3618422, MGI:MGI:5285150 NCBI chr 3:71,113,269...71,205,958
Ensembl chr 3:71,114,100...71,202,411
JBrowse link
G Itgb3 integrin subunit beta 3 ISO UniProtKB:O54890 (PMID:20826760)
UniProtKB:P05106 (MGI:MGI:5285150|PMID:20826760)
RGD PMID:20826760 MGI:MGI:5285150 NCBI chr10:92,667,869...92,783,413
Ensembl chr10:92,667,869...92,783,410
JBrowse link
G Jmjd6 jumonji domain containing 6, arginine demethylase and lysine hydroxylase NOT ISO MGI:MGI:3580706 (MGI:MGI:3580691|PMID:15345036)
MGI:MGI:3043930 (MGI:MGI:3042820|PMID:14715629), (MGI:MGI:3618422|PMID:15647754)
RGD PMID:14715629, PMID:15345036, PMID:15647754 MGI:MGI:3042820, MGI:MGI:3580691, MGI:MGI:3618422 NCBI chr10:105,781,752...105,787,803
Ensembl chr10:105,781,753...105,787,803
JBrowse link
G Lrp1 LDL receptor related protein 1 ISO (MGI:MGI:3618422|PMID:15647754) RGD PMID:15647754 MGI:MGI:3618422 NCBI chr 7:70,846,313...70,927,028
Ensembl chr 7:70,846,344...70,926,903
JBrowse link
G Marco macrophage receptor with collagenous structure ISO (MGI:MGI:3831958|PMID:19201851) RGD PMID:19201851 MGI:MGI:3831958 NCBI chr16:85,115,199...85,147,683
Ensembl chr16:85,115,201...85,135,859
JBrowse link
G Megf10 multiple EGF-like domains 10 IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr18:52,215,652...52,366,212
Ensembl chr18:52,215,682...52,366,238
JBrowse link
G Mertk MER proto-oncogene, tyrosine kinase ISO MGI:MGI:104294|MGI:MGI:1347244|MGI:MGI:2387768 (MGI:MGI:3778590|PMID:18159085), (MGI:MGI:3836130|PMID:17442946), (MGI:MGI:5509105|PMID:23878224), (MGI:MGI:6120635|PMID:29440417) RGD PMID:17442946, PMID:18159085, PMID:23878224, PMID:29440417 MGI:MGI:3778590, MGI:MGI:3836130, MGI:MGI:5509105, MGI:MGI:6120635 NCBI chr 3:121,235,230...121,340,932
Ensembl chr 3:121,235,119...121,342,444
JBrowse link
G Mfge8 milk fat globule EGF and factor V/VIII domain containing IEA
ISO
GO_REF:0000107
(MGI:MGI:5285150|PMID:20826760)
Ensembl
RGD
PMID:20826760 GO_REF:0000107, MGI:MGI:5285150 NCBI chr 1:140,845,478...140,860,882
Ensembl chr 1:140,845,465...140,860,894
JBrowse link
G Nr1h3 nuclear receptor subfamily 1, group H, member 3 ISO (PMID:19628791) RGD PMID:19628791 NCBI chr 3:80,004,130...80,014,197
Ensembl chr 3:80,004,130...80,012,750
JBrowse link
G Rara retinoic acid receptor, alpha ISO (PMID:19628791) RGD PMID:19628791 NCBI chr10:86,838,819...86,884,224
Ensembl chr10:86,860,685...86,884,210
JBrowse link
G Tgm2 transglutaminase 2 ISO (PMID:19628791) RGD PMID:19628791 NCBI chr 3:154,597,165...154,627,257
Ensembl chr 3:154,597,168...154,627,257
JBrowse link
G Timd4 T-cell immunoglobulin and mucin domain containing 4 ISO (MGI:MGI:6120635|PMID:29440417) RGD PMID:29440417 MGI:MGI:6120635 NCBI chr10:31,880,822...31,917,215 JBrowse link
G Trem2 triggering receptor expressed on myeloid cells 2 ISO (MGI:MGI:3531054|PMID:15728241) RGD PMID:15728241 MGI:MGI:3531054 NCBI chr 9:14,611,541...14,618,076
Ensembl chr 9:14,611,561...14,618,013
JBrowse link
G Trex1 three prime repair exonuclease 1 ISO MGI:MGI:3052754 (MGI:MGI:5554502|PMID:24218451) RGD PMID:24218451 MGI:MGI:5554502 NCBI chr 8:117,796,127...117,797,427
Ensembl chr 8:117,796,128...117,797,427
JBrowse link
G Txndc5 thioredoxin domain containing 5 IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr17:26,925,828...26,953,981
Ensembl chr17:26,925,828...26,953,970
JBrowse link
G Tyro3 TYRO3 protein tyrosine kinase IEA
ISO
ISS
GO_REF:0000107
MGI:MGI:1347244|MGI:MGI:96965 (MGI:MGI:3778590|PMID:18159085), (MGI:MGI:3836130|PMID:17442946)
GO_REF:0000024
Ensembl
RGD
UniProt
PMID:17442946, PMID:18159085 GO_REF:0000024, GO_REF:0000107, MGI:MGI:3778590, MGI:MGI:3836130 NCBI chr 3:111,597,102...111,616,142
Ensembl chr 3:111,597,102...111,616,142
JBrowse link
G Tyrobp transmembrane immune signaling adaptor Tyrobp ISS
ISO
GO_REF:0000024
(MGI:MGI:3531054|PMID:15728241)
UniProt
RGD
PMID:15728241 GO_REF:0000024, MGI:MGI:3531054 NCBI chr 1:88,875,370...88,879,305
Ensembl chr 1:88,875,375...88,879,303
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 ISO
IBA
(PMID:24509909)
PMID:21873635
(MGI:MGI:3764740|PMID:17960134)
RGD PMID:17960134, PMID:24509909, PMID:21873635 MGI:MGI:3764740, RGD:13792537 NCBI chr 7:115,766,484...115,828,514 JBrowse link
G Becn1 beclin 1 ISO (MGI:MGI:5619450|PMID:22393062) RGD PMID:22393062 MGI:MGI:5619450 NCBI chr10:89,209,944...89,225,297
Ensembl chr10:89,209,940...89,225,297
JBrowse link
G Megf10 multiple EGF-like domains 10 ISO MGI:MGI:4454190 (MGI:MGI:5775214|PMID:27170117) RGD PMID:27170117 MGI:MGI:5775214 NCBI chr18:52,215,652...52,366,212
Ensembl chr18:52,215,682...52,366,238
JBrowse link
G Rac1 Rac family small GTPase 1 ISO
IBA
(MGI:MGI:4943793|PMID:20691665)
PMID:21873635
RGD PMID:20691665, PMID:21873635 MGI:MGI:4943793, RGD:13792537 NCBI chr12:13,090,316...13,111,841
Ensembl chr12:13,090,172...13,111,873
JBrowse link
G Rac2 Rac family small GTPase 2 IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr 7:119,769,708...119,797,111
Ensembl chr 7:119,783,849...119,797,098
JBrowse link
G Rhobtb1 Rho-related BTB domain containing 1 IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr20:20,638,579...20,715,437
Ensembl chr20:20,638,579...20,713,128
JBrowse link
G Rhobtb2 Rho-related BTB domain containing 2 IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr15:51,465,148...51,485,562
Ensembl chr15:51,465,148...51,485,692
JBrowse link
G Rhog ras homolog family member G IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr 1:167,336,147...167,347,720
Ensembl chr 1:167,335,248...167,347,671
JBrowse link
G Rhoh ras homolog family member H IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr14:43,961,756...43,992,587
Ensembl chr14:43,961,756...43,992,587
JBrowse link
G Thbs1 thrombospondin 1 ISO (PMID:16882710) RGD PMID:16882710 NCBI chr 3:109,862,120...109,873,466
Ensembl chr 3:109,862,117...109,873,466
JBrowse link
G Xkr4 XK related 4 IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr 5:15,746,012...16,141,059
Ensembl chr 5:15,747,614...16,140,896
JBrowse link
G Xkr5 XK related 5 IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr16:75,744,786...75,762,694
Ensembl chr16:75,744,786...75,762,693
JBrowse link
G Xkr6 XK related 6 IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr15:46,784,963...47,173,352
Ensembl chr15:46,784,963...47,173,335
JBrowse link
G Xkr7 XK related 7 IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr 3:148,508,622...148,537,904
Ensembl chr 3:148,510,779...148,533,404
JBrowse link
G Xkr8 XK related 8 ISO
IBA
(PMID:23845944)
PMID:21873635
RGD PMID:23845944, PMID:21873635 RGD:13792537 NCBI chr 5:150,918,600...150,925,727
Ensembl chr 5:150,918,603...150,925,727
JBrowse link
G Xkr9 XK related 9 IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr 5:4,946,332...4,975,436
Ensembl chr 5:4,946,006...4,975,436
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 ISO
ISS
(MGI:MGI:5819329|PMID:26768664)
GO_REF:0000024
RGD
UniProt
PMID:26768664 GO_REF:0000024, MGI:MGI:5819329 NCBI chr10:103,669,781...103,690,584
Ensembl chr10:103,670,028...103,687,425
JBrowse link
G Hmgb1 high mobility group box 1 ISO (PMID:20826760) RGD PMID:20826760 NCBI chr12:7,082,529...7,090,246
Ensembl chr16:37,500,017...37,502,237
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
(PMID:21957127)
PMID:21873635
RGD PMID:21957127, PMID:21873635 RGD:13792537 NCBI chr 1:237,893,983...237,910,002
Ensembl chr 1:237,893,966...237,910,012
JBrowse link
G Axl Axl receptor tyrosine kinase ISO MGI:MGI:96965 (MGI:MGI:5509105|PMID:23878224) RGD PMID:23878224 MGI:MGI:5509105 NCBI chr 1:82,550,892...82,580,761
Ensembl chr 1:82,549,420...82,580,761
JBrowse link
G Ccr2 C-C motif chemokine receptor 2 ISO MGI:MGI:2158345 (MGI:MGI:1100445|PMID:9342361) RGD PMID:9342361 MGI:MGI:1100445
G Hmgb1 high mobility group box 1 ISO
ISS
(PMID:18768881)
GO_REF:0000024
RGD
UniProt
PMID:18768881 GO_REF:0000024 NCBI chr12:7,082,529...7,090,246
Ensembl chr16:37,500,017...37,502,237
JBrowse link
G Mertk MER proto-oncogene, tyrosine kinase ISO MGI:MGI:1347244 (MGI:MGI:5509105|PMID:23878224) RGD PMID:23878224 MGI:MGI:5509105 NCBI chr 3:121,235,230...121,340,932
Ensembl chr 3:121,235,119...121,342,444
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 RGD:13792537 NCBI chr 3:14,373,270...14,395,357
Ensembl chr 3:14,373,275...14,395,362
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 ISO MGI:MGI:4377985 (MGI:MGI:5749311|PMID:26284655) RGD PMID:26284655 MGI:MGI:5749311 NCBI chr 3:113,999,600...114,064,438
Ensembl chr 3:113,999,719...114,065,170
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 ISO (PMID:19302245) RGD PMID:19302245 NCBI chr20:4,542,340...4,561,152
Ensembl chr20:4,542,340...4,561,152
JBrowse link
G C3 complement C3 ISO
IEA
(PMID:19302245)
GO_REF:0000107
RGD
Ensembl
PMID:19302245 GO_REF:0000107 NCBI chr 9:9,721,137...9,747,084
Ensembl chr 9:9,721,105...9,747,167
JBrowse link
G C4a complement C4A ISO UniProtKB:P0C0L5 (PMID:19302245) RGD PMID:19302245 NCBI chr20:2,651,599...2,678,183
Ensembl chr20:2,651,599...2,678,141
JBrowse link
G C4b complement C4B (Chido blood group) ISO UniProtKB:P0C0L4|UniProtKB:P0C0L5 (PMID:19302245) RGD PMID:19302245 NCBI chr20:4,302,344...4,316,752
Ensembl chr20:4,302,344...4,316,715
JBrowse link
G Ccl2 C-C motif chemokine ligand 2 ISO (MGI:MGI:4943793|PMID:20691665) RGD PMID:20691665 MGI:MGI:4943793 NCBI chr10:69,412,065...69,413,863
Ensembl chr10:69,412,017...69,413,870
JBrowse link
G Cd300lf Cd300 molecule-like family member F ISS
ISO
GO_REF:0000024
(MGI:MGI:5301804|PMID:21865548), (MGI:MGI:5819329|PMID:26768664)
UniProt
RGD
PMID:21865548, PMID:26768664 GO_REF:0000024, MGI:MGI:5301804, MGI:MGI:5819329 NCBI chr10:103,669,781...103,690,584
Ensembl chr10:103,670,028...103,687,425
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 ISO
ISS
(MGI:MGI:3662940|PMID:16908670)
GO_REF:0000024
RGD
Alzheimers_University_of_Toronto
PMID:16908670 GO_REF:0000024, MGI:MGI:3662940 NCBI chr 7:12,742,433...12,762,423
Ensembl chr 7:12,742,433...12,762,341
JBrowse link
G Trem2 triggering receptor expressed on myeloid cells 2 ISO (PMID:24990881) RGD PMID:24990881 NCBI chr 9:14,611,541...14,618,076
Ensembl chr 9:14,611,561...14,618,013
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) RGD PMID:15804047 NCBI chr 3:2,850,006...2,853,230
Ensembl chr 3:2,849,984...2,853,272
JBrowse link
G Fcnb ficolin B ISO (PMID:15804047) RGD PMID:15804047 NCBI chr 3:6,617,816...6,626,193
Ensembl chr 3:6,617,751...6,626,284
JBrowse link
G Jmjd6 jumonji domain containing 6, arginine demethylase and lysine hydroxylase ISO MGI:MGI:2686850 (MGI:MGI:1855743|PMID:10811223), (MGI:MGI:2682078|PMID:14645847) RGD PMID:10811223, PMID:14645847 MGI:MGI:1855743, MGI:MGI:2682078 NCBI chr10:105,781,752...105,787,803
Ensembl chr10:105,781,753...105,787,803
JBrowse link
G Megf10 multiple EGF-like domains 10 ISO (MGI:MGI:4414741|PMID:19915564) RGD PMID:19915564 MGI:MGI:4414741 NCBI chr18:52,215,652...52,366,212
Ensembl chr18:52,215,682...52,366,238
JBrowse link
G Pear1 platelet endothelial aggregation receptor 1 ISO (MGI:MGI:4414741|PMID:19915564) RGD PMID:19915564 MGI:MGI:4414741 NCBI chr 2:187,114,219...187,134,209
Ensembl chr 2:187,114,217...187,133,993
JBrowse link
G Scarb1 scavenger receptor class B, member 1 ISO
ISS
IDA
(PMID:9211901)
GO_REF:0000024
PMID:12016218
RGD
BHF-UCL
PMID:9211901, PMID:12016218 GO_REF:0000024, RGD:1304245 NCBI chr12:36,694,952...36,761,445
Ensembl chr12:36,694,960...36,761,455
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
ISO
GO_REF:0000024
(MGI:MGI:5436199|PMID:22503541), (MGI:MGI:5508294|PMID:11278875)
UniProt
RGD
PMID:11278875, PMID:22503541 GO_REF:0000024, MGI:MGI:5436199, MGI:MGI:5508294 NCBI chr10:56,953,692...56,962,145
Ensembl chr10:56,953,691...56,962,161
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 20014
    cellular process 18788
      vesicle-mediated transport 1652
        phagocytosis 350
          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 + 10
Path 2
Term Annotations click to browse term
  biological_process 20014
    localization 6486
      establishment of localization 4918
        transport 4774
          vesicle-mediated transport 1652
            phagocytosis 350
              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 + 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.