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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) UniProtKB PMID:24509909 NCBI chr 8:139,154,065...139,251,115
Ensembl chr 8:142,220,827...142,301,070
JBrowse link
G ALOX15 arachidonate 15-lipoxygenase ISO (MGI:MGI:5436199|PMID:22503541) UniProtKB PMID:22503541 MGI:MGI:5436199 NCBI chr17:4,686,339...4,696,877
Ensembl chr17:4,677,125...4,687,669
JBrowse link
G AXL AXL receptor tyrosine kinase ISO (MGI:MGI:3778590|PMID:18159085)
(MGI:MGI:3841855|PMID:18804096)
(MGI:MGI:3836130|PMID:17442946)
(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 chr19:38,211,555...38,254,464
Ensembl chr19:46,719,615...46,761,747
JBrowse link
G CD36 CD36 molecule ISO (MGI:MGI:3618422|PMID:15647754) MGI PMID:15647754 MGI:MGI:3618422 NCBI chr 7:72,566,478...72,643,517
Ensembl chr 7:86,265,114...86,305,865
JBrowse link
G HMGB1 high mobility group box 1 ISO (PMID:18768881) UniProtKB PMID:18768881 NCBI chr13:11,737,942...11,894,923 JBrowse link
G ITGAV integrin subunit alpha V ISO (MGI:MGI:3618422|PMID:15647754)
(MGI:MGI:5285150|PMID:20826760)
(PMID:20826760)
MGI
BHF-UCL
PMID:15647754, PMID:20826760 MGI:MGI:3618422, MGI:MGI:5285150 NCBI chr2B:73,880,962...73,972,486
Ensembl chr2B:191,680,655...191,773,028
JBrowse link
G ITGB3 integrin subunit beta 3 ISO (PMID:20826760)
(MGI:MGI:5285150|PMID:20826760)
BHF-UCL PMID:20826760 MGI:MGI:5285150 NCBI chr17:10,134,450...10,194,596 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 chr17:70,789,922...70,803,791
Ensembl chr17:76,356,142...76,370,117
JBrowse link
G LRP1 LDL receptor related protein 1 ISO (MGI:MGI:3618422|PMID:15647754) MGI PMID:15647754 MGI:MGI:3618422 NCBI chr12:31,713,938...31,799,287
Ensembl chr12:31,966,149...32,051,979
JBrowse link
G MARCO macrophage receptor with collagenous structure ISO (MGI:MGI:3831958|PMID:19201851) MGI PMID:19201851 MGI:MGI:3831958 NCBI chr2B:5,896,433...5,940,284
Ensembl chr2B:119,475,677...119,520,385
JBrowse link
G MERTK MER proto-oncogene, tyrosine kinase ISO (MGI:MGI:3778590|PMID:18159085)
(MGI:MGI:6120635|PMID:29440417)
(MGI:MGI:5509105|PMID:23878224)
(MGI:MGI:3836130|PMID:17442946)
UniProtKB
MGI
PMID:17442946, PMID:18159085, PMID:23878224, PMID:29440417 MGI:MGI:3778590, MGI:MGI:3836130, MGI:MGI:5509105, MGI:MGI:6120635 NCBI chr2A:89,977,226...90,109,970
Ensembl chr2A:113,056,852...113,162,052
JBrowse link
G MFGE8 milk fat globule EGF and factor V/VIII domain containing ISO (MGI:MGI:5285150|PMID:20826760) BHF-UCL PMID:20826760 MGI:MGI:5285150 NCBI chr15:67,587,360...67,602,029
Ensembl chr15:86,795,135...86,809,876
JBrowse link
G NR1H3 nuclear receptor subfamily 1 group H member 3 ISO (PMID:19628791) UniProtKB PMID:19628791 NCBI chr11:47,195,122...47,215,277
Ensembl chr11:47,748,353...47,768,672
JBrowse link
G RARA retinoic acid receptor alpha ISO (PMID:19628791) UniProtKB PMID:19628791 NCBI chr17:16,932,485...16,980,958 JBrowse link
G TGM2 transglutaminase 2 ISO (PMID:19628791) UniProtKB PMID:19628791 NCBI chr20:34,450,845...34,488,106
Ensembl chr20:35,561,819...35,599,042
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 5:152,321,962...152,365,717
Ensembl chr 5:158,305,721...158,349,336
JBrowse link
G TREM2 triggering receptor expressed on myeloid cells 2 ISO (MGI:MGI:3531054|PMID:15728241) UniProt PMID:15728241 MGI:MGI:3531054 NCBI chr 6:40,735,483...40,740,208
Ensembl chr 6:42,043,900...42,048,578
JBrowse link
G TREX1 three prime repair exonuclease 1 ISO (MGI:MGI:5554502|PMID:24218451) MGI PMID:24218451 MGI:MGI:5554502 NCBI chr 3:48,387,762...48,389,693
Ensembl chr 3:49,470,222...49,471,331
JBrowse link
G TYRO3 TYRO3 protein tyrosine kinase ISO (MGI:MGI:3778590|PMID:18159085)
(MGI:MGI:3836130|PMID:17442946)
MGI PMID:17442946, PMID:18159085 MGI:MGI:3778590, MGI:MGI:3836130 NCBI chr15:20,499,789...20,520,152
Ensembl chr15:38,739,509...38,760,288
JBrowse link
G TYROBP transmembrane immune signaling adaptor TYROBP ISO (MGI:MGI:3531054|PMID:15728241) UniProt PMID:15728241 MGI:MGI:3531054 NCBI chr19:32,821,279...32,825,488
Ensembl chr19:41,570,683...41,575,226
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 (PMID:24509909)
(MGI:MGI:3764740|PMID:17960134)
UniProtKB PMID:17960134, PMID:24509909 MGI:MGI:3764740 NCBI chr 8:139,154,065...139,251,115
Ensembl chr 8:142,220,827...142,301,070
JBrowse link
G BECN1 beclin 1 ISO (MGI:MGI:5619450|PMID:22393062) CACAO PMID:22393062 MGI:MGI:5619450 NCBI chr17:14,493,619...14,507,809
Ensembl chr17:14,719,781...14,733,286
JBrowse link
G MEGF10 multiple EGF like domains 10 ISO (MGI:MGI:5775214|PMID:27170117) MGI PMID:27170117 MGI:MGI:5775214 NCBI chr 5:122,639,155...122,877,324
Ensembl chr 5:128,466,095...128,641,043
JBrowse link
G RAC1 Rac family small GTPase 1 ISO (MGI:MGI:4943793|PMID:20691665) BHF-UCL PMID:20691665 MGI:MGI:4943793 NCBI chr 7:7,039,379...7,068,866 JBrowse link
G THBS1 thrombospondin 1 ISO (PMID:16882710) BHF-UCL PMID:16882710 NCBI chr15:18,521,802...18,538,172
Ensembl chr15:36,776,756...36,793,170
JBrowse link
G XKR8 XK related 8 ISO (PMID:23845944) UniProtKB PMID:23845944 NCBI chr 1:27,219,682...27,228,381
Ensembl chr 1:28,259,993...28,266,978
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 (MGI:MGI:5819329|PMID:26768664) UniProtKB PMID:26768664 MGI:MGI:5819329 NCBI chr17:68,638,855...68,658,017
Ensembl chr17:74,197,131...74,215,038
JBrowse link
G HMGB1 high mobility group box 1 ISO (PMID:20826760) BHF-UCL PMID:20826760 NCBI chr13:11,737,942...11,894,923 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 (PMID:21957127) BHF-UCL PMID:21957127 NCBI chr 9:51,647,404...51,665,990
Ensembl chr 9:71,929,728...71,948,779
JBrowse link
G AXL AXL receptor tyrosine kinase ISO (MGI:MGI:5509105|PMID:23878224) MGI PMID:23878224 MGI:MGI:5509105 NCBI chr19:38,211,555...38,254,464
Ensembl chr19:46,719,615...46,761,747
JBrowse link
G CCR2 C-C motif chemokine receptor 2 ISO (MGI:MGI:1100445|PMID:9342361) MGI PMID:9342361 MGI:MGI:1100445 NCBI chr 3:46,255,725...46,263,285
Ensembl chr 3:47,361,124...47,368,312
JBrowse link
G HMGB1 high mobility group box 1 ISO (PMID:18768881) UniProtKB PMID:18768881 NCBI chr13:11,737,942...11,894,923 JBrowse link
G MERTK MER proto-oncogene, tyrosine kinase ISO (MGI:MGI:5509105|PMID:23878224) MGI PMID:23878224 MGI:MGI:5509105 NCBI chr2A:89,977,226...90,109,970
Ensembl chr2A:113,056,852...113,162,052
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:5749311|PMID:26284655) MGI PMID:26284655 MGI:MGI:5749311 NCBI chr15:23,519,311...23,620,532
Ensembl chr15:41,688,081...41,788,616
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) BHF-UCL PMID:19302245 NCBI chr 6:31,590,135...31,606,368 JBrowse link
G C3 complement C3 ISO (PMID:19302245) BHF-UCL PMID:19302245 NCBI chr19:5,708,211...5,753,178
Ensembl chr19:6,629,287...6,674,699
JBrowse link
G CCL2 C-C motif chemokine ligand 2 ISO (MGI:MGI:4943793|PMID:20691665) BHF-UCL PMID:20691665 MGI:MGI:4943793 NCBI chr17:22,528,154...22,530,091
Ensembl chr17:22,820,890...22,823,384
JBrowse link
G CD300LF CD300 molecule like family member f ISO (MGI:MGI:5301804|PMID:21865548)
(MGI:MGI:5819329|PMID:26768664)
UniProtKB PMID:21865548, PMID:26768664 MGI:MGI:5301804, MGI:MGI:5819329 NCBI chr17:68,638,855...68,658,017
Ensembl chr17:74,197,131...74,215,038
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 (MGI:MGI:3662940|PMID:16908670) Alzheimers_University_of_Toronto PMID:16908670 MGI:MGI:3662940 NCBI chr19:62,811...77,897
Ensembl chr19:1,018,095...1,042,104
JBrowse link
G TREM2 triggering receptor expressed on myeloid cells 2 ISO (PMID:24990881) UniProt PMID:24990881 NCBI chr 6:40,735,483...40,740,208
Ensembl chr 6:42,043,900...42,048,578
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 ISO (PMID:15804047) UniProtKB PMID:15804047 NCBI chr 9:106,039,315...106,047,648 JBrowse link
G FCN2 ficolin 2 ISO (PMID:15804047) UniProtKB PMID:15804047 NCBI chr 9:105,995,807...106,020,389
Ensembl chr 9:134,997,038...135,018,992
JBrowse link
G FCN3 ficolin 3 ISO (PMID:15804047) UniProtKB PMID:15804047 NCBI chr 1:26,620,373...26,636,424
Ensembl chr 1:27,676,866...27,683,861
JBrowse link
G JMJD6 jumonji domain containing 6, arginine demethylase and lysine hydroxylase ISO (MGI:MGI:1855743|PMID:10811223)
(MGI:MGI:2682078|PMID:14645847)
MGI PMID:10811223, PMID:14645847 MGI:MGI:1855743, MGI:MGI:2682078 NCBI chr17:70,789,922...70,803,791
Ensembl chr17:76,356,142...76,370,117
JBrowse link
G MEGF10 multiple EGF like domains 10 ISO (MGI:MGI:4414741|PMID:19915564) MGI PMID:19915564 MGI:MGI:4414741 NCBI chr 5:122,639,155...122,877,324
Ensembl chr 5:128,466,095...128,641,043
JBrowse link
G PEAR1 platelet endothelial aggregation receptor 1 ISO (MGI:MGI:4414741|PMID:19915564) MGI PMID:19915564 MGI:MGI:4414741 NCBI chr 1:132,236,550...132,259,273
Ensembl chr 1:136,069,341...136,080,165
JBrowse link
G SCARB1 scavenger receptor class B member 1 ISO PMID:12016218
(PMID:9211901)
BHF-UCL PMID:9211901, PMID:12016218 RGD:1304245 NCBI chr12:122,293,803...122,455,314 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 ISO (MGI:MGI:5436199|PMID:22503541), (MGI:MGI:5508294|PMID:11278875) UniProtKB PMID:11278875, PMID:22503541 MGI:MGI:5436199, MGI:MGI:5508294 NCBI chr17:4,686,339...4,696,877
Ensembl chr17:4,677,125...4,687,669
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 12561
    cellular process 11665
      vesicle-mediated transport 1145
        phagocytosis 189
          apoptotic cell clearance 38
            engulfment of apoptotic cell + 9
            negative regulation of apoptotic cell clearance + 2
            neutrophil clearance 5
            phagosome maturation involved in apoptotic cell clearance + 1
            positive regulation of apoptotic cell clearance + 6
            recognition of apoptotic cell 7
            regulation of apoptotic cell clearance + 7
Path 2
Term Annotations click to browse term
  biological_process 12561
    localization 4922
      establishment of localization 3510
        transport 3358
          vesicle-mediated transport 1145
            phagocytosis 189
              apoptotic cell clearance 38
                engulfment of apoptotic cell + 9
                negative regulation of apoptotic cell clearance + 2
                neutrophil clearance 5
                phagosome maturation involved in apoptotic cell clearance + 1
                positive regulation of apoptotic cell clearance + 6
                recognition of apoptotic cell 7
                regulation of apoptotic cell clearance + 7
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.