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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 chr13:36,627,791...36,649,013
Ensembl chr13:36,614,498...36,690,936
JBrowse link
G ALOX12 arachidonate 12-lipoxygenase, 12S type IEA Ensembl GO_REF:0000107 NCBI chr 5:32,026,193...32,038,698
Ensembl chr 5:31,882,501...32,038,119
JBrowse link
G ALOX15 arachidonate 15-lipoxygenase IEA Ensembl GO_REF:0000107 NCBI chr 5:31,883,544...31,891,357
Ensembl chr 5:31,882,501...32,038,119
JBrowse link
G AXL AXL receptor tyrosine kinase ISO (MGI:MGI:3778590|PMID:18159085)
(MGI:MGI:5509105|PMID:23878224)
(MGI:MGI:3836130|PMID:17442946)
(MGI:MGI:3841855|PMID:18804096)
MGI PMID:17442946, PMID:18159085, PMID:18804096, PMID:23878224 MGI:MGI:3778590, MGI:MGI:3836130, MGI:MGI:3841855, MGI:MGI:5509105 NCBI chr 1:112,699,679...112,727,434
Ensembl chr 1:112,700,365...112,726,960
JBrowse link
G CD36 CD36 molecule IEA Ensembl GO_REF:0000107 NCBI chr18:20,299,808...20,375,856
Ensembl chr18:20,339,050...20,372,639
JBrowse link
G GAS6 growth arrest specific 6 IEA Ensembl GO_REF:0000107 NCBI chr22:60,975,196...61,005,869
Ensembl chr22:60,974,849...61,005,875
JBrowse link
G HMGB1 high mobility group box 1 ISS UniProtKB GO_REF:0000024 NCBI chr25:9,431,223...9,558,167
Ensembl chr25:9,431,218...9,558,165
JBrowse link
G ITGAV integrin subunit alpha V IEA Ensembl GO_REF:0000107 NCBI chr36:28,815,215...28,890,569
Ensembl chr36:28,804,013...28,887,430
JBrowse link
G ITGB3 integrin subunit beta 3 IEA Ensembl GO_REF:0000107 NCBI chr 9:9,179,667...9,231,061
Ensembl chr 9:9,182,562...9,231,451
JBrowse link
G JMJD6 jumonji domain containing 6, arginine demethylase and lysine hydroxylase NOT ISO (MGI:MGI:3618422|PMID:15647754)
(MGI:MGI:3580691|PMID:15345036)
(MGI:MGI:3042820|PMID:14715629)
MGI PMID:14715629, PMID:15345036, PMID:15647754 MGI:MGI:3042820, MGI:MGI:3580691, MGI:MGI:3618422 NCBI chr 9:4,037,307...4,076,119
Ensembl chr 9:4,037,439...4,076,123
JBrowse link
G LRP1 LDL receptor related protein 1 ISO (MGI:MGI:3618422|PMID:15647754) MGI PMID:15647754 MGI:MGI:3618422 NCBI chr10:1,260,256...1,341,705
Ensembl chr10:1,260,719...1,352,271
JBrowse link
G MARCO macrophage receptor with collagenous structure IEA Ensembl GO_REF:0000107 NCBI chr19:30,996,209...31,034,520
Ensembl chr19:30,996,347...31,034,487
JBrowse link
G MEGF10 multiple EGF like domains 10 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr11:16,359,648...16,574,882
Ensembl chr11:16,378,669...16,617,335
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)
MGI
UniProtKB
PMID:17442946, PMID:18159085, PMID:23878224, PMID:29440417 MGI:MGI:3778590, MGI:MGI:3836130, MGI:MGI:5509105, MGI:MGI:6120635 NCBI chr17:36,336,787...36,445,796
Ensembl chr17:36,336,861...36,445,380
JBrowse link
G MFGE8 milk fat globule EGF and factor V/VIII domain containing IEA Ensembl GO_REF:0000107 NCBI chr 3:52,054,243...52,064,423
Ensembl chr 3:52,054,831...52,080,240
JBrowse link
G NR1H3 nuclear receptor subfamily 1 group H member 3 ISO (PMID:19628791) UniProtKB PMID:19628791 NCBI chr18:42,333,173...42,346,152
Ensembl chr18:42,333,202...42,341,236
JBrowse link
G RARA retinoic acid receptor alpha IEA Ensembl GO_REF:0000107 NCBI chr 9:22,254,803...22,298,614
Ensembl chr 9:22,254,806...22,289,459
JBrowse link
G TGM2 transglutaminase 2 IEA Ensembl GO_REF:0000107 NCBI chr24:26,631,339...26,662,723
Ensembl chr24:26,628,009...26,663,840
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 4:53,070,950...53,133,617 JBrowse link
G TREX1 three prime repair exonuclease 1 IEA Ensembl GO_REF:0000107 NCBI chr20:40,624,845...40,626,840
Ensembl chr20:40,624,891...40,626,906
JBrowse link
G TXNDC5 thioredoxin domain containing 5 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr35:7,834,135...7,854,836
Ensembl chr35:7,834,331...7,854,852
JBrowse link
G TYRO3 TYRO3 protein tyrosine kinase ISS
IEA
UniProt
Ensembl
GO_REF:0000024, GO_REF:0000107 NCBI chr30:8,571,230...8,602,655
Ensembl chr30:8,571,475...8,598,721
JBrowse link
G TYROBP transmembrane immune signaling adaptor TYROBP IEA Ensembl GO_REF:0000107 NCBI chr 1:116,757,271...116,760,453
Ensembl chr 1:116,757,289...116,772,325
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 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr13:36,627,791...36,649,013
Ensembl chr13:36,614,498...36,690,936
JBrowse link
G BECN1 beclin 1 ISO (MGI:MGI:5619450|PMID:22393062) CACAO PMID:22393062 MGI:MGI:5619450 NCBI chr 9:20,204,203...20,215,081
Ensembl chr 9:20,204,220...20,214,236
JBrowse link
G MEGF10 multiple EGF like domains 10 IEA Ensembl GO_REF:0000107 NCBI chr11:16,359,648...16,574,882
Ensembl chr11:16,378,669...16,617,335
JBrowse link
G RAC1 Rac family small GTPase 1 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 6:11,726,259...11,758,532
Ensembl chr 6:11,655,494...11,757,216
JBrowse link
G RAC2 Rac family small GTPase 2 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr10:27,295,597...27,311,864
Ensembl chr10:27,295,640...27,311,397
JBrowse link
G RHOBTB1 Rho related BTB domain containing 1 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 4:12,971,624...13,089,520
Ensembl chr 4:12,973,412...13,035,505
JBrowse link
G RHOBTB2 Rho related BTB domain containing 2 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr25:34,299,363...34,329,052
Ensembl chr25:34,300,780...34,322,217
JBrowse link
G RHOG ras homolog family member G IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr21:26,371,868...26,373,395
Ensembl chr21:26,372,462...26,373,037
JBrowse link
G RHOG2 RHOG family member 2 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr  X:55,679,373...55,689,161
Ensembl chr  X:55,678,892...55,686,322
JBrowse link
G RHOH ras homolog family member H IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 3:72,272,446...72,277,015
Ensembl chr 3:72,276,418...72,276,993
JBrowse link
G THBS1 thrombospondin 1 IEA Ensembl GO_REF:0000107 NCBI chr30:6,770,212...6,786,875
Ensembl chr30:6,769,470...6,784,915
JBrowse link
G XKR4 XK related 4 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr29:6,640,108...7,081,182
Ensembl chr29:6,640,108...7,064,029
JBrowse link
G XKR5 XK related 5 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr16:58,836,581...58,861,698
Ensembl chr16:58,841,135...58,852,668
JBrowse link
G XKR7 XK related 7 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr24:21,403,557...21,432,207
Ensembl chr24:21,403,557...21,426,295
JBrowse link
G XKR8 XK related 8 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 2:72,419,950...72,426,315
Ensembl chr 2:72,418,872...72,450,737
JBrowse link
G XKR9 XK related 9 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr29:19,709,517...19,794,811
Ensembl chr29:19,753,291...19,794,747
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 chr 9:5,700,915...5,714,868 JBrowse link
G HMGB1 high mobility group box 1 IEA Ensembl GO_REF:0000107 NCBI chr25:9,431,223...9,558,167
Ensembl chr25:9,431,218...9,558,165
JBrowse link
neutrophil clearance term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ANXA1 annexin A1 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 1:84,744,159...84,763,011
Ensembl chr 1:84,744,163...84,763,011
JBrowse link
G AXL AXL receptor tyrosine kinase IEA Ensembl GO_REF:0000107 NCBI chr 1:112,699,679...112,727,434
Ensembl chr 1:112,700,365...112,726,960
JBrowse link
G CCR2 C-C motif chemokine receptor 2 IEA Ensembl GO_REF:0000107 NCBI chr20:42,305,344...42,313,258
Ensembl chr20:42,307,580...42,308,698
JBrowse link
G HMGB1 high mobility group box 1 ISS UniProtKB GO_REF:0000024 NCBI chr25:9,431,223...9,558,167
Ensembl chr25:9,431,218...9,558,165
JBrowse link
G MERTK MER proto-oncogene, tyrosine kinase IEA Ensembl GO_REF:0000107 NCBI chr17:36,336,787...36,445,796
Ensembl chr17:36,336,861...36,445,380
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 NCBI chr11:74,157,497...74,172,817
Ensembl chr11:74,159,414...74,172,810
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 IEA Ensembl GO_REF:0000107 NCBI chr30:11,233,709...11,305,454
Ensembl chr30:11,233,718...11,305,485
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 IEA Ensembl GO_REF:0000107 NCBI chr12:1,363,656...1,399,732
Ensembl chr12:1,363,803...1,399,728
JBrowse link
G C3 complement C3 IEA Ensembl GO_REF:0000107 NCBI chr20:53,566,226...53,598,365
Ensembl chr20:53,566,261...53,598,761
JBrowse link
G CCL2 C-C motif chemokine ligand 2 ISO (MGI:MGI:4943793|PMID:20691665) BHF-UCL PMID:20691665 MGI:MGI:4943793 NCBI chr 9:39,008,187...39,009,932 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 chr 9:5,700,915...5,714,868 JBrowse link
G LOC481722 complement C4-A ISO (PMID:19302245) BHF-UCL PMID:19302245 NCBI chr12:1,433,185...1,448,056 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 chr20:57,668,371...57,684,111
Ensembl chr20:57,667,706...57,677,342
JBrowse link
G TREM2 triggering receptor expressed on myeloid cells 2 ISO (PMID:24990881) UniProt PMID:24990881 NCBI chr12:9,915,692...9,928,322
Ensembl chr12:9,915,677...9,928,174
JBrowse link
recognition of apoptotic cell term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G FCN2 ficolin 2 IEA Ensembl GO_REF:0000107 NCBI chr 9:50,868,942...50,876,001
Ensembl chr 9:50,868,973...50,875,792
JBrowse link
G JMJD6 jumonji domain containing 6, arginine demethylase and lysine hydroxylase IEA Ensembl GO_REF:0000107 NCBI chr 9:4,037,307...4,076,119
Ensembl chr 9:4,037,439...4,076,123
JBrowse link
G MEGF10 multiple EGF like domains 10 IEA Ensembl GO_REF:0000107 NCBI chr11:16,359,648...16,574,882
Ensembl chr11:16,378,669...16,617,335
JBrowse link
G PEAR1 platelet endothelial aggregation receptor 1 IEA Ensembl GO_REF:0000107 NCBI chr 7:41,110,925...41,130,532
Ensembl chr 7:41,110,909...41,123,390
JBrowse link
G SCARB1 scavenger receptor class B member 1 IEA Ensembl GO_REF:0000107 NCBI chr26:5,035,797...5,122,383
Ensembl chr26:5,049,407...5,121,468
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 ALOX12 arachidonate 12-lipoxygenase, 12S type IEA Ensembl GO_REF:0000107 NCBI chr 5:32,026,193...32,038,698
Ensembl chr 5:31,882,501...32,038,119
JBrowse link
G ALOX15 arachidonate 15-lipoxygenase IEA Ensembl GO_REF:0000107 NCBI chr 5:31,883,544...31,891,357
Ensembl chr 5:31,882,501...32,038,119
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 16187
    cellular process 15465
      vesicle-mediated transport 1456
        phagocytosis 216
          apoptotic cell clearance 51
            engulfment of apoptotic cell + 20
            negative regulation of apoptotic cell clearance + 2
            neutrophil clearance 5
            phagosome maturation involved in apoptotic cell clearance + 2
            positive regulation of apoptotic cell clearance + 7
            recognition of apoptotic cell 5
            regulation of apoptotic cell clearance + 8
Path 2
Term Annotations click to browse term
  biological_process 16187
    localization 5957
      establishment of localization 4452
        transport 4303
          vesicle-mediated transport 1456
            phagocytosis 216
              apoptotic cell clearance 51
                engulfment of apoptotic cell + 20
                negative regulation of apoptotic cell clearance + 2
                neutrophil clearance 5
                phagosome maturation involved in apoptotic cell clearance + 2
                positive regulation of apoptotic cell clearance + 7
                recognition of apoptotic cell 5
                regulation of apoptotic cell clearance + 8
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.