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ONTOLOGY REPORT - ANNOTATIONS


Term:lytic vacuole organization
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Accession:GO:0080171 term browser browse the term
Definition:A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a lytic vacuole.
Synonyms:exact_synonym: lytic vacuole organisation
 narrow_synonym: lytic vacuolar assembly
 related_synonym: lytic vacuole biogenesis;   lytic vacuole organization and biogenesis


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lysosomal lumen acidification term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ATP6AP2 ATPase H+ transporting accessory protein 2 IEA Ensembl GO_REF:0000107 NCBI chr  X:36,271,154...36,300,240
Ensembl chr  X:36,271,223...36,304,183
JBrowse link
G CCDC115 coiled-coil domain containing 115 IEA Ensembl GO_REF:0000107 NCBI chr15:31,974,715...31,979,062
Ensembl chr15:31,974,724...31,979,059
JBrowse link
G CLN3 CLN3 lysosomal/endosomal transmembrane protein, battenin IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 3:18,433,564...18,450,296 JBrowse link
G CLN5 CLN5 intracellular trafficking protein ISO (PMID:11722572) UniProtKB PMID:11722572 NCBI chr11:49,105,822...49,128,425 JBrowse link
G CLN6 CLN6 transmembrane ER protein IEA Ensembl GO_REF:0000107 NCBI chr 1:166,107,895...166,126,054
Ensembl chr 1:166,107,228...166,126,584
JBrowse link
G GRN granulin precursor IEA Ensembl GO_REF:0000107 NCBI chr12:18,893,772...18,900,444
Ensembl chr12:18,893,770...18,900,446
JBrowse link
G PPT1 palmitoyl-protein thioesterase 1 IEA Ensembl GO_REF:0000107 NCBI chr 6:95,840,906...95,860,858
Ensembl chr 6:95,840,905...95,860,837
JBrowse link
G SNAPIN SNAP associated protein IEA Ensembl GO_REF:0000107 NCBI chr 4:95,987,524...95,989,527
Ensembl chr 4:95,984,358...95,989,474
JBrowse link
G TMEM199 transmembrane protein 199 IEA Ensembl GO_REF:0000107 NCBI chr12:44,636,379...44,641,536
Ensembl chr12:44,636,378...44,641,530
JBrowse link
G TMEM9 transmembrane protein 9 ISO (PMID:30374053) UniProt PMID:30374053 NCBI chr10:23,586,487...23,600,042
Ensembl chr10:23,586,488...23,610,716
JBrowse link
lysosomal lumen pH elevation term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CLN3 CLN3 lysosomal/endosomal transmembrane protein, battenin ISO (PMID:10924275) UniProtKB PMID:10924275 NCBI chr 3:18,433,564...18,450,296 JBrowse link
lysosomal membrane organization term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ARF1 ADP ribosylation factor 1 ISO RGD PMID:9538255 RGD:9684948 NCBI chr 2:51,219,597...51,237,640
Ensembl chr 2:51,219,667...51,237,639
JBrowse link
lysosome organization term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G ABCA1 ATP binding cassette subfamily A member 1 IEA Ensembl GO_REF:0000107 NCBI chr 1:246,144,277...246,278,492
Ensembl chr 1:246,144,277...246,278,492
JBrowse link
G ACP2 acid phosphatase 2, lysosomal IEA
IBA
(PMID:21873635) Ensembl
GO_Central
PMID:21873635 GO_REF:0000107 NCBI chr 2:15,334,015...15,342,531
Ensembl chr 2:15,334,025...15,347,774
JBrowse link
G ACP3 acid phosphatase 3 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr13:73,471,837...73,530,778
Ensembl chr13:73,471,881...73,571,052
JBrowse link
G ACP4 acid phosphatase 4 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 6:55,535,406...55,541,929
Ensembl chr 6:55,537,076...55,541,928
JBrowse link
G AKTIP AKT interacting protein IEA Ensembl GO_REF:0000107 NCBI chr 6:31,706,253...31,757,878
Ensembl chr 6:31,747,606...31,758,280
JBrowse link
G AP3B1 adaptor related protein complex 3 subunit beta 1 IEA Ensembl GO_REF:0000107 NCBI chr 2:86,875,922...87,142,722
Ensembl chr 2:86,873,081...87,142,744
JBrowse link
G BECN1 beclin 1 IEA Ensembl GO_REF:0000107 NCBI chr12:20,041,914...20,054,249
Ensembl chr12:20,041,956...20,054,373
JBrowse link
G CHMP5 charged multivesicular body protein 5 IEA Ensembl GO_REF:0000107 NCBI chr10:33,212,769...33,227,237
Ensembl chr10:33,212,766...33,227,405
JBrowse link
G CLN3 CLN3 lysosomal/endosomal transmembrane protein, battenin IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 3:18,433,564...18,450,296 JBrowse link
G CLN5 CLN5 intracellular trafficking protein IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr11:49,105,822...49,128,425 JBrowse link
G CLN6 CLN6 transmembrane ER protein IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 1:166,107,895...166,126,054
Ensembl chr 1:166,107,228...166,126,584
JBrowse link
G CLN8 CLN8 transmembrane ER and ERGIC protein IEA Ensembl GO_REF:0000107 NCBI chr15:33,282,524...33,325,598 JBrowse link
G CLVS1 clavesin 1 IEA
IBA
(PMID:21873635) InterPro
GO_Central
PMID:21873635 GO_REF:0000002 NCBI chr 4:72,104,521...72,257,259
Ensembl chr 4:72,082,685...72,257,226
JBrowse link
G CLVS2 clavesin 2 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 1:39,680,741...39,755,398
Ensembl chr 1:39,682,688...39,752,487
JBrowse link
G FAM160A2 family with sequence similarity 160 member A2 IEA Ensembl GO_REF:0000107 NCBI chr 9:3,441,613...3,464,237
Ensembl chr 9:3,446,075...3,464,226
JBrowse link
G GAA glucosidase alpha, acid IEA Ensembl GO_REF:0000107 NCBI chr12:2,315,807...2,339,867
Ensembl chr12:2,314,591...2,336,988
JBrowse link
G GBA glucosylceramidase beta ISS
IEA
UniProt
Ensembl
GO_REF:0000024, GO_REF:0000107 NCBI chr 4:94,583,905...94,606,689
Ensembl chr 4:94,584,196...94,609,745
JBrowse link
G GNPTAB N-acetylglucosamine-1-phosphate transferase subunits alpha and beta IEA Ensembl GO_REF:0000107 NCBI chr 5:82,264,640...82,460,819
Ensembl chr 5:82,361,871...82,460,814
JBrowse link
G GRN granulin precursor ISO (MGI:MGI:6274951|PMID:27789271) UniProt PMID:27789271 MGI:MGI:6274951 NCBI chr12:18,893,772...18,900,444
Ensembl chr12:18,893,770...18,900,446
JBrowse link
G HEXA hexosaminidase subunit alpha IEA Ensembl GO_REF:0000107 NCBI chr 7:60,878,531...60,911,537 JBrowse link
G HEXB hexosaminidase subunit beta IEA Ensembl GO_REF:0000107 NCBI chr 2:83,745,263...83,784,762
Ensembl chr 2:83,744,627...83,784,759
JBrowse link
G HOOK1 hook microtubule tethering protein 1 ISO (PMID:18799622) UniProtKB PMID:18799622 NCBI chr 6:152,636,118...152,709,422 JBrowse link
G HOOK2 hook microtubule tethering protein 2 IEA Ensembl GO_REF:0000107 NCBI chr 2:66,227,562...66,239,671
Ensembl chr 2:66,213,823...66,242,511
JBrowse link
G HOOK3 hook microtubule tethering protein 3 IEA Ensembl GO_REF:0000107 NCBI chr17:11,817,963...11,919,152
Ensembl chr17:11,817,987...11,924,884
JBrowse link
G HPS1 HPS1 biogenesis of lysosomal organelles complex 3 subunit 1 ISO (MGI:MGI:6415001|PMID:30786955) MGI PMID:30786955 MGI:MGI:6415001 NCBI chr14:109,730,597...109,755,288
Ensembl chr14:109,730,594...109,755,213
JBrowse link
G HPS4 HPS4 biogenesis of lysosomal organelles complex 3 subunit 2 IEA Ensembl GO_REF:0000107 NCBI chr14:44,041,684...44,073,661
Ensembl chr14:44,049,707...44,073,622
JBrowse link
G IDUA alpha-L-iduronidase ISO (MGI:MGI:4414887|PMID:19751987)
(MGI:MGI:86916|PMID:9097952)
MGI PMID:9097952, PMID:19751987 MGI:MGI:4414887, MGI:MGI:86916 NCBI chr 8:334,604...351,970
Ensembl chr 8:334,599...351,970
JBrowse link
G LAMTOR1 late endosomal/lysosomal adaptor, MAPK and MTOR activator 1 IEA InterPro
Ensembl
GO_REF:0000002, GO_REF:0000107 NCBI chr 9:6,674,045...6,680,067
Ensembl chr 9:6,672,475...6,680,053
JBrowse link
G LRRK2 leucine rich repeat kinase 2 ISO (PMID:25416817) ParkinsonsUK-UCL PMID:25416817 NCBI chr 5:71,800,337...71,945,828
Ensembl chr 5:71,800,240...71,944,938
JBrowse link
G LYST lysosomal trafficking regulator IEA InterPro GO_REF:0000002 NCBI chr14:55,433,163...55,634,011
Ensembl chr14:55,433,018...55,633,484
JBrowse link
G MBTPS1 membrane bound transcription factor peptidase, site 1 IEA Ensembl GO_REF:0000107 NCBI chr 6:4,503,530...4,558,601
Ensembl chr 6:4,503,573...4,558,609
JBrowse link
G MFSD8 major facilitator superfamily domain containing 8 IEA Ensembl GO_REF:0000107 NCBI chr 8:96,925,063...96,972,390
Ensembl chr 8:96,925,080...96,971,339
JBrowse link
G MTOR mechanistic target of rapamycin kinase IEA Ensembl GO_REF:0000107 NCBI chr 6:71,286,989...71,412,913
Ensembl chr 6:71,286,989...71,412,888
JBrowse link
G MYO7A myosin VIIA ISO (PMID:16001398) UniProtKB PMID:16001398 NCBI chr 9:11,251,187...11,337,618
Ensembl chr 9:11,249,075...11,666,296
JBrowse link
G NAGLU N-acetyl-alpha-glucosaminidase IEA Ensembl GO_REF:0000107 Ensembl chr12:20,269,930...20,279,582 JBrowse link
G PPT1 palmitoyl-protein thioesterase 1 ISO (MGI:MGI:3612221|PMID:16368712)
(MGI:MGI:3654230|PMID:16542649)
MGI PMID:16368712, PMID:16542649 MGI:MGI:3612221, MGI:MGI:3654230 NCBI chr 6:95,840,906...95,860,858
Ensembl chr 6:95,840,905...95,860,837
JBrowse link
G SNAPIN SNAP associated protein IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 4:95,987,524...95,989,527
Ensembl chr 4:95,984,358...95,989,474
JBrowse link
G SPG11 SPG11 vesicle trafficking associated, spatacsin ISO (MGI:MGI:5749311|PMID:26284655) MGI PMID:26284655 MGI:MGI:5749311 NCBI chr 1:126,890,464...126,998,014
Ensembl chr 1:126,890,892...126,998,059
JBrowse link
G TFEB transcription factor EB ISO (PMID:23434374)
(PMID:22692423)
UniProtKB
UniProt
PMID:22692423, PMID:23434374 NCBI chr 7:36,870,240...36,920,887
Ensembl chr 7:36,869,565...36,920,875
JBrowse link
G TMEM106B transmembrane protein 106B IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 9:81,837,654...81,864,215
Ensembl chr 9:81,837,688...81,864,193
JBrowse link
G TPCN2 two pore segment channel 2 ISO (PMID:25416817) ParkinsonsUK-UCL PMID:25416817 NCBI chr 2:4,069,267...4,105,065 JBrowse link
G TPP1 tripeptidyl peptidase 1 IEA Ensembl GO_REF:0000107 NCBI chr 9:3,135,580...3,143,408
Ensembl chr 9:3,135,642...3,143,408
JBrowse link
G VPS18 VPS18 core subunit of CORVET and HOPS complexes IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 1:130,409,121...130,420,467
Ensembl chr 1:130,409,122...130,420,450
JBrowse link
G VPS35 VPS35 retromer complex component IEA Ensembl GO_REF:0000107 NCBI chr 6:37,944,099...37,977,091
Ensembl chr 6:37,944,127...37,986,203
JBrowse link
G WASHC5 WASH complex subunit 5 IEA Ensembl GO_REF:0000107 NCBI chr 4:14,598,133...14,667,535
Ensembl chr 4:14,598,148...14,668,327
JBrowse link
negative regulation of lysosome organization term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G BECN1 beclin 1 ISO RGD PMID:25561470 RGD:11561937 NCBI chr12:20,041,914...20,054,249
Ensembl chr12:20,041,956...20,054,373
JBrowse link
phagolysosome assembly term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CORO1A coronin 1A IEA InterPro
Ensembl
GO_REF:0000002, GO_REF:0000107 NCBI chr 3:18,336,813...18,342,381
Ensembl chr 3:18,336,899...18,342,380
JBrowse link
G MYO7A myosin VIIA IEA Ensembl GO_REF:0000107 NCBI chr 9:11,251,187...11,337,618
Ensembl chr 9:11,249,075...11,666,296
JBrowse link
G P2RX7 purinergic receptor P2X 7 IEA Ensembl GO_REF:0000107 NCBI chr14:31,415,188...31,476,502
Ensembl chr14:31,415,192...31,476,472
JBrowse link
G SRPX sushi repeat containing protein X-linked IEA Ensembl GO_REF:0000107 NCBI chr  X:34,075,577...34,198,462
Ensembl chr  X:34,075,577...34,198,467
JBrowse link
phagosome-lysosome docking term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CLN3 CLN3 lysosomal/endosomal transmembrane protein, battenin IEA Ensembl GO_REF:0000107 NCBI chr 3:18,433,564...18,450,296 JBrowse link
phagosome-lysosome fusion term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CLN3 CLN3 lysosomal/endosomal transmembrane protein, battenin IEA Ensembl GO_REF:0000107 NCBI chr 3:18,433,564...18,450,296 JBrowse link
G PIKFYVE phosphoinositide kinase, FYVE-type zinc finger containing IEA Ensembl GO_REF:0000107 NCBI chr15:111,372,148...111,468,720
Ensembl chr15:111,372,173...111,467,919
JBrowse link
G PLA2G5 phospholipase A2 group V ISO (MGI:MGI:3841317|PMID:19342668) UniProt PMID:19342668 MGI:MGI:3841317 NCBI chr 6:78,365,697...78,376,383
Ensembl chr 6:78,365,700...78,406,457
JBrowse link
G RAB20 RAB20, member RAS oncogene family IEA Ensembl GO_REF:0000107 NCBI chr11:77,167,052...77,188,893
Ensembl chr11:77,167,055...77,188,902
JBrowse link
G RAB34 RAB34, member RAS oncogene family ISS
IBA
(PMID:21873635) UniProt
GO_Central
PMID:21873635 GO_REF:0000024 NCBI chr12:44,951,989...44,956,458
Ensembl chr12:44,949,892...44,956,119
JBrowse link
G RAB39A RAB39A, member RAS oncogene family IEA Ensembl GO_REF:0000107 NCBI chr 9:36,341,339...36,403,690
Ensembl chr 9:36,341,339...36,403,696
JBrowse link
G RAB7A RAB7A, member RAS oncogene family IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr13:71,777,422...71,886,758
Ensembl chr13:71,777,420...71,886,581
JBrowse link
G RAB7B RAB7B, member RAS oncogene family IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 9:66,635,636...66,666,034
Ensembl chr 9:66,635,637...66,666,037
JBrowse link
G SYT7 synaptotagmin 7 IEA Ensembl GO_REF:0000107 NCBI chr 2:9,947,962...10,012,713
Ensembl chr 2:9,947,925...10,012,521
JBrowse link
G TMEM175 transmembrane protein 175 IEA Ensembl GO_REF:0000107 NCBI chr 8:295,693...313,974
Ensembl chr 8:297,007...313,973
JBrowse link
phagosome-lysosome fusion involved in apoptotic cell clearance term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G SPG11 SPG11 vesicle trafficking associated, spatacsin IEA Ensembl GO_REF:0000107 NCBI chr 1:126,890,464...126,998,014
Ensembl chr 1:126,890,892...126,998,059
JBrowse link
positive regulation of lysosomal membrane permeability term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G HSPA8 heat shock protein family A (Hsp70) member 8 ISO RGD PMID:9038169 RGD:10059368 NCBI chr 9:49,982,278...49,986,760
Ensembl chr 9:49,982,284...49,990,508
JBrowse link
G MT3 metallothionein 3 ISS
IEA
UniProt
Ensembl
GO_REF:0000024, GO_REF:0000107 NCBI chr 6:18,634,735...18,636,134
Ensembl chr 6:18,634,721...18,789,137
JBrowse link
positive regulation of lysosome organization term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G GRN granulin precursor IEA Ensembl GO_REF:0000107 NCBI chr12:18,893,772...18,900,444
Ensembl chr12:18,893,770...18,900,446
JBrowse link
regulation of lysosomal lumen pH term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G LRRK2 leucine rich repeat kinase 2 IEA Ensembl GO_REF:0000107 NCBI chr 5:71,800,337...71,945,828
Ensembl chr 5:71,800,240...71,944,938
JBrowse link
G SH3BGRL SH3 domain binding glutamate rich protein like IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr  X:64,617,350...64,709,006 JBrowse link
G TASL TLR adaptor interacting with endolysosomal SLC15A4 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr  X:26,363,808...26,384,933
Ensembl chr  X:26,363,810...26,393,041
JBrowse link
G TMEM165 transmembrane protein 165 IEA Ensembl GO_REF:0000107 NCBI chr 8:54,751,570...54,796,352
Ensembl chr 8:54,751,572...54,788,426
JBrowse link
G TMEM175 transmembrane protein 175 IEA Ensembl GO_REF:0000107 NCBI chr 8:295,693...313,974
Ensembl chr 8:297,007...313,973
JBrowse link
G VPS33A VPS33A core subunit of CORVET and HOPS complexes ISO (PMID:28013294) UniProtKB PMID:28013294 NCBI chr14:30,469,003...30,496,626 JBrowse link
regulation of lysosomal membrane permeability term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G LAPTM4B lysosomal protein transmembrane 4 beta IEA Ensembl GO_REF:0000107 NCBI chr 4:38,932,735...39,015,219
Ensembl chr 4:38,932,736...39,023,925
JBrowse link
regulation of lysosome organization term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G LAPTM4B lysosomal protein transmembrane 4 beta IEA Ensembl GO_REF:0000107 NCBI chr 4:38,932,735...39,015,219
Ensembl chr 4:38,932,736...39,023,925
JBrowse link
G TREX1 three prime repair exonuclease 1 IEA Ensembl GO_REF:0000107 NCBI chr13:31,177,604...31,180,764
Ensembl chr13:31,178,601...31,180,592
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 16524
    cellular process 15759
      cellular component organization or biogenesis 5963
        cellular component organization 5794
          organelle organization 3643
            vacuole organization 175
              lytic vacuole organization 70
                lysosome organization + 70
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.