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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 ISO (PMID:32276428) UniProt PMID:32276428 NCBI chrNW_004936502:7,206,226...7,232,798 JBrowse link
G Ccdc115 coiled-coil domain containing 115 ISO (PMID:28296633) UniProtKB PMID:28296633 NCBI chrNW_004936469:41,083,713...41,087,106 JBrowse link
G Cln3 CLN3 lysosomal/endosomal transmembrane protein, battenin ISO (PMID:11722572) UniProtKB PMID:11722572 NCBI chrNW_004936501:11,955,334...11,967,338 JBrowse link
G Cln5 CLN5 intracellular trafficking protein ISO (PMID:11722572) UniProtKB PMID:11722572 NCBI chrNW_004936511:4,283,016...4,291,968 JBrowse link
G Cln6 CLN6 transmembrane ER protein ISO (PMID:11722572) UniProtKB PMID:11722572 NCBI chrNW_004936471:28,069,058...28,084,607 JBrowse link
G Grn granulin precursor ISO (PMID:28073925) UniProt PMID:28073925 NCBI chrNW_004936541:793,548...800,271 JBrowse link
G Ppt1 palmitoyl-protein thioesterase 1 ISO (PMID:11722572) UniProtKB PMID:11722572 NCBI chrNW_004936474:21,881,692...21,906,564 JBrowse link
G Snapin SNAP associated protein ISO (MGI:MGI:4879078|PMID:20920792) MGI PMID:20920792 MGI:MGI:4879078 NCBI chrNW_004936580:3,449,585...3,464,709 JBrowse link
G Tmem199 transmembrane protein 199 ISO (PMID:28296633) UniProtKB PMID:28296633 NCBI chrNW_004936538:4,512,866...4,517,404 JBrowse link
G Tmem9 transmembrane protein 9 ISO (PMID:30374053) UniProt PMID:30374053 NCBI chrNW_004936567:3,232,628...3,250,596 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 chrNW_004936501:11,955,334...11,967,338 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 chrNW_004936864:117,510...119,612 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 ISO (PMID:15163665) BHF-UCL PMID:15163665 NCBI chrNW_004936559:7,177,887...7,312,660 JBrowse link
G Acp2 acid phosphatase 2, lysosomal ISO (MGI:MGI:894905|PMID:9228031)
(MGI:MGI:3522374|PMID:15604265)
MGI PMID:9228031, PMID:15604265 MGI:MGI:3522374, MGI:MGI:894905 NCBI chrNW_004936562:1,952,581...1,960,327 JBrowse link
G Aktip AKT interacting protein ISO (PMID:18799622) UniProtKB PMID:18799622 NCBI chrNW_004936475:6,139,875...6,150,132 JBrowse link
G Ap3b1 adaptor related protein complex 3 subunit beta 1 ISO (MGI:MGI:1330543|PMID:9931340), (MGI:MGI:6415001|PMID:30786955) MGI PMID:9931340, PMID:30786955 MGI:MGI:1330543, MGI:MGI:6415001 NCBI chrNW_004936549:5,964,240...6,205,245 JBrowse link
G Becn1 beclin 1 ISO (MGI:MGI:3801567|PMID:18497889) MGI PMID:18497889 MGI:MGI:3801567 NCBI chrNW_004936490:17,518,100...17,531,126 JBrowse link
G Chmp5 charged multivesicular body protein 5 ISO (MGI:MGI:3622513|PMID:16567502) MGI PMID:16567502 MGI:MGI:3622513 NCBI chrNW_004936524:1,804,643...1,820,491 JBrowse link
G Cln3 CLN3 lysosomal/endosomal transmembrane protein, battenin ISO (MGI:MGI:1343910|PMID:10440905)
(MGI:MGI:1337525|PMID:10191119), (MGI:MGI:1346962|PMID:10527801)
(MGI:MGI:3527911|PMID:15588329)
MGI PMID:10191119, PMID:10440905, PMID:10527801, PMID:15588329 MGI:MGI:1337525, MGI:MGI:1343910, MGI:MGI:1346962, MGI:MGI:3527911 NCBI chrNW_004936501:11,955,334...11,967,338 JBrowse link
G Cln5 CLN5 intracellular trafficking protein ISO (MGI:MGI:3512689|PMID:15459177) MGI PMID:15459177 MGI:MGI:3512689 NCBI chrNW_004936511:4,283,016...4,291,968 JBrowse link
G Cln6 CLN6 transmembrane ER protein ISO (MGI:MGI:1203267|PMID:9600738), (MGI:MGI:5751614|PMID:26681805) MGI PMID:9600738, PMID:26681805 MGI:MGI:1203267, MGI:MGI:5751614 NCBI chrNW_004936471:28,069,058...28,084,607 JBrowse link
G Cln8 CLN8 transmembrane ER and ERGIC protein ISO (MGI:MGI:1333651|PMID:10087069), (MGI:MGI:65559|PMID:8144516), (MGI:MGI:66707|PMID:8160780), (MGI:MGI:71226|PMID:7613514) MGI PMID:7613514, PMID:8144516, PMID:8160780, PMID:10087069 MGI:MGI:1333651, MGI:MGI:65559, MGI:MGI:66707, MGI:MGI:71226 NCBI chrNW_004936615:993,092...999,976 JBrowse link
G Clvs1 clavesin 1 ISO PMID:19651769 UniProt PMID:19651769 RGD:8553526 NCBI chrNW_004936496:11,814,627...12,008,233 JBrowse link
G Clvs2 clavesin 2 ISO PMID:19651769 UniProt PMID:19651769 RGD:8553526 NCBI chrNW_004936802:872,224...936,660 JBrowse link
G Fam160a2 family with sequence similarity 160 member A2 ISO (PMID:18799622) UniProtKB PMID:18799622 NCBI chrNW_004936842:280,718...306,311 JBrowse link
G Gaa glucosidase alpha, acid ISO (PMID:7717400)
(MGI:MGI:1275872|PMID:9668092), (MGI:MGI:3618942|PMID:15169761)
(MGI:MGI:1195358|PMID:9384603), (MGI:MGI:1346721|PMID:10547605), (MGI:MGI:2136118|PMID:11328962), (MGI:MGI:3664400|PMID:12115977)
BHF-UCL
MGI
PMID:7717400, PMID:9384603, PMID:9668092, PMID:10547605, PMID:11328962, PMID:12115977, PMID:15169761 MGI:MGI:1195358, MGI:MGI:1275872, MGI:MGI:1346721, MGI:MGI:2136118, MGI:MGI:3618942, MGI:MGI:3664400 NCBI chrNW_004936594:4,125,595...4,142,261 JBrowse link
G Gba glucosylceramidase beta ISO (PMID:27378698)
(MGI:MGI:5817293|PMID:27378698)
UniProt PMID:27378698 MGI:MGI:5817293 NCBI chrNW_004936580:4,715,869...4,720,752 JBrowse link
G Gnptab N-acetylglucosamine-1-phosphate transferase subunits alpha and beta ISO (PMID:21719679) UniProtKB PMID:21719679 NCBI chrNW_004936492:12,233,943...12,310,014 JBrowse link
G Grn granulin precursor ISO (MGI:MGI:6274951|PMID:27789271) UniProt PMID:27789271 MGI:MGI:6274951 NCBI chrNW_004936541:793,548...800,271 JBrowse link
G Hexa hexosaminidase subunit alpha ISO (MGI:MGI:77946|PMID:8747922)
(MGI:MGI:69059|PMID:7937929), (MGI:MGI:86923|PMID:9103204)
(MGI:MGI:1097747|PMID:9302266), (MGI:MGI:1271008|PMID:9645704), (MGI:MGI:1352198|PMID:10591619), (MGI:MGI:3033296|PMID:14972652)
(MGI:MGI:83770|PMID:8896570), (MGI:MGI:894634|PMID:9184660)
MGI PMID:7937929, PMID:8747922, PMID:8896570, PMID:9103204, PMID:9184660, PMID:9302266, PMID:9645704, PMID:10591619, PMID:14972652 MGI:MGI:1097747, MGI:MGI:1271008, MGI:MGI:1352198, MGI:MGI:3033296, MGI:MGI:69059, MGI:MGI:77946, MGI:MGI:83770, MGI:MGI:86923, MGI:MGI:894634 NCBI chrNW_004936471:31,712,485...31,738,273 JBrowse link
G Hexb hexosaminidase subunit beta ISO (MGI:MGI:1271008|PMID:9645704), (MGI:MGI:78473|PMID:8789434)
(MGI:MGI:83770|PMID:8896570), (MGI:MGI:894634|PMID:9184660)
MGI PMID:8789434, PMID:8896570, PMID:9184660, PMID:9645704 MGI:MGI:1271008, MGI:MGI:78473, MGI:MGI:83770, MGI:MGI:894634 NCBI chrNW_004936549:1,918,482...1,943,665 JBrowse link
G Hook1 hook microtubule tethering protein 1 ISO (PMID:18799622) UniProtKB PMID:18799622 NCBI chrNW_004936522:2,102,787...2,159,525 JBrowse link
G Hook2 hook microtubule tethering protein 2 ISO (PMID:18799622) UniProtKB PMID:18799622 NCBI chrNW_004936659:1,869,622...1,879,213 JBrowse link
G Hook3 hook microtubule tethering protein 3 ISO (PMID:18799622) UniProtKB PMID:18799622 NCBI chrNW_004937108:873...110,949 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 chrNW_004936636:1,407,666...1,430,683 JBrowse link
G Hps4 HPS4 biogenesis of lysosomal organelles complex 3 subunit 2 ISO (PMID:12663659) UniProtKB PMID:12663659 NCBI chrNW_004936657:1,075,300...1,104,328 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 chrNW_004936477:22,200,471...22,215,473 JBrowse link
G Lamtor1 late endosomal/lysosomal adaptor, MAPK and MTOR activator 1 ISO (MGI:MGI:4887551|PMID:19177150) UniProtKB PMID:19177150 MGI:MGI:4887551 NCBI chrNW_004936498:1,446,794...1,459,590 JBrowse link
G Lrrk2 leucine rich repeat kinase 2 ISO (PMID:25416817) ParkinsonsUK-UCL PMID:25416817 NCBI chrNW_004936607:628,469...761,117 JBrowse link
G Lyst lysosomal trafficking regulator ISO (MGI:MGI:1099544|PMID:9368050)
(MGI:MGI:53816|PMID:4697831), (MGI:MGI:53992|PMID:1113502), (MGI:MGI:55104|PMID:6170520), (MGI:MGI:56449|PMID:4031470)
MGI PMID:1113502, PMID:4031470, PMID:4697831, PMID:6170520, PMID:9368050 MGI:MGI:1099544, MGI:MGI:53816, MGI:MGI:53992, MGI:MGI:55104, MGI:MGI:56449 NCBI chrNW_004936484:16,750,976...16,915,999 JBrowse link
G Mbtps1 membrane bound transcription factor peptidase, site 1 ISO (PMID:21719679) UniProtKB PMID:21719679 NCBI chrNW_004936641:3,696,506...3,751,558 JBrowse link
G Mfsd8 major facilitator superfamily domain containing 8 ISO (MGI:MGI:5575728|PMID:24423645)
(MGI:MGI:5751614|PMID:26681805)
MGI PMID:24423645, PMID:26681805 MGI:MGI:5575728, MGI:MGI:5751614 NCBI chrNW_004936642:2,745,889...2,833,286 JBrowse link
G Mtor mechanistic target of rapamycin kinase ISO (PMID:22692423) UniProt PMID:22692423 NCBI chrNW_004936474:158,376...282,310 JBrowse link
G Myo7a myosin VIIA ISO (PMID:16001398) UniProtKB PMID:16001398 NCBI chrNW_004936498:5,758,572...5,824,526 JBrowse link
G Naglu N-acetyl-alpha-glucosaminidase ISO (MGI:MGI:3769195|PMID:17712420) MGI PMID:17712420 MGI:MGI:3769195 NCBI chrNW_004936490:17,305,033...17,312,167 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 chrNW_004936474:21,881,692...21,906,564 JBrowse link
G Snapin SNAP associated protein ISO (MGI:MGI:4879078|PMID:20920792) MGI PMID:20920792 MGI:MGI:4879078 NCBI chrNW_004936580:3,449,585...3,464,709 JBrowse link
G Spg11 SPG11 vesicle trafficking associated, spatacsin ISO (MGI:MGI:5749311|PMID:26284655) MGI PMID:26284655 MGI:MGI:5749311 NCBI chrNW_004936471:7,540,647...7,618,783 JBrowse link
G Tfeb transcription factor EB ISO (PMID:23434374)
(PMID:22692423)
UniProtKB
UniProt
PMID:22692423, PMID:23434374 NCBI chrNW_004936476:18,189,096...18,233,622 JBrowse link
G Tmem106b transmembrane protein 106B ISO (MGI:MGI:5588048|PMID:25066864) MGI PMID:25066864 MGI:MGI:5588048 NCBI chrNW_004936761:1,663,099...1,689,580 JBrowse link
G Tpcn2 two pore segment channel 2 ISO (PMID:25416817) ParkinsonsUK-UCL PMID:25416817 NCBI chrNW_004936599:1,301,937...1,343,046 JBrowse link
G Tpp1 tripeptidyl peptidase 1 ISO (MGI:MGI:3522013|PMID:15483130) MGI PMID:15483130 MGI:MGI:3522013 NCBI chrNW_004936842:669,869...676,706 JBrowse link
G Vps18 VPS18 core subunit of CORVET and HOPS complexes ISO (PMID:18799622) UniProtKB PMID:18799622 NCBI chrNW_004936471:4,289,487...4,297,634 JBrowse link
G Vps35 VPS35 retromer complex component ISO (MGI:MGI:5694519|PMID:26203154) ParkinsonsUK-UCL PMID:26203154 MGI:MGI:5694519 NCBI chrNW_004936475:50,476...77,797 JBrowse link
G Washc5 WASH complex subunit 5 ISO (MGI:MGI:6199426|PMID:30061306) MGI PMID:30061306 MGI:MGI:6199426 NCBI chrNW_004936470:22,667,354...22,725,538 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 chrNW_004936490:17,518,100...17,531,126 JBrowse link
phagolysosome assembly term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Coro1a coronin 1A ISO (PMID:12132654) UniProtKB PMID:12132654 NCBI chrNW_004936501:12,338,542...12,344,236 JBrowse link
G Myo7a myosin VIIA ISO (MGI:MGI:2662763|PMID:12743369) MGI PMID:12743369 MGI:MGI:2662763 NCBI chrNW_004936498:5,758,572...5,824,526 JBrowse link
G P2rx7 purinergic receptor P2X 7 ISO (MGI:MGI:3699774|PMID:11544318) MGI PMID:11544318 MGI:MGI:3699774 NCBI chrNW_004936558:3,106,819...3,149,689 JBrowse link
G Srpx sushi repeat containing protein X-linked ISO (MGI:MGI:3852261|PMID:19368996) MGI PMID:19368996 MGI:MGI:3852261 NCBI chrNW_004936502:5,010,692...5,107,221 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 ISO (MGI:MGI:5698740|PMID:26450516) UniProt PMID:26450516 MGI:MGI:5698740 NCBI chrNW_004936501:11,955,334...11,967,338 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 ISO (MGI:MGI:5698740|PMID:26450516) UniProt PMID:26450516 MGI:MGI:5698740 NCBI chrNW_004936501:11,955,334...11,967,338 JBrowse link
G Pikfyve phosphoinositide kinase, FYVE-type zinc finger containing ISO (PMID:28779020)
(MGI:MGI:6103777|PMID:28779020)
UniProt PMID:28779020 MGI:MGI:6103777 NCBI chrNW_004936950:242,071...323,204 JBrowse link
G Pla2g5 phospholipase A2 group V ISO (MGI:MGI:3841317|PMID:19342668) UniProt PMID:19342668 MGI:MGI:3841317 NCBI chrNW_004936474:6,131,915...6,150,810 JBrowse link
G Rab20 RAB20, member RAS oncogene family ISO (PMID:21255211) UniProtKB PMID:21255211 NCBI chrNW_004936472:2,234,826...2,264,613 JBrowse link
G Rab34 RAB34, member RAS oncogene family ISO (PMID:21255211)
(MGI:MGI:5467668|PMID:23197834)
UniProtKB
ParkinsonsUK-UCL
PMID:21255211, PMID:23197834 MGI:MGI:5467668 NCBI chrNW_004936538:4,923,740...4,928,798 JBrowse link
G Rab39a RAB39A, member RAS oncogene family ISO (PMID:21255211) UniProtKB PMID:21255211 NCBI chrNW_004936551:750,940...778,432 JBrowse link
G Rab7a RAB7A, member RAS oncogene family ISO (PMID:21255211) UniProtKB PMID:21255211 NCBI chrNW_004936798:297,600...304,929 JBrowse link
G Syt7 synaptotagmin 7 ISO (MGI:MGI:3690533|PMID:16982801) UniProtKB PMID:16982801 MGI:MGI:3690533 NCBI chrNW_004936581:1,516,199...1,557,992 JBrowse link
G Tmem175 transmembrane protein 175 ISO (MGI:MGI:5693670|PMID:26317472) UniProtKB PMID:26317472 MGI:MGI:5693670 NCBI chrNW_004936477:22,239,093...22,254,028 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 ISO (MGI:MGI:5749311|PMID:26284655) MGI PMID:26284655 MGI:MGI:5749311 NCBI chrNW_004936471:7,540,647...7,618,783 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 chrNW_004936542:7,577,192...7,581,598 JBrowse link
G Mt3 metallothionein 3 ISO (MGI:MGI:4881636|PMID:20544854) UniProtKB PMID:20544854 MGI:MGI:4881636 NCBI chrNW_004936475:8,864,512...8,866,516 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 ISO (MGI:MGI:5905514|PMID:28073925)
(PMID:28073925)
UniProt PMID:28073925 MGI:MGI:5905514 NCBI chrNW_004936541:793,548...800,271 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 ISO (PMID:22012985) ParkinsonsUK-UCL PMID:22012985 NCBI chrNW_004936607:628,469...761,117 JBrowse link
G Tasl TLR adaptor interacting with endolysosomal SLC15A4 ISO (PMID:31001245) UniProt PMID:31001245 NCBI chrNW_004936553:6,628,131...6,629,027 JBrowse link
G Tmem165 transmembrane protein 165 ISO (PMID:23569283) UniProtKB PMID:23569283 NCBI chrNW_004936482:17,760,532...17,785,466 JBrowse link
G Tmem175 transmembrane protein 175 ISO (MGI:MGI:5693670|PMID:26317472) UniProtKB PMID:26317472 MGI:MGI:5693670 NCBI chrNW_004936477:22,239,093...22,254,028 JBrowse link
G Vps33a VPS33A core subunit of CORVET and HOPS complexes ISO (PMID:28013294) UniProtKB PMID:28013294 NCBI chrNW_004936558:2,227,305...2,257,725 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 ISO (PMID:26280656) UniProtKB PMID:26280656 NCBI chrNW_004936470:44,917,462...44,981,773 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 ISO (PMID:26280656) UniProtKB PMID:26280656 NCBI chrNW_004936470:44,917,462...44,981,773 JBrowse link
G Trex1 three prime repair exonuclease 1 ISO (MGI:MGI:5460923|PMID:23160154) MGI PMID:23160154 MGI:MGI:5460923 NCBI chrNW_004936529:264,535...266,451 JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 11962
    cellular process 11135
      cellular component organization or biogenesis 4887
        cellular component organization 4809
          organelle organization 2971
            vacuole organization 147
              lytic vacuole organization 66
                lysosome organization + 66
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.