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ONTOLOGY REPORT - ANNOTATIONS


Term:lysosome organization
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Accession:GO:0007040 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 lysosome. A lysosome is a cytoplasmic, membrane-bounded organelle that is found in most animal cells and that contains a variety of hydrolases.
Synonyms:exact_synonym: lysosome organisation
 related_synonym: lysosome organization and biogenesis


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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_004955419:21,553,863...21,681,626 JBrowse link
G Acp2 acid phosphatase 2, lysosomal ISO (MGI:MGI:3522374|PMID:15604265)
(MGI:MGI:894905|PMID:9228031)
MGI PMID:9228031, PMID:15604265 MGI:MGI:3522374, MGI:MGI:894905 NCBI chrNW_004955422:954,108...961,522 JBrowse link
G Aktip AKT interacting protein ISO (PMID:18799622) UniProtKB PMID:18799622 NCBI chrNW_004955433:11,237,717...11,248,638 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_004955425:22,792,616...23,051,509 JBrowse link
G Becn1 beclin 1 ISO (MGI:MGI:3801567|PMID:18497889) MGI PMID:18497889 MGI:MGI:3801567 NCBI chrNW_004955451:16,616,595...16,625,731 JBrowse link
G Cln3 CLN3 lysosomal/endosomal transmembrane protein, battenin ISO (MGI:MGI:1337525|PMID:10191119), (MGI:MGI:1346962|PMID:10527801)
(MGI:MGI:3527911|PMID:15588329)
(MGI:MGI:1343910|PMID:10440905)
MGI PMID:10191119, PMID:10440905, PMID:10527801, PMID:15588329 MGI:MGI:1337525, MGI:MGI:1343910, MGI:MGI:1346962, MGI:MGI:3527911 NCBI chrNW_004955493:6,696,520...6,707,849 JBrowse link
G Cln5 CLN5 intracellular trafficking protein ISO (MGI:MGI:3512689|PMID:15459177) MGI PMID:15459177 MGI:MGI:3512689 NCBI chrNW_004955404:30,229,632...30,235,677 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_004955450:7,876,572...7,885,305 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_004955403:57,926,711...57,938,698 JBrowse link
G Clvs1 clavesin 1 ISO PMID:19651769 UniProt PMID:19651769 RGD:8553526 NCBI chrNW_004955444:17,319,905...17,515,397 JBrowse link
G Clvs2 clavesin 2 ISO PMID:19651769 UniProt PMID:19651769 RGD:8553526 NCBI chrNW_004955436:4,758,749...4,823,383 JBrowse link
G Fam160a2 family with sequence similarity 160 member A2 ISO (PMID:18799622) UniProtKB PMID:18799622 NCBI chrNW_004955414:21,954,103...21,977,877 JBrowse link
G Gaa glucosidase alpha, acid ISO (PMID:7717400)
(MGI:MGI:1195358|PMID:9384603), (MGI:MGI:1346721|PMID:10547605), (MGI:MGI:2136118|PMID:11328962), (MGI:MGI:3664400|PMID:12115977)
(MGI:MGI:1275872|PMID:9668092), (MGI:MGI:3618942|PMID:15169761)
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_004955506:2,764,959...2,783,231 JBrowse link
G Gba glucosylceramidase beta ISO (PMID:27378698)
(MGI:MGI:5817293|PMID:27378698)
UniProt PMID:27378698 MGI:MGI:5817293 NCBI chrNW_004955545:1,682,097...1,689,373 JBrowse link
G Gnptab N-acetylglucosamine-1-phosphate transferase subunits alpha and beta ISO (PMID:21719679) UniProtKB PMID:21719679 NCBI chrNW_004955405:37,107,902...37,136,993 JBrowse link
G Grn granulin precursor ISO (MGI:MGI:6274951|PMID:27789271) UniProt PMID:27789271 MGI:MGI:6274951 NCBI chrNW_004955451:17,368,600...17,371,981 JBrowse link
G Hexa hexosaminidase subunit alpha ISO (MGI:MGI:83770|PMID:8896570), (MGI:MGI:894634|PMID:9184660)
(MGI:MGI:1097747|PMID:9302266), (MGI:MGI:1271008|PMID:9645704), (MGI:MGI:1352198|PMID:10591619), (MGI:MGI:3033296|PMID:14972652)
(MGI:MGI:77946|PMID:8747922)
(MGI:MGI:69059|PMID:7937929), (MGI:MGI:86923|PMID:9103204)
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_004955450:4,790,342...4,806,862 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_004955425:25,942,341...25,961,312 JBrowse link
G Hook1 hook microtubule tethering protein 1 ISO (PMID:18799622) UniProtKB PMID:18799622 NCBI chrNW_004955464:47,895...129,414 JBrowse link
G Hook2 hook microtubule tethering protein 2 ISO (PMID:18799622) UniProtKB PMID:18799622 NCBI chrNW_004955415:31,855,183...31,865,413 JBrowse link
G Hook3 hook microtubule tethering protein 3 ISO (PMID:18799622) UniProtKB PMID:18799622 NCBI chrNW_004955457:13,149,013...13,249,524 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_004955507:4,408,428...4,433,219 JBrowse link
G Hps4 HPS4 biogenesis of lysosomal organelles complex 3 subunit 2 ISO (PMID:12663659) UniProtKB PMID:12663659 NCBI chrNW_004955455:1,048,946...1,076,097 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_004955514:474,830...488,007 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_004955414:19,228,615...19,235,523 JBrowse link
G Lrrk2 leucine rich repeat kinase 2 ISO (PMID:25416817) ParkinsonsUK-UCL PMID:25416817 NCBI chrNW_004955505:84,324...216,923 JBrowse link
G Lyst lysosomal trafficking regulator ISO (MGI:MGI:53816|PMID:4697831), (MGI:MGI:53992|PMID:1113502), (MGI:MGI:55104|PMID:6170520), (MGI:MGI:56449|PMID:4031470)
(MGI:MGI:1099544|PMID:9368050)
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_004955492:4,161,976...4,371,637 JBrowse link
G Mbtps1 membrane bound transcription factor peptidase, site 1 ISO (PMID:21719679) UniProtKB PMID:21719679 NCBI chrNW_004955564:176,230...226,555 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_004955428:13,519,285...13,548,007 JBrowse link
G Mtor mechanistic target of rapamycin kinase ISO (PMID:22692423) UniProt PMID:22692423 NCBI chrNW_004955486:2,487,642...2,599,694 JBrowse link
G Myo7a myosin VIIA ISO (PMID:16001398) UniProtKB PMID:16001398 NCBI chrNW_004955414:14,576,356...14,647,500 JBrowse link
G Naglu N-acetyl-alpha-glucosaminidase ISO (MGI:MGI:3769195|PMID:17712420) MGI PMID:17712420 MGI:MGI:3769195 NCBI chrNW_004955451:16,445,338...16,449,243 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_004955452:17,518,345...17,549,112 JBrowse link
G Snapin SNAP associated protein ISO (MGI:MGI:4879078|PMID:20920792) MGI PMID:20920792 MGI:MGI:4879078 NCBI chrNW_004955545:306,546...308,229 JBrowse link
G Spg11 SPG11 vesicle trafficking associated, spatacsin ISO (MGI:MGI:5749311|PMID:26284655) MGI PMID:26284655 MGI:MGI:5749311 NCBI chrNW_004955416:11,084,448...11,168,478 JBrowse link
G Tfeb transcription factor EB ISO (PMID:23434374)
(PMID:22692423)
UniProtKB
UniProt
PMID:22692423, PMID:23434374 NCBI chrNW_004955437:8,102,241...8,141,001 JBrowse link
G Tmem106b transmembrane protein 106B ISO (MGI:MGI:5588048|PMID:25066864) MGI PMID:25066864 MGI:MGI:5588048 NCBI chrNW_004955432:18,619,418...18,644,876 JBrowse link
G Tpcn2 two pore segment channel 2 ISO (PMID:25416817) ParkinsonsUK-UCL PMID:25416817 NCBI chrNW_004955422:16,899,730...16,923,962 JBrowse link
G Tpp1 tripeptidyl peptidase 1 ISO (MGI:MGI:3522013|PMID:15483130) MGI PMID:15483130 MGI:MGI:3522013 NCBI chrNW_004955414:22,324,847...22,330,912 JBrowse link
G Vps18 VPS18 core subunit of CORVET and HOPS complexes ISO (PMID:18799622) UniProtKB PMID:18799622 NCBI chrNW_004955416:7,772,653...7,780,408 JBrowse link
G Vps35 VPS35 retromer complex component ISO (MGI:MGI:5694519|PMID:26203154) ParkinsonsUK-UCL PMID:26203154 MGI:MGI:5694519 NCBI chrNW_004955448:207,582...240,264 JBrowse link
G Washc5 WASH complex subunit 5 ISO (MGI:MGI:6199426|PMID:30061306) MGI PMID:30061306 MGI:MGI:6199426 NCBI chrNW_004955461:145,993...199,274 JBrowse link
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_004955565:2,006,154...2,029,921 JBrowse link
G Ccdc115 coiled-coil domain containing 115 ISO (PMID:28296633) UniProtKB PMID:28296633 NCBI chrNW_004955459:25,649...30,215 JBrowse link
G Cln3 CLN3 lysosomal/endosomal transmembrane protein, battenin ISO (PMID:11722572) UniProtKB PMID:11722572 NCBI chrNW_004955493:6,696,520...6,707,849 JBrowse link
G Cln5 CLN5 intracellular trafficking protein ISO (PMID:11722572) UniProtKB PMID:11722572 NCBI chrNW_004955404:30,229,632...30,235,677 JBrowse link
G Cln6 CLN6 transmembrane ER protein ISO (PMID:11722572) UniProtKB PMID:11722572 NCBI chrNW_004955450:7,876,572...7,885,305 JBrowse link
G Grn granulin precursor ISO (PMID:28073925) UniProt PMID:28073925 NCBI chrNW_004955451:17,368,600...17,371,981 JBrowse link
G Ppt1 palmitoyl-protein thioesterase 1 ISO (PMID:11722572) UniProtKB PMID:11722572 NCBI chrNW_004955452:17,518,345...17,549,112 JBrowse link
G Snapin SNAP associated protein ISO (MGI:MGI:4879078|PMID:20920792) MGI PMID:20920792 MGI:MGI:4879078 NCBI chrNW_004955545:306,546...308,229 JBrowse link
G Tmem199 transmembrane protein 199 ISO (PMID:28296633) UniProtKB PMID:28296633 NCBI chrNW_004955481:4,772,394...4,776,524 JBrowse link
G Tmem9 transmembrane protein 9 ISO (PMID:30374053) UniProt PMID:30374053 NCBI chrNW_004955406:37,279,885...37,299,196 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_004955493:6,696,520...6,707,849 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_004955581:319,942...335,112 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_004955451:16,616,595...16,625,731 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_004955493:6,815,148...6,820,295 JBrowse link
G Myo7a myosin VIIA ISO (MGI:MGI:2662763|PMID:12743369) MGI PMID:12743369 MGI:MGI:2662763 NCBI chrNW_004955414:14,576,356...14,647,500 JBrowse link
G P2rx7 purinergic receptor P2X 7 ISO (MGI:MGI:3699774|PMID:11544318) MGI PMID:11544318 MGI:MGI:3699774 NCBI chrNW_004955482:7,048,674...7,087,525 JBrowse link
G Srpx sushi repeat containing protein X-linked ISO (MGI:MGI:3852261|PMID:19368996) MGI PMID:19368996 MGI:MGI:3852261 NCBI chrNW_004955601:286,092...364,235 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_004955493:6,696,520...6,707,849 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_004955493:6,696,520...6,707,849 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_004955457:6,749,226...6,841,855 JBrowse link
G Pla2g5 phospholipase A2 group V ISO (MGI:MGI:3841317|PMID:19342668) UniProt PMID:19342668 MGI:MGI:3841317 NCBI chrNW_004955452:662,281...721,507 JBrowse link
G Rab20 RAB20, member RAS oncogene family ISO (PMID:21255211) UniProtKB PMID:21255211 NCBI chrNW_004955404:2,087,580...2,088,545 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_004955481:4,441,290...4,445,969 JBrowse link
G Rab39a RAB39A, member RAS oncogene family ISO (PMID:21255211) UniProtKB PMID:21255211 NCBI chrNW_004955412:10,224,074...10,240,270 JBrowse link
G Rab7a RAB7A, member RAS oncogene family ISO (PMID:21255211) UniProtKB PMID:21255211 NCBI chrNW_004955429:15,103,792...15,167,498 JBrowse link
G Syt7 synaptotagmin 7 ISO (MGI:MGI:3690533|PMID:16982801) UniProtKB PMID:16982801 MGI:MGI:3690533 NCBI chrNW_004955511:6,051,392...6,093,651 JBrowse link
G Tmem175 transmembrane protein 175 ISO (MGI:MGI:5693670|PMID:26317472) UniProtKB PMID:26317472 MGI:MGI:5693670 NCBI chrNW_004955514:434,283...453,239 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_004955416:11,084,448...11,168,478 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_004955412:23,863,513...23,867,984 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_004955451:17,368,600...17,371,981 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_004955505:84,324...216,923 JBrowse link
G Tasl TLR adaptor interacting with endolysosomal SLC15A4 ISO (PMID:31001245) UniProt PMID:31001245 NCBI chrNW_004955531:207,614...293,127 JBrowse link
G Tmem165 transmembrane protein 165 ISO (PMID:23569283) UniProtKB PMID:23569283 NCBI chrNW_004955447:15,538,958...15,543,885 JBrowse link
G Tmem175 transmembrane protein 175 ISO (MGI:MGI:5693670|PMID:26317472) UniProtKB PMID:26317472 MGI:MGI:5693670 NCBI chrNW_004955514:434,283...453,239 JBrowse link
G Vps33a VPS33A core subunit of CORVET and HOPS complexes ISO (PMID:28013294) UniProtKB PMID:28013294 NCBI chrNW_004955482:6,333,282...6,352,369 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_004955417:13,574,493...13,625,669 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_004955417:13,574,493...13,625,669 JBrowse link
G Trex1 three prime repair exonuclease 1 ISO (MGI:MGI:5460923|PMID:23160154) MGI PMID:23160154 MGI:MGI:5460923 NCBI chrNW_004955532:533,877...535,767 JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 11860
    cellular process 11055
      cellular component organization or biogenesis 4837
        cellular component organization 4757
          organelle organization 2937
            vacuole organization 143
              lytic vacuole organization 64
                lysosome organization 64
                  lysosomal membrane organization + 3
                  negative regulation of lysosome organization 1
                  phagolysosome assembly + 14
                  positive regulation of lysosome organization 1
                  regulation of lysosomal lumen pH + 15
                  regulation of lysosome organization + 4
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.