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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 IEA Ensembl GO_REF:0000107 NCBI chr11:60,761,669...60,869,753
Ensembl chr11:60,761,655...60,890,496
JBrowse link
G ACP2 acid phosphatase 2, lysosomal IEA
IBA
(PMID:21873635) Ensembl
GO_Central
PMID:21873635 GO_REF:0000107 NCBI chr18:42,346,207...42,356,447
Ensembl chr18:42,345,608...42,354,352
JBrowse link
G ACP3 acid phosphatase 3 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr23:29,294,641...29,353,970
Ensembl chr23:29,294,843...29,343,499
JBrowse link
G ACP4 acid phosphatase 4 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 1:106,051,901...106,056,137
Ensembl chr 1:106,051,901...106,056,137
JBrowse link
G AKTIP AKT interacting protein IEA Ensembl GO_REF:0000107 NCBI chr 2:62,253,005...62,263,918
Ensembl chr 2:62,254,320...62,263,337
JBrowse link
G AP3B1 adaptor related protein complex 3 subunit beta 1 IEA Ensembl GO_REF:0000107 NCBI chr 3:28,481,974...28,748,095
Ensembl chr 3:28,481,038...28,751,258
JBrowse link
G BECN1 beclin 1 ISO (MGI:MGI:3801567|PMID:18497889) MGI PMID:18497889 MGI:MGI:3801567 NCBI chr 9:20,204,203...20,215,081
Ensembl chr 9:20,204,220...20,214,236
JBrowse link
G CHMP5 charged multivesicular body protein 5 IEA Ensembl GO_REF:0000107 NCBI chr11:50,363,488...50,376,081 JBrowse link
G CLN3 CLN3 lysosomal/endosomal transmembrane protein, battenin IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 6:18,252,543...18,266,033
Ensembl chr 6:18,254,139...18,266,033
JBrowse link
G CLN5 CLN5 intracellular trafficking protein IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr22:30,568,572...30,575,890
Ensembl chr22:30,568,572...30,575,890
JBrowse link
G CLN6 CLN6 transmembrane ER protein IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr30:32,246,394...32,264,251
Ensembl chr30:32,246,411...32,264,240
JBrowse link
G CLN8 CLN8 transmembrane ER and ERGIC protein IEA Ensembl GO_REF:0000107 NCBI chr37:30,863,098...30,885,831
Ensembl chr37:30,867,479...30,884,895
JBrowse link
G CLVS1 clavesin 1 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr29:11,638,550...11,811,853
Ensembl chr29:11,638,024...11,812,396
JBrowse link
G CLVS2 clavesin 2 IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 1:62,217,473...62,286,853
Ensembl chr 1:62,217,837...62,282,449
JBrowse link
G FAM160A2 family with sequence similarity 160 member A2 IEA Ensembl GO_REF:0000107 NCBI chr21:29,547,361...29,570,900
Ensembl chr21:29,547,522...29,566,536
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 chr 9:1,601,092...1,615,582
Ensembl chr 9:1,601,121...1,656,597
JBrowse link
G GBA glucosylceramidase beta IEA Ensembl GO_REF:0000107 NCBI chr 7:42,317,704...42,322,285
Ensembl chr 7:42,317,862...42,322,864
JBrowse link
G GNPTAB N-acetylglucosamine-1-phosphate transferase subunits alpha and beta IEA Ensembl GO_REF:0000107 NCBI chr15:40,659,108...40,724,498
Ensembl chr15:40,631,279...40,704,365
JBrowse link
G GRN granulin precursor ISO (MGI:MGI:6274951|PMID:27789271) UniProt PMID:27789271 MGI:MGI:6274951 NCBI chr 9:19,077,430...19,085,443
Ensembl chr 9:19,077,427...19,082,268
JBrowse link
G HEXA hexosaminidase subunit alpha IEA Ensembl GO_REF:0000107 NCBI chr30:35,836,788...35,862,525 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 chr 2:57,221,809...57,248,432
Ensembl chr 2:57,222,186...57,248,417
JBrowse link
G HOOK1 hook microtubule tethering protein 1 IEA Ensembl GO_REF:0000107 NCBI chr 5:49,994,930...50,060,513
Ensembl chr 5:49,998,241...50,060,525
JBrowse link
G HOOK2 hook microtubule tethering protein 2 IEA Ensembl GO_REF:0000107 NCBI chr20:49,367,450...49,383,109
Ensembl chr20:49,367,876...49,382,813
JBrowse link
G HOOK3 hook microtubule tethering protein 3 IEA Ensembl GO_REF:0000107 NCBI chr16:22,791,198...22,940,168
Ensembl chr16:22,784,267...22,901,991
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 chr28:11,547,457...11,572,248
Ensembl chr28:11,547,741...11,571,613
JBrowse link
G HPS4 HPS4 biogenesis of lysosomal organelles complex 3 subunit 2 IEA Ensembl GO_REF:0000107 NCBI chr26:20,131,658...20,157,532
Ensembl chr26:19,933,281...20,157,058
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 3:91,517,225...91,534,593
Ensembl chr 3:91,522,035...91,534,593
JBrowse link
G LAMTOR1 late endosomal/lysosomal adaptor, MAPK and MTOR activator 1 IEA Ensembl
InterPro
GO_REF:0000002, GO_REF:0000107 NCBI chr21:25,981,170...25,986,942
Ensembl chr21:25,981,254...25,996,432
JBrowse link
G LRRK2 leucine rich repeat kinase 2 ISO (PMID:25416817) ParkinsonsUK-UCL PMID:25416817 NCBI chr27:13,282,824...13,420,917
Ensembl chr27:13,283,756...13,420,870
JBrowse link
G LYST lysosomal trafficking regulator IEA InterPro GO_REF:0000002 NCBI chr 4:4,106,869...4,296,042
Ensembl chr 4:4,089,837...4,294,593
JBrowse link
G MBTPS1 membrane bound transcription factor peptidase, site 1 IEA Ensembl GO_REF:0000107 NCBI chr 5:68,228,176...68,281,175
Ensembl chr 5:68,228,238...68,280,515
JBrowse link
G MFSD8 major facilitator superfamily domain containing 8 IEA Ensembl GO_REF:0000107 NCBI chr19:12,905,336...13,030,901
Ensembl chr19:12,982,394...13,020,083
JBrowse link
G MTOR mechanistic target of rapamycin kinase IEA Ensembl GO_REF:0000107 NCBI chr 2:84,818,893...84,939,283
Ensembl chr 2:84,787,708...84,939,114
JBrowse link
G MYO7A myosin VIIA ISO (PMID:16001398) UniProtKB PMID:16001398 NCBI chr21:21,539,735...21,624,063
Ensembl chr21:21,539,785...21,624,279
JBrowse link
G NAGLU N-acetyl-alpha-glucosaminidase IEA Ensembl GO_REF:0000107 NCBI chr 9:20,407,296...20,414,094
Ensembl chr 9:20,407,281...20,414,056
JBrowse link
G PPT1 palmitoyl-protein thioesterase 1 ISO (MGI:MGI:3654230|PMID:16542649)
(MGI:MGI:3612221|PMID:16368712)
MGI PMID:16368712, PMID:16542649 MGI:MGI:3612221, MGI:MGI:3654230 NCBI chr15:2,815,428...2,886,474
Ensembl chr15:2,859,979...2,894,425
JBrowse link
G SNAPIN SNAP associated protein IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 7:43,410,554...43,411,929
Ensembl chr 7:43,410,998...43,412,323
JBrowse link
G SPG11 SPG11 vesicle trafficking associated, spatacsin ISO (MGI:MGI:5749311|PMID:26284655) MGI PMID:26284655 MGI:MGI:5749311 NCBI chr30:11,233,709...11,305,454
Ensembl chr30:11,233,718...11,305,485
JBrowse link
G SYCP3 synaptonemal complex protein 3 IEA Ensembl GO_REF:0000107 NCBI chr15:40,630,976...40,641,398
Ensembl chr15:40,631,279...40,704,365
JBrowse link
G TFEB transcription factor EB ISO (PMID:23434374)
(PMID:22692423)
UniProtKB
UniProt
PMID:22692423, PMID:23434374 NCBI chr12:10,367,979...10,423,478
Ensembl chr12:10,368,599...10,452,619
JBrowse link
G TMEM106B transmembrane protein 106B IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr14:27,140,692...27,166,652
Ensembl chr14:27,140,687...27,161,333
JBrowse link
G TPCN2 two pore segment channel 2 ISO (PMID:25416817) ParkinsonsUK-UCL PMID:25416817 NCBI chr18:48,956,833...48,984,499
Ensembl chr18:48,957,249...48,984,564
JBrowse link
G TPP1 tripeptidyl peptidase 1 IEA Ensembl GO_REF:0000107 NCBI chr21:29,921,764...29,926,974
Ensembl chr21:29,921,764...29,926,986
JBrowse link
G VPS18 VPS18 core subunit of CORVET and HOPS complexes IBA
IEA
(PMID:21873635) GO_Central
Ensembl
PMID:21873635 GO_REF:0000107 NCBI chr30:8,027,877...8,036,773
Ensembl chr30:8,027,128...8,036,153
JBrowse link
G VPS35 VPS35 retromer complex component IEA Ensembl GO_REF:0000107 NCBI chr15:8,428,073...8,454,601
Ensembl chr15:8,428,172...8,454,049
JBrowse link
G WASHC5 WASH complex subunit 5 IEA Ensembl GO_REF:0000107 NCBI chr13:23,019,422...23,078,073
Ensembl chr13:23,019,636...23,078,280
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 IEA Ensembl GO_REF:0000107 NCBI chr  X:35,050,588...35,073,633
Ensembl chr  X:35,050,606...35,073,067
JBrowse link
G CCDC115 coiled-coil domain containing 115 IEA Ensembl GO_REF:0000107 NCBI chr25:19,027,014...19,031,467
Ensembl chr25:19,027,342...19,030,887
JBrowse link
G CLN3 CLN3 lysosomal/endosomal transmembrane protein, battenin ISS
IBA
(PMID:21873635) UniProtKB
GO_Central
PMID:21873635 GO_REF:0000024 NCBI chr 6:18,252,543...18,266,033
Ensembl chr 6:18,254,139...18,266,033
JBrowse link
G CLN5 CLN5 intracellular trafficking protein ISS UniProtKB GO_REF:0000024 NCBI chr22:30,568,572...30,575,890
Ensembl chr22:30,568,572...30,575,890
JBrowse link
G CLN6 CLN6 transmembrane ER protein ISS
IEA
UniProtKB
Ensembl
GO_REF:0000024, GO_REF:0000107 NCBI chr30:32,246,394...32,264,251
Ensembl chr30:32,246,411...32,264,240
JBrowse link
G GRN granulin precursor IEA Ensembl GO_REF:0000107 NCBI chr 9:19,077,430...19,085,443
Ensembl chr 9:19,077,427...19,082,268
JBrowse link
G PPT1 palmitoyl-protein thioesterase 1 ISO (PMID:11722572) UniProtKB PMID:11722572 NCBI chr15:2,815,428...2,886,474
Ensembl chr15:2,859,979...2,894,425
JBrowse link
G SNAPIN SNAP associated protein IEA Ensembl GO_REF:0000107 NCBI chr 7:43,410,554...43,411,929
Ensembl chr 7:43,410,998...43,412,323
JBrowse link
G TMEM199 transmembrane protein 199 IEA Ensembl GO_REF:0000107 NCBI chr 9:42,607,688...42,614,776
Ensembl chr 9:42,607,733...42,611,445
JBrowse link
G TMEM9 transmembrane protein 9 ISO (PMID:30374053) UniProt PMID:30374053 NCBI chr 7:2,069,017...2,087,961 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 ISS UniProtKB GO_REF:0000024 NCBI chr 6:18,252,543...18,266,033
Ensembl chr 6:18,254,139...18,266,033
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 chr14:835,476...836,424
Ensembl chr14:835,476...836,424
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 chr 9:20,204,203...20,215,081
Ensembl chr 9:20,204,220...20,214,236
JBrowse link
phagolysosome assembly term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CORO1A coronin 1A IEA Ensembl
InterPro
GO_REF:0000002, GO_REF:0000107 NCBI chr 6:18,161,850...18,167,915
Ensembl chr 6:18,160,601...18,167,818
JBrowse link
G MYO7A myosin VIIA IEA Ensembl GO_REF:0000107 NCBI chr21:21,539,735...21,624,063
Ensembl chr21:21,539,785...21,624,279
JBrowse link
G P2RX7 purinergic receptor P2X 7 IEA Ensembl GO_REF:0000107 NCBI chr26:7,928,863...7,983,956
Ensembl chr26:7,940,985...7,983,740
JBrowse link
G SRPX sushi repeat containing protein X-linked ISO (MGI:MGI:3852261|PMID:19368996) MGI PMID:19368996 MGI:MGI:3852261 NCBI chr  X:32,905,380...33,017,642
Ensembl chr  X:32,745,020...33,330,841
JBrowse link
phagolysosome assembly involved in apoptotic cell clearance term browser
Symbol Object Name 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 docking term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G CLN3 CLN3 lysosomal/endosomal transmembrane protein, battenin ISS
IEA
UniProt
Ensembl
GO_REF:0000024, GO_REF:0000107 NCBI chr 6:18,252,543...18,266,033
Ensembl chr 6:18,254,139...18,266,033
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
ISS
Ensembl
UniProt
GO_REF:0000024, GO_REF:0000107 NCBI chr 6:18,252,543...18,266,033
Ensembl chr 6:18,254,139...18,266,033
JBrowse link
G PIKFYVE phosphoinositide kinase, FYVE-type zinc finger containing IEA Ensembl GO_REF:0000107 NCBI chr37:16,537,095...16,620,427
Ensembl chr37:16,541,562...16,619,554
JBrowse link
G PLA2G5 phospholipase A2 group V ISO (MGI:MGI:3841317|PMID:19342668) UniProt PMID:19342668 MGI:MGI:3841317 NCBI chr 2:78,762,851...78,781,642
Ensembl chr 2:78,762,852...78,781,983
JBrowse link
G RAB20 RAB20, member RAS oncogene family IEA Ensembl GO_REF:0000107 NCBI chr22:58,825,147...58,853,921
Ensembl chr22:58,825,667...58,853,667
JBrowse link
G RAB34 RAB34, member RAS oncogene family IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr 9:42,909,843...42,913,935
Ensembl chr 9:42,910,011...42,913,985
JBrowse link
G RAB39A RAB39A, member RAS oncogene family IEA Ensembl GO_REF:0000107 NCBI chr 5:24,516,541...24,546,743
Ensembl chr 5:24,519,240...24,546,606
JBrowse link
G RAB7A RAB7A, member RAS oncogene family ISS
IBA
(PMID:21873635) UniProtKB
GO_Central
PMID:21873635 GO_REF:0000024 NCBI chr20:2,704,716...2,776,518
Ensembl chr20:2,704,752...2,826,636
JBrowse link
G RAB7B RAB7B, member RAS oncogene family IBA (PMID:21873635) GO_Central PMID:21873635 NCBI chr38:2,333,939...2,359,531
Ensembl chr38:2,335,535...2,359,469
JBrowse link
G SYT7 synaptotagmin 7 IEA Ensembl GO_REF:0000107 NCBI chr18:54,863,072...54,926,121
Ensembl chr18:54,861,754...54,921,367
JBrowse link
G TMEM175 transmembrane protein 175 IEA Ensembl GO_REF:0000107 NCBI chr 3:91,554,001...91,576,845
Ensembl chr 3:91,553,778...91,670,930
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 chr30:11,233,709...11,305,454
Ensembl chr30:11,233,718...11,305,485
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 5:11,292,219...11,296,851
Ensembl chr 5:11,292,262...11,296,797
JBrowse link
G MT3 metallothionein 3 IEA Ensembl GO_REF:0000107 Ensembl chr 2:59,624,849...59,626,424 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 chr 9:19,077,430...19,085,443
Ensembl chr 9:19,077,427...19,082,268
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 chr27:13,282,824...13,420,917
Ensembl chr27:13,283,756...13,420,870
JBrowse link
G TASL TLR adaptor interacting with endolysosomal SLC15A4 ISO (PMID:31001245) UniProt PMID:31001245 NCBI chr  X:25,664,361...25,679,044 JBrowse link
G TMEM165 transmembrane protein 165 IEA Ensembl GO_REF:0000107 NCBI chr13:47,658,408...47,683,519
Ensembl chr13:47,658,330...47,682,866
JBrowse link
G TMEM175 transmembrane protein 175 IEA Ensembl GO_REF:0000107 NCBI chr 3:91,554,001...91,576,845
Ensembl chr 3:91,553,778...91,670,930
JBrowse link
G VPS33A VPS33A core subunit of CORVET and HOPS complexes ISO (PMID:28013294) UniProtKB PMID:28013294 NCBI chr26:7,090,669...7,119,913 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 chr13:41,134...127,399
Ensembl chr13:41,121...127,182
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 chr13:41,134...127,399
Ensembl chr13:41,121...127,182
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

Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 16162
    cellular process 15439
      cellular component organization or biogenesis 6022
        cellular component organization 5853
          organelle organization 3700
            vacuole organization 179
              lytic vacuole organization 71
                lysosome organization 71
                  lysosomal membrane organization + 4
                  negative regulation of lysosome organization 1
                  phagolysosome assembly + 16
                  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.