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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: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
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
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 15442
      cellular component organization or biogenesis 6021
        cellular component organization 5852
          organelle organization 3698
            vacuole organization 179
              lytic vacuole organization 71
                lysosome organization + 71
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.