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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 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
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
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 15756
      cellular component organization or biogenesis 5964
        cellular component organization 5795
          organelle organization 3644
            vacuole organization 175
              lytic vacuole organization 70
                lysosome organization 70
                  lysosomal membrane organization + 4
                  negative regulation of lysosome organization 1
                  phagolysosome assembly + 15
                  positive regulation of lysosome organization 1
                  regulation of lysosomal lumen pH + 16
                  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.