KEGG   PATHWAY: xla04142
Entry
xla04142                    Pathway                                
Name
Lysosome - Xenopus laevis (African clawed frog)
Description
Lysosomes are membrane-delimited organelles in animal cells serving as the cell's main digestive compartment to which all sorts of macromolecules are delivered for degradation. They contain more than 40 hydrolases in an acidic environment (pH of about 5). After synthesis in the ER, lysosomal enzymes are decorated with mannose-6-phosphate residues, which are recognized by mannose-6-phosphate receptors in the trans-Golgi network. They are packaged into clathrin-coated vesicles and are transported to late endosomes. Substances for digestion are acquired by the lysosomes via a series of processes including endocytosis, phagocytosis, and autophagy.
Class
Cellular Processes; Transport and catabolism
Pathway map
xla04142  Lysosome
xla04142

Other DBs
GO: 0005764
Organism
Xenopus laevis (African clawed frog) [GN:xla]
Gene
100036800  cd63l.L; uncharacterized protein LOC100036800 [KO:K06497]
100036849  ap1b1.S; adaptor related protein complex 1 subunit beta 1 S homeolog [KO:K12392]
100036898  arsa.2.L; LOW QUALITY PROTEIN: arylsulfatase A [KO:K01134] [EC:3.1.6.8]
100036949  ctsh.L; cathepsin H [KO:K01368] [EC:3.4.22.27]
100036952  ppt1.S; palmitoyl-protein thioesterase 1 isoform X1 [KO:K01074] [EC:3.1.2.22]
100037210  ppt1.L; palmitoyl-protein thioesterase 1 L homeolog precursor [KO:K01074] [EC:3.1.2.22]
100127265  ctsk.L; cathepsin K L homeolog precursor [KO:K01371] [EC:3.4.22.38]
100158266  hexb.L; beta-hexosaminidase subunit beta isoform X1 [KO:K12373] [EC:3.2.1.52]
100158274  acp2.S; lysosomal acid phosphatase S homeolog precursor [KO:K14410] [EC:3.1.3.2]
100158281  sort1.S; sortilin 1 S homeolog precursor [KO:K12388]
100158286  cln5.L; ceroid-lipofuscinosis neuronal protein 5 [KO:K12390]
100158325  laptm4b.L; uncharacterized protein LOC100158325 [KO:K12387]
100158341  slc17a5.S; solute carrier family 17 member 5 S homeolog [KO:K12301]
100158367  glb1l.L; galactosidase beta 1 like L homeolog precursor [KO:K12309] [EC:3.2.1.23]
100337508  hyal2.L; hyaluronidase 2 L homeolog precursor [KO:K01197] [EC:3.2.1.35]
100337617  atp6ap1.1.L; ATPase, H+ transporting, lysosomal accessory protein 1, gene 1 L homeolog precursor [KO:K03662]
100380957  ap3d1.S; AP-3 complex subunit delta-1 [KO:K12396]
108695292  atp6v1h.S; V-type proton ATPase subunit H [KO:K02144]
108695399  laptm4b.S; lysosomal-associated transmembrane protein 4B [KO:K12387]
108695792  [KO:K10532] [EC:2.3.1.78]
108696325  tcirg1.L; V-type proton ATPase 116 kDa subunit a3 [KO:K02154]
108696664  [KO:K01319] [EC:3.4.21.20]
108698079  atp6ap1.2.L; V-type proton ATPase subunit S1 [KO:K03662]
108698149  abca2.L; ATP-binding cassette sub-family A member 2 isoform X1 [KO:K05642]
108698425  ids.L; iduronate 2-sulfatase [KO:K01136] [EC:3.1.6.13]
108699062  [KO:K01368] [EC:3.4.22.27]
108699063  [KO:K01368] [EC:3.4.22.27]
108699249  ctso.L; cathepsin O isoform X1 [KO:K01374] [EC:3.4.22.42]
108699333  [KO:K01368] [EC:3.4.22.27]
108699334  [KO:K01368] [EC:3.4.22.27]
108699348  [KO:K01371] [EC:3.4.22.38]
108699349  [KO:K01371] [EC:3.4.22.38]
108699410  [KO:K01368] [EC:3.4.22.27]
108699819  lgmn.S; legumain [KO:K01369] [EC:3.4.22.34]
108700331  [KO:K01368] [EC:3.4.22.27]
108700332  [KO:K01368] [EC:3.4.22.27]
108700335  [KO:K01368] [EC:3.4.22.27]
108700336  [KO:K01368] [EC:3.4.22.27]
108700337  [KO:K01371] [EC:3.4.22.38]
108701202  [KO:K12381] [EC:3.1.6.-]
108701517  litafd.L; LITAF domain-containing protein [KO:K19363]
108701526  litaf.L; lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog [KO:K19363]
108702456  atp6v0a1.S; V-type proton ATPase 116 kDa subunit a1 isoform X1 [KO:K02154]
108702815  gga3.S; ADP-ribosylation factor-binding protein GGA3 isoform X1 [KO:K12404]
108703100  litafd.S; LITAF domain-containing protein [KO:K19363]
108703175  atp6v0c.S; V-type proton ATPase 16 kDa proteolipid subunit [KO:K02155]
108703274  [KO:K12316] [EC:3.2.1.20]
108703509  ap1s1.S; AP-1 complex subunit sigma-1A isoform X1 [KO:K12394]
108704163  slc17a5.L; sialin [KO:K12301]
108704291  [KO:K01444] [EC:3.5.1.26]
108705351  [KO:K12373] [EC:3.2.1.52]
108705472  [KO:K08569] [EC:3.4.22.-]
108705476  ctsw.L; cathepsin W [KO:K08569] [EC:3.4.22.-]
108707022  ap1g2.S; AP-1 complex subunit gamma-1 isoform X1 [KO:K12391]
108707079  [KO:K12387]
108707125  cltcl1.S; clathrin heavy chain 1 isoform X1 [KO:K04646]
108707330  wdr7.S; WD repeat-containing protein 7 isoform X2 [KO:K24738]
108707923  ap1s2.L; AP-1 complex subunit sigma-2 isoform X1 [KO:K12394]
108708030  nagpa.L; N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase [KO:K01125] [EC:3.1.4.45]
108708166  ap4b1.L; AP-4 complex subunit beta-1 isoform X1 [KO:K12401]
108708220  laptm5.L; lysosomal-associated transmembrane protein 5 isoform X1 [KO:K12387]
108708332  gusb.L; beta-glucuronidase isoform X1 [KO:K01195] [EC:3.2.1.31]
108708604  slc11a2.L; natural resistance-associated macrophage protein 2 isoform X4 [KO:K21398]
108708792  smpd1.L; sphingomyelin phosphodiesterase [KO:K12350] [EC:3.1.4.12]
108708997  slc11a2.S; natural resistance-associated macrophage protein 2 isoform X1 [KO:K21398]
108709563  laptm5.S; lysosomal-associated transmembrane protein 5 isoform X1 [KO:K12387]
108709605  cltc.S; clathrin heavy chain 1 isoform X4 [KO:K04646]
108709643  gusb.S; beta-glucuronidase isoform X1 [KO:K01195] [EC:3.2.1.31]
108710023  ctsc.S; dipeptidyl peptidase 1 [KO:K01275] [EC:3.4.14.1]
108710286  [KO:K12397]
108711016  gnptab.L; N-acetylglucosamine-1-phosphotransferase subunits alpha/beta [KO:K08239] [EC:2.7.8.17]
108711078  gns.L; N-acetylglucosamine-6-sulfatase isoform X1 [KO:K01137] [EC:3.1.6.14]
108711150  hyal4.L; hyaluronidase-1 [KO:K01197] [EC:3.2.1.35]
108711337  [KO:K01365] [EC:3.4.22.15]
108711393  dmxl2.L; dmX-like protein 2 isoform X1 [KO:K24155]
108711630  ap3m2.L; AP-3 complex subunit mu-2 [KO:K12398]
108711713  man2b1.L; lysosomal alpha-mannosidase [KO:K12311] [EC:3.2.1.24]
108712227  hgsnat.L; heparan-alpha-glucosaminide N-acetyltransferase isoform X1 [KO:K10532] [EC:2.3.1.78]
108712381  [KO:K12393]
108712486  [KO:K01382] [EC:3.4.23.34]
108712507  [KO:K12393]
108712719  entpd4.S; ectonucleoside triphosphate diphosphohydrolase 4 isoform X1 [KO:K12305] [EC:3.6.1.6]
108712874  ap3d1.L; AP-3 complex subunit delta-1 [KO:K12396]
108712915  dmxl2.S; dmX-like protein 2 isoform X1 [KO:K24155]
108712917  ap4e1.S; AP-4 complex subunit epsilon-1 [KO:K12400]
108712967  [KO:K12397]
108713209  gnptab.S; N-acetylglucosamine-1-phosphotransferase subunits alpha/beta [KO:K08239] [EC:2.7.8.17]
108713957  ctsf.L; cathepsin F [KO:K01373] [EC:3.4.22.41]
108713973  pla2g15.L; phospholipase A2 group XV isoform X4 [KO:K06129] [EC:3.1.1.5]
108714554  gga1.L; ADP-ribosylation factor-binding protein GGA1 [KO:K12404]
108714598  hyal1.L; hyaluronidase-1 [KO:K01197] [EC:3.2.1.35]
108715409  ap1b1.L; AP-1 complex subunit beta-1 [KO:K12392]
108715415  ap1g1.S; AP-1 complex subunit gamma-1 isoform X1 [KO:K12391]
108715496  dnase2b.S; deoxyribonuclease-2-beta [KO:K01158] [EC:3.1.22.1]
108715574  atp6v0b.S; V-type proton ATPase 21 kDa proteolipid subunit [KO:K03661]
108716047  cltcl1.L; clathrin heavy chain 1 isoform X1 [KO:K04646]
108716355  [KO:K06562]
108716525  naglu.L; alpha-N-acetylglucosaminidase [KO:K01205] [EC:3.2.1.50]
108716527  atp6v0a2.L; V-type proton ATPase 116 kDa subunit a2 [KO:K02154]
108716664  igf2r.L; cation-independent mannose-6-phosphate receptor [KO:K06564]
108716685  abcb9.L; ATP-binding cassette sub-family B member 9 isoform X1 [KO:K05656]
108716764  ncoa7.L; nuclear receptor coactivator 7 isoform X1 [KO:K25442]
108716811  [KO:K01134] [EC:3.1.6.8]
108716837  [KO:K06546]
108716938  XB5954440.L; major facilitator superfamily domain-containing protein 8-like [KO:K12307]
108717084  [KO:K12395]
108717339  dmxl1.L; dmX-like protein 1 isoform X4 [KO:K24155]
108717342  [KO:K12399]
108717994  arsb.L; arylsulfatase B [KO:K01135] [EC:3.1.6.12]
108718085  [KO:K06562]
108719222  npc1.L; NPC intracellular cholesterol transporter 1 [KO:K12385]
113939961  [KO:K01365] [EC:3.4.22.15]
373572  ctse.L; cathepsin E-A precursor [KO:K01382] [EC:3.4.23.34]
373573  ctse.S; cathepsin E-B precursor [KO:K01382] [EC:3.4.23.34]
379225  ap1g2.L; adaptor related protein complex 1 subunit gamma 2 L homeolog [KO:K12391]
379257  ctsb.S; cathepsin B precursor [KO:K01363] [EC:3.4.22.1]
379512  psap.S; uncharacterized protein LOC379512 precursor [KO:K12382]
379601  lgmn.L; legumain L homeolog precursor [KO:K01369] [EC:3.4.22.34]
379689  ppt2.L; lysosomal thioesterase PPT2-A precursor [KO:K01074] [EC:3.1.2.22]
379798  scarb2.L; scavenger receptor class B member 2 L homeolog [KO:K12384]
379829  ap3s1.S; adaptor related protein complex 3 subunit sigma 1 S homeolog [KO:K12399]
379892  atp6v0d1.L; ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d1 L homeolog [KO:K02146]
379953  gns.S; glucosamine (N-acetyl)-6-sulfatase S homeolog [KO:K01137] [EC:3.1.6.14]
379986  atp6v0a1.L; V-type proton ATPase 116 kDa subunit a1 isoform X1 [KO:K02154]
380102  ctsb.L; uncharacterized protein LOC380102 precursor [KO:K01363] [EC:3.4.22.1]
380203  ctsc.L; cathepsin C L homeolog precursor [KO:K01275] [EC:3.4.14.1]
380212  cd63.S; CD63 molecule S homeolog [KO:K06497]
380470  hyal2.S; hyaluronidase 2 S homeolog precursor [KO:K01197] [EC:3.2.1.35]
380516  ctss.L; cathepsin S precursor [KO:K01368] [EC:3.4.22.27]
380564  m6pr.L; mannose-6-phosphate receptor (cation dependent) L homeolog precursor [KO:K10089]
398013  atp6ap1.2.S; ATPase, H+ transporting, lysosomal accessory protein 1, gene 2 S homeolog precursor [KO:K03662]
398285  spam1.L; sperm adhesion molecule 1 (PH-20 hyaluronidase, zona pellucida binding) L homeolog [KO:K01197] [EC:3.2.1.35]
398555  cd63.L; CD63 molecule L homeolog [KO:K06497]
398647  atp6v0c.L; ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c L homeolog [KO:K02155]
398801  fuca2.L; alpha-L-fucosidase 2 L homeolog precursor [KO:K01206] [EC:3.2.1.51]
398897  atp6v0a4.L; ATPase H+ transporting V0 subunit a4 L homeolog [KO:K02154]
398898  cltb.L; clathrin, light chain B L homeolog [KO:K04645]
398927  [KO:K01368] [EC:3.4.22.27]
398947  npc2.S; uncharacterized protein LOC398947 precursor [KO:K13443]
398994  napsa.L; napsin A aspartic peptidase L homeolog precursor [KO:K01379] [EC:3.4.23.5]
399079  ap1s1.L; adaptor related protein complex 1 subunit sigma 1 L homeolog [KO:K12394]
399225  fuca1.S; tissue alpha-L-fucosidase [KO:K01206] [EC:3.2.1.51]
399243  ap1g1.L; adaptor related protein complex 1 gamma 1 subunit [KO:K12391]
414505  tpp1.L; tripeptidyl peptidase I L homeolog precursor [KO:K01279] [EC:3.4.14.9]
414558  npc2.L; uncharacterized protein LOC414558 precursor [KO:K13443]
431937  ctns.L; cystinosin, lysosomal cystine transporter L homeolog precursor [KO:K12386]
431991  ap1m2.S; uncharacterized protein LOC431991 [KO:K12393]
432087  fuca1.L; alpha-L-fucosidase 1 L homeolog precursor [KO:K01206] [EC:3.2.1.51]
432187  ctsz.L; uncharacterized protein LOC432187 precursor [KO:K08568] [EC:3.4.18.1]
432261  sumf1.L; formylglycine-generating enzyme [KO:K13444] [EC:1.8.3.7]
432322  acp5.S; acid phosphatase 5, tartrate resistant S homeolog precursor [KO:K14379] [EC:3.1.3.2]
443592  naga.S; N-acetylgalactosaminidase, alpha- S homeolog precursor [KO:K01204] [EC:3.2.1.49]
443609  ap1s3.S; adaptor related protein complex 1 subunit sigma 3 S homeolog [KO:K12395]
443661  XB5914295.S; cathepsin S isoform X1 [KO:K01368] [EC:3.4.22.27]
443663  ap3b2.S; AP-3 complex subunit beta-1 isoform X1 [KO:K12397]
443721  ctsd.S; cathepsin D precursor [KO:K01379] [EC:3.4.23.5]
443722  [KO:K01368] [EC:3.4.22.27]
443724  ap3b1.L; adaptor related protein complex 3 subunit beta 1 L homeolog [KO:K12397]
443753  naga.L; alpha-N-acetylgalactosaminidase [KO:K01204] [EC:3.2.1.49]
443829  [KO:K01379] [EC:3.4.23.5]
444026  gga1.S; ADP-ribosylation factor-binding protein GGA1 isoform X1 [KO:K12404]
444062  mfsd8.L; major facilitator superfamily domain-containing protein 8 [KO:K12307]
444090  acp2.l; lysosomal acid phosphatase L homeolog [KO:K14410] [EC:3.1.3.2]
444113  mcoln1.L; mucolipin TRP cation channel 1 L homeolog [KO:K04992]
444163  ctsl.L; cathepsin L L homeolog [KO:K01365] [EC:3.4.22.15]
444201  laptm4a.S; lysosomal-associated protein transmembrane 4 alpha S homeolog [KO:K12387]
444228  ppt2l.L; lysosomal thioesterase PPT2-B precursor [KO:K01074] [EC:3.1.2.22]
444287  cltc.L; clathrin, heavy chain (Hc) L homeolog [KO:K04646]
444356  acp5.L; acid phosphatase 5, tartrate resistant L homeolog precursor [KO:K14379] [EC:3.1.3.2]
444511  neu1.L; neuraminidase 1 (lysosomal sialidase) L homeolog [KO:K01186] [EC:3.2.1.18]
444713  gm2a.S; GM2 ganglioside activator S homeolog precursor [KO:K12383]
446283  gnptg.L; N-acetylglucosamine-1-phosphate transferase subunit gamma L homeolog precursor [KO:K10087]
446498  cln3.L; ceroid-lipofuscinosis, neuronal 3 L homeolog [KO:K12389]
446505  ctss.S; cathepsin S [KO:K01368] [EC:3.4.22.27]
446506  dnase2.L; deoxyribonuclease II, lysosomal L homeolog precursor [KO:K01158] [EC:3.1.22.1]
446523  cltb.S; clathrin, light chain B S homeolog [KO:K04645]
446550  ap4m1.S; adaptor related protein complex 4 subunit mu 1 S homeolog [KO:K12402]
446554  meak7.L; MTOR-associated protein MEAK7 [KO:K27947]
446701  ap1m2.L; adaptor related protein complex 1 subunit mu 2 L homeolog [KO:K12393]
446866  idua.L; alpha-L-iduronidase L homeolog [KO:K01217] [EC:3.2.1.76]
446877  lamp1.L; lysosomal-associated membrane protein 1 L homeolog precursor [KO:K06528]
446948  galc.L; galactocerebrosidase isoform X2 [KO:K01202] [EC:3.2.1.46]
447024  manba.L; mannosidase, beta A, lysosomal L homeolog [KO:K01192] [EC:3.2.1.25]
447203  lamp1.S; lysosomal-associated membrane protein 1 S homeolog precursor [KO:K06528]
447252  arsa.1.S; arylsulfatase A [KO:K01134] [EC:3.1.6.8]
447313  ctsv.L; cathepsin L2 precursor [KO:K01365] [EC:3.4.22.15]
447327  asah1.L; N-acylsphingosine amidohydrolase (acid ceramidase) 1 L homeolog precursor [KO:K12348] [EC:3.5.1.23]
447436  psap.L; prosaposin (variant Gaucher disease and variant metachromatic leukodystrophy) L homeolog precursor [KO:K12382]
447489  atp6v0d2.L; ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d2 L homeolog [KO:K02146]
447565  atp6v0b.L; ATPase, H+ transporting, lysosomal 21kDa, V0 subunit b L homeolog [KO:K03661]
447570  gba.L; lysosomal acid glucosylceramidase [KO:K01201] [EC:3.2.1.45]
447742  lamp2.S; lysosome-associated membrane glycoprotein 2 precursor [KO:K06528]
494699  slc11a1.L; solute carrier family 11 member 1 L homeolog [KO:K12347]
494800  ctsz.S; cathepsin Z precursor [KO:K08568] [EC:3.4.18.1]
494802  gzmh.S; granzyme H S homeolog precursor [KO:K01319] [EC:3.4.21.20]
494810  ctsa.L; cathepsin A L homeolog precursor [KO:K13289] [EC:3.4.16.5]
494858  [KO:K12387]
495077  scarb2.S; uncharacterized protein LOC495077 [KO:K12384]
495089  atp6ap1.1.S; ATPase, H+ transporting, lysosomal accessory protein 1, gene 1 S homeolog [KO:K03662]
495185  ap1s2.S; adaptor related protein complex 1 subunit sigma 2 S homeolog [KO:K12394]
495239  galns.L; galactosamine (N-acetyl)-6-sulfatase L homeolog precursor [KO:K01132] [EC:3.1.6.4]
495422  entpd4.L; ectonucleoside triphosphate diphosphohydrolase 4 L homeolog [KO:K12305] [EC:3.6.1.6]
495504  sgsh.L; N-sulphoglucosamine sulphohydrolase [KO:K01565] [EC:3.10.1.1]
496032  laptm4a.L; lysosomal-associated protein transmembrane 4 alpha L homeolog [KO:K12387]
496052  ap3m2.S; adaptor related protein complex 3 subunit mu 2 S homeolog [KO:K12398]
496207  m6pr.S; mannose-6-phosphate receptor (cation dependent) S homeolog [KO:K10089]
496244  ap3s2.S; adaptor related protein complex 3 subunit sigma 2 S homeolog [KO:K12399]
496249  aga.L; aspartylglucosaminidase L homeolog precursor [KO:K01444] [EC:3.5.1.26]
733384  lamp2.L; lysosome-associated membrane glycoprotein 2 isoform X2 [KO:K06528]
734359  atp6v1h.L; ATPase, H+ transporting, lysosomal 50/57kDa, V1 subunit H L homeolog [KO:K02144]
734389  clta.S; clathrin light chain A S homeolog [KO:K04644]
734415  pla2g15.S; phospholipase A2 group XV S homeolog [KO:K06129] [EC:3.1.1.5]
734471  MGC115291; uncharacterized protein LOC734471 [KO:K04992]
734499  ap1m1.S; adaptor related protein complex 1 subunit mu 1 S homeolog [KO:K12393]
734749  gla.S; galactosidase alpha S homeolog precursor [KO:K01189] [EC:3.2.1.22]
734759  lipa.L; lysosomal acid lipase/cholesteryl ester hydrolase precursor [KO:K01052] [EC:3.1.1.13]
734760  ap4s1.L; adaptor related protein complex 4, sigma 1 subunit L homeolog [KO:K12403]
734870  litaf.S; lipopolysaccharide-induced TNF factor S homeolog [KO:K19363]
779153  gm2a.L; GM2 ganglioside activator L homeolog precursor [KO:K12383]
779405  clta.L; clathrin light chain A L homeolog [KO:K04644]
Compound
C00002  ATP
C00008  ADP
C00159  D-Mannose
C00275  D-Mannose 6-phosphate
Reference
  Authors
Eskelinen EL, Tanaka Y, Saftig P
  Title
At the acidic edge: emerging functions for lysosomal membrane proteins.
  Journal
Trends Cell Biol 13:137-45 (2003)
DOI:10.1016/S0962-8924(03)00005-9
Reference
PMID:1883197
  Authors
Neufeld EF
  Title
Lysosomal storage diseases.
  Journal
Annu Rev Biochem 60:257-80 (1991)
DOI:10.1146/annurev.bi.60.070191.001353
Reference
PMID:2943218
  Authors
von Figura K, Hasilik A
  Title
Lysosomal enzymes and their receptors.
  Journal
Annu Rev Biochem 55:167-93 (1986)
DOI:10.1146/annurev.bi.55.070186.001123
Reference
  Authors
Janvier K, Bonifacino JS
  Title
Role of the endocytic machinery in the sorting of lysosome-associated membrane proteins.
  Journal
Mol Biol Cell 16:4231-42 (2005)
DOI:10.1091/mbc.E05-03-0213
Reference
  Authors
Vergarajauregui S, Puertollano R
  Title
Mucolipidosis type IV: the importance of functional lysosomes for efficient autophagy.
  Journal
Autophagy 4:832-4 (2008)
DOI:10.4161/auto.6567
Reference
  Authors
Jaskolka MC, Winkley SR, Kane PM
  Title
RAVE and Rabconnectin-3 Complexes as Signal Dependent Regulators of Organelle Acidification.
  Journal
Front Cell Dev Biol 9:698190 (2021)
DOI:10.3389/fcell.2021.698190
Reference
  Authors
Majdoul S, Compton AA
  Title
Lessons in self-defence: inhibition of virus entry by intrinsic immunity.
  Journal
Nat Rev Immunol 10.1038/s41577-021-00626-8 (2021)
DOI:10.1038/s41577-021-00626-8
Related
pathway
xla00511  Other glycan degradation
xla00531  Glycosaminoglycan degradation
xla04130  SNARE interactions in vesicular transport
xla04140  Autophagy - animal
xla04144  Endocytosis
KO pathway
ko04142   

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