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UniProtKB - Q5ST30 (SYVM_HUMAN)

Protein

Valine--tRNA ligase, mitochondrial

Gene

VARS2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Catalytic activityi

ATP + L-valine + tRNA(Val) = AMP + diphosphate + L-valyl-tRNA(Val).

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei661ATPBy similarity1

GO - Molecular functioni

  • aminoacyl-tRNA editing activity Source: InterPro
  • ATP binding Source: UniProtKB-KW
  • valine-tRNA ligase activity Source: GO_Central
View the complete GO annotation on QuickGO ...

GO - Biological processi

View the complete GO annotation on QuickGO ...

Keywordsi

Molecular functionAminoacyl-tRNA synthetase, Ligase
Biological processProtein biosynthesis
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

ReactomeiR-HSA-379726 Mitochondrial tRNA aminoacylation

Names & Taxonomyi

Protein namesi
Recommended name:
Valine--tRNA ligase, mitochondrial (EC:6.1.1.9)
Alternative name(s):
Valyl-tRNA synthetase
Short name:
ValRS
Valyl-tRNA synthetase-like
Gene namesi
Name:VARS2
Synonyms:KIAA1885, VARS2L, VARSL
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

EuPathDBiHostDB:ENSG00000137411.16
HGNCiHGNC:21642 VARS2
MIMi612802 gene
neXtProtiNX_Q5ST30

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Mitochondrion

Pathology & Biotechi

Involvement in diseasei

Combined oxidative phosphorylation deficiency 20 (COXPD20)2 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA disorder due to mitochondrial respiratory chain complex defects. Clinical features are variable and include muscle weakness with hypotonia, central neurological disease with progressive external ophthalmoplegia, ptosis and ataxia, delayed psychomotor development, cardiomyopathy, abnormal liver function, facial dysmorphism, microcephaly and epilepsy.
See also OMIM:615917
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_071850337T → I in COXPD20; decreased levels of the protein. 1 PublicationCorresponds to variant dbSNP:rs587777585Ensembl.1
Natural variantiVAR_071851349A → T in COXPD20. 1 PublicationCorresponds to variant dbSNP:rs587777583Ensembl.1
Natural variantiVAR_071852596A → D in COXPD20. 1 PublicationCorresponds to variant dbSNP:rs587777584Ensembl.1

Keywords - Diseasei

Disease mutation, Primary mitochondrial disease

Organism-specific databases

DisGeNETi57176
MalaCardsiVARS2
MIMi615917 phenotype
OpenTargetsiENSG00000137411
Orphaneti420728 Combined oxidative phosphorylation defect type 20
PharmGKBiPA164742816

Polymorphism and mutation databases

BioMutaiVARS2
DMDMi296452917

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 26MitochondrionSequence analysisAdd BLAST26
ChainiPRO_000033800027 – 1063Valine--tRNA ligase, mitochondrialAdd BLAST1037

Proteomic databases

EPDiQ5ST30
MaxQBiQ5ST30
PaxDbiQ5ST30
PeptideAtlasiQ5ST30
PRIDEiQ5ST30
ProteomicsDBi63892
63893 [Q5ST30-2]

PTM databases

iPTMnetiQ5ST30
PhosphoSitePlusiQ5ST30

Expressioni

Gene expression databases

BgeeiENSG00000137411 Expressed in 198 organ(s), highest expression level in right hemisphere of cerebellum
CleanExiHS_VARS2
ExpressionAtlasiQ5ST30 baseline and differential
GenevisibleiQ5ST30 HS

Organism-specific databases

HPAiHPA062449
HPA070267

Interactioni

Binary interactionsi

Protein-protein interaction databases

BioGridi121426, 11 interactors
IntActiQ5ST30, 13 interactors
MINTiQ5ST30
STRINGi9606.ENSP00000441000

Structurei

3D structure databases

ProteinModelPortaliQ5ST30
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi146 – 156"HIGH" regionAdd BLAST11
Motifi658 – 662"KMSKS" region5

Sequence similaritiesi

Belongs to the class-I aminoacyl-tRNA synthetase family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiKOG0432 Eukaryota
COG0525 LUCA
GeneTreeiENSGT00550000074727
HOVERGENiHBG017878
InParanoidiQ5ST30
KOiK01873
OMAiRQWYIRN
OrthoDBiEOG091G01XH
PhylomeDBiQ5ST30
TreeFamiTF354250

Family and domain databases

CDDicd07962 Anticodon_Ia_Val, 1 hit
Gene3Di3.40.50.620, 2 hits
3.90.740.10, 2 hits
InterProiView protein in InterPro
IPR001412 aa-tRNA-synth_I_CS
IPR002300 aa-tRNA-synth_Ia
IPR033705 Anticodon_Ia_Val
IPR013155 M/V/L/I-tRNA-synth_anticd-bd
IPR014729 Rossmann-like_a/b/a_fold
IPR009080 tRNAsynth_Ia_anticodon-bd
IPR009008 Val/Leu/Ile-tRNA-synth_edit
IPR002303 Valyl-tRNA_ligase
PfamiView protein in Pfam
PF08264 Anticodon_1, 1 hit
PF00133 tRNA-synt_1, 1 hit
PRINTSiPR00986 TRNASYNTHVAL
SUPFAMiSSF47323 SSF47323, 1 hit
SSF50677 SSF50677, 1 hit
TIGRFAMsiTIGR00422 valS, 1 hit
PROSITEiView protein in PROSITE
PS00178 AA_TRNA_LIGASE_I, 1 hit

Sequences (4+)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 4 described isoforms and 8 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: Q5ST30-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MPHLPLASFR PPFWGLRHSR GLPRFHSVST QSEPHGSPIS RRNREAKQKR 
        60         70         80         90        100
LREKQATLEA EIAGESKSPA ESIKAWRPKE LVLYEIPTKP GEKKDVSGPL 
       110        120        130        140        150
PPAYSPRYVE AAWYPWWVRE GFFKPEYQAR LPQATGETFS MCIPPPNVTG 
       160        170        180        190        200
SLHIGHALTV AIQDALVRWH RMRGDQVLWV PGSDHAGIAT QAVVEKQLWK 
       210        220        230        240        250
ERGVRRHELS REAFLREVWQ WKEAKGGEIC EQLRALGASL DWDRECFTMD 
       260        270        280        290        300
VGSSVAVTEA FVRLYKAGLL YRNHQLVNWS CALRSAISDI EVENRPLPGH 
       310        320        330        340        350
TQLRLPGCPT PVSFGLLFSV AFPVDGEPDA EVVVGTTRPE TLPGDVAVAV 
       360        370        380        390        400
HPDDSRYTHL HGRQLRHPLM GQPLPLITDY AVQPHVGTGA VKVTPAHSPA 
       410        420        430        440        450
DAEMGARHGL SPLNVIAEDG TMTSLCGDWL QGLHRFVARE KIMSVLSEWG 
       460        470        480        490        500
LFRGLQNHPM VLPICSRSGD VIEYLLKNQW FVRCQEMGAR AAKAVESGAL 
       510        520        530        540        550
ELSPSFHQKN WQHWFSHIGD WCVSRQLWWG HQIPAYLVVE DHAQGEEDCW 
       560        570        580        590        600
VVGRSEAEAR EVAAELTGRP GAELTLERDP DVLDTWFSSA LFPFSALGWP 
       610        620        630        640        650
QETPDLARFY PLSLLETGSD LLLFWVGRMV MLGTQLTGQL PFSKVLLHPM 
       660        670        680        690        700
VRDRQGRKMS KSLGNVLDPR DIISGVEMQV LQEKLRSGNL DPAELAIVAA 
       710        720        730        740        750
AQKKDFPHGI PECGTDALRF TLCSHGVQAG DLHLSVSEVQ SCRHFCNKIW 
       760        770        780        790        800
NALRFILNAL GEKFVPQPAE ELSPSSPMDA WILSRLALAA QECERGFLTR 
       810        820        830        840        850
ELSLVTHALH HFWLHNLCDV YLEAVKPVLW HSPRPLGPPQ VLFSCADLGL 
       860        870        880        890        900
RLLAPLMPFL AEELWQRLPP RPGCPPAPSI SVAPYPSACS LEHWRQPELE 
       910        920        930        940        950
RRFSRVQEVV QVLRALRATY QLTKARPRVL LQSSEPGDQG LFEAFLEPLG 
       960        970        980        990       1000
TLGYCGAVGL LPPGAAAPSG WAQAPLSDTA QVYMELQGLV DPQIQLPLLA 
      1010       1020       1030       1040       1050
ARRYKLQKQL DSLTARTPSE GEAGTQRQQK LSSLQLELSK LDKAASHLRQ 
      1060 
LMDEPPAPGS PEL
Length:1,063
Mass (Da):118,490
Last modified:May 18, 2010 - v2
Checksum:i0212C6361A87DF8B
GO
Isoform 2 (identifier: Q5ST30-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-644: MPHLPLASFR...QLTGQLPFSK → MVFFCPVPLF...PPLLTPPCPQ

Note: No experimental confirmation available.
Show »
Length:501
Mass (Da):55,078
Checksum:i6F274961A95460AF
GO
Isoform 3 (identifier: Q5ST30-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-140: Missing.

Note: No experimental confirmation available.
Show »
Length:923
Mass (Da):102,416
Checksum:i2949E6A77692F99D
GO
Isoform 4 (identifier: Q5ST30-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MGGKAWPRRAVGTAGGPCAEQISAPFQTLLM

Note: No experimental confirmation available.
Show »
Length:1,093
Mass (Da):121,543
Checksum:i6CE3ECF0345D3D78
GO

Computationally mapped potential isoform sequencesi

There are 8 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
B4E0K6B4E0K6_HUMAN
Valine--tRNA ligase, mitochondrial
VARS2
1,063Annotation score:
A0A0G2JIA5A0A0G2JIA5_HUMAN
Valine--tRNA ligase, mitochondrial
VARS2
1,063Annotation score:
A0A140T8Y0A0A140T8Y0_HUMAN
Valine--tRNA ligase, mitochondrial
VARS2
1,063Annotation score:
A0A0G2JL52A0A0G2JL52_HUMAN
VARS2
VARS2
1,093Annotation score:
A0A140TA35A0A140TA35_HUMAN
VARS2
VARS2
1,093Annotation score:
A0A140TA36A0A140TA36_HUMAN
VARS2
VARS2
1,093Annotation score:
B7ZCJ6B7ZCJ6_HUMAN
Valine--tRNA ligase, mitochondrial
VARS2
326Annotation score:
A2ABL6A2ABL6_HUMAN
Valine--tRNA ligase, mitochondrial
VARS2
115Annotation score:

Sequence cautioni

The sequence BAB15191 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence BAB67778 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
The sequence BAD92716 differs from that shown. The sequence differs from that shown because it seems to be derived from a pre-mRNA.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti25F → S in BAG65557 (PubMed:14702039).Curated1
Sequence conflicti156H → R in BAG57195 (PubMed:14702039).Curated1
Sequence conflicti985E → G in BAB15191 (PubMed:14702039).Curated1
Sequence conflicti1060S → G in BAG65557 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_05265126H → Y. Corresponds to variant dbSNP:rs6926224Ensembl.1
Natural variantiVAR_04373064G → R. Corresponds to variant dbSNP:rs6926723Ensembl.1
Natural variantiVAR_071850337T → I in COXPD20; decreased levels of the protein. 1 PublicationCorresponds to variant dbSNP:rs587777585Ensembl.1
Natural variantiVAR_071851349A → T in COXPD20. 1 PublicationCorresponds to variant dbSNP:rs587777583Ensembl.1
Natural variantiVAR_043731449W → R4 PublicationsCorresponds to variant dbSNP:rs2249464Ensembl.1
Natural variantiVAR_071852596A → D in COXPD20. 1 PublicationCorresponds to variant dbSNP:rs587777584Ensembl.1
Natural variantiVAR_043732680V → L4 PublicationsCorresponds to variant dbSNP:rs2074506Ensembl.1
Natural variantiVAR_061910765V → M. Corresponds to variant dbSNP:rs55865499Ensembl.1
Natural variantiVAR_043733917R → Q3 PublicationsCorresponds to variant dbSNP:rs9394021Ensembl.1
Natural variantiVAR_043734965A → T5 PublicationsCorresponds to variant dbSNP:rs2252863Ensembl.1
Natural variantiVAR_0437351049R → Q3 PublicationsCorresponds to variant dbSNP:rs4678Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0340321 – 644MPHLP…LPFSK → MVFFCPVPLFCPGLAPRDPR PCSFLPPVTFGNGQRPSAVL GGPHGHVGDPAHRAAALQQV WRPEIPRHLQGNPPLLTPPC PQ in isoform 2. 1 PublicationAdd BLAST644
Alternative sequenceiVSP_0454831 – 140Missing in isoform 3. 1 PublicationAdd BLAST140
Alternative sequenceiVSP_0461021M → MGGKAWPRRAVGTAGGPCAE QISAPFQTLLM in isoform 4. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB067472 mRNA Translation: BAB67778.1 Different initiation.
AK025618 mRNA Translation: BAB15191.1 Different initiation.
AK125069 mRNA No translation available.
AK293780 mRNA Translation: BAG57195.1
AK304807 mRNA Translation: BAG65557.1
AB209479 Transcribed RNA Translation: BAD92716.1 Sequence problems.
AL662854 Genomic DNA No translation available.
AL669830 Genomic DNA No translation available.
AL773541 Genomic DNA No translation available.
BX927194 Genomic DNA No translation available.
CR759747 Genomic DNA No translation available.
CR936875 Genomic DNA No translation available.
BC008844 mRNA Translation: AAH08844.2
BC009355 mRNA Translation: AAH09355.2
BC073838 mRNA Translation: AAH73838.1
BC112054 mRNA Translation: AAI12055.1
BC113605 mRNA Translation: AAI13606.1
AL122037 mRNA Translation: CAB59177.1
CCDSiCCDS34387.1 [Q5ST30-1]
CCDS54980.1 [Q5ST30-4]
CCDS54981.1 [Q5ST30-3]
RefSeqiNP_001161205.1, NM_001167733.2 [Q5ST30-3]
NP_001161206.1, NM_001167734.1 [Q5ST30-4]
NP_065175.4, NM_020442.5 [Q5ST30-1]
UniGeneiHs.597526

Genome annotation databases

EnsembliENST00000321897; ENSP00000316092; ENSG00000137411 [Q5ST30-1]
ENST00000541562; ENSP00000441000; ENSG00000137411 [Q5ST30-4]
ENST00000625423; ENSP00000485818; ENSG00000137411 [Q5ST30-3]
GeneIDi57176
KEGGihsa:57176
UCSCiuc003nsc.3 human [Q5ST30-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB067472 mRNA Translation: BAB67778.1 Different initiation.
AK025618 mRNA Translation: BAB15191.1 Different initiation.
AK125069 mRNA No translation available.
AK293780 mRNA Translation: BAG57195.1
AK304807 mRNA Translation: BAG65557.1
AB209479 Transcribed RNA Translation: BAD92716.1 Sequence problems.
AL662854 Genomic DNA No translation available.
AL669830 Genomic DNA No translation available.
AL773541 Genomic DNA No translation available.
BX927194 Genomic DNA No translation available.
CR759747 Genomic DNA No translation available.
CR936875 Genomic DNA No translation available.
BC008844 mRNA Translation: AAH08844.2
BC009355 mRNA Translation: AAH09355.2
BC073838 mRNA Translation: AAH73838.1
BC112054 mRNA Translation: AAI12055.1
BC113605 mRNA Translation: AAI13606.1
AL122037 mRNA Translation: CAB59177.1
CCDSiCCDS34387.1 [Q5ST30-1]
CCDS54980.1 [Q5ST30-4]
CCDS54981.1 [Q5ST30-3]
RefSeqiNP_001161205.1, NM_001167733.2 [Q5ST30-3]
NP_001161206.1, NM_001167734.1 [Q5ST30-4]
NP_065175.4, NM_020442.5 [Q5ST30-1]
UniGeneiHs.597526

3D structure databases

ProteinModelPortaliQ5ST30
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121426, 11 interactors
IntActiQ5ST30, 13 interactors
MINTiQ5ST30
STRINGi9606.ENSP00000441000

PTM databases

iPTMnetiQ5ST30
PhosphoSitePlusiQ5ST30

Polymorphism and mutation databases

BioMutaiVARS2
DMDMi296452917

Proteomic databases

EPDiQ5ST30
MaxQBiQ5ST30
PaxDbiQ5ST30
PeptideAtlasiQ5ST30
PRIDEiQ5ST30
ProteomicsDBi63892
63893 [Q5ST30-2]

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000321897; ENSP00000316092; ENSG00000137411 [Q5ST30-1]
ENST00000541562; ENSP00000441000; ENSG00000137411 [Q5ST30-4]
ENST00000625423; ENSP00000485818; ENSG00000137411 [Q5ST30-3]
GeneIDi57176
KEGGihsa:57176
UCSCiuc003nsc.3 human [Q5ST30-1]

Organism-specific databases

CTDi57176
DisGeNETi57176
EuPathDBiHostDB:ENSG00000137411.16
GeneCardsiVARS2
H-InvDBiHIX0166334
HIX0166693
HIX0200924
HGNCiHGNC:21642 VARS2
HPAiHPA062449
HPA070267
MalaCardsiVARS2
MIMi612802 gene
615917 phenotype
neXtProtiNX_Q5ST30
OpenTargetsiENSG00000137411
Orphaneti420728 Combined oxidative phosphorylation defect type 20
PharmGKBiPA164742816
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0432 Eukaryota
COG0525 LUCA
GeneTreeiENSGT00550000074727
HOVERGENiHBG017878
InParanoidiQ5ST30
KOiK01873
OMAiRQWYIRN
OrthoDBiEOG091G01XH
PhylomeDBiQ5ST30
TreeFamiTF354250

Enzyme and pathway databases

ReactomeiR-HSA-379726 Mitochondrial tRNA aminoacylation

Miscellaneous databases

ChiTaRSiVARS2 human
GenomeRNAii57176
PROiPR:Q5ST30
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000137411 Expressed in 198 organ(s), highest expression level in right hemisphere of cerebellum
CleanExiHS_VARS2
ExpressionAtlasiQ5ST30 baseline and differential
GenevisibleiQ5ST30 HS

Family and domain databases

CDDicd07962 Anticodon_Ia_Val, 1 hit
Gene3Di3.40.50.620, 2 hits
3.90.740.10, 2 hits
InterProiView protein in InterPro
IPR001412 aa-tRNA-synth_I_CS
IPR002300 aa-tRNA-synth_Ia
IPR033705 Anticodon_Ia_Val
IPR013155 M/V/L/I-tRNA-synth_anticd-bd
IPR014729 Rossmann-like_a/b/a_fold
IPR009080 tRNAsynth_Ia_anticodon-bd
IPR009008 Val/Leu/Ile-tRNA-synth_edit
IPR002303 Valyl-tRNA_ligase
PfamiView protein in Pfam
PF08264 Anticodon_1, 1 hit
PF00133 tRNA-synt_1, 1 hit
PRINTSiPR00986 TRNASYNTHVAL
SUPFAMiSSF47323 SSF47323, 1 hit
SSF50677 SSF50677, 1 hit
TIGRFAMsiTIGR00422 valS, 1 hit
PROSITEiView protein in PROSITE
PS00178 AA_TRNA_LIGASE_I, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiSYVM_HUMAN
AccessioniPrimary (citable) accession number: Q5ST30
Secondary accession number(s): A2ABL7
, B4DET4, B4E3P5, F5GXJ0, F5H323, Q2M2A0, Q59FI1, Q5SQ96, Q5SS98, Q6DKJ5, Q6ZV24, Q96GN2, Q96H77, Q96Q02, Q9H6R2, Q9UFH7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: May 18, 2010
Last modified: November 7, 2018
This is version 141 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. Human chromosome 6
    Human chromosome 6: entries, gene names and cross-references to MIM
  6. Aminoacyl-tRNA synthetases
    List of aminoacyl-tRNA synthetase entries
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