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    USP40 ubiquitin specific peptidase 40 [ Homo sapiens (human) ]

    Gene ID: 55230, updated on 10-Dec-2024

    Summary

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    Official Symbol
    USP40provided by HGNC
    Official Full Name
    ubiquitin specific peptidase 40provided by HGNC
    Primary source
    HGNC:HGNC:20069
    See related
    Ensembl:ENSG00000085982 MIM:610570; AllianceGenome:HGNC:20069
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Modification of cellular proteins by ubiquitin is an essential regulatory mechanism controlled by the coordinated action of multiple ubiquitin-conjugating and deubiquitinating enzymes. USP40 belongs to a large family of cysteine proteases that function as deubiquitinating enzymes (Quesada et al., 2004 [PubMed 14715245]).[supplied by OMIM, Mar 2008]
    Expression
    Ubiquitous expression in testis (RPKM 7.5), thyroid (RPKM 6.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See USP40 in Genome Data Viewer
    Location:
    2q37.1
    Exon count:
    44
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (233475526..233566782, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (233964044..234055315, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (234384172..234475428, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:234227861-234228828 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:234228829-234229795 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:234234987-234235964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:234237262-234238093 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:234238124-234238905 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17339 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17340 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12470 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17341 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17342 Neighboring gene S-antigen visual arrestin Neighboring gene MPRA-validated peak4087 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17343 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17344 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17345 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:234307646-234308151 Neighboring gene diacylglycerol kinase delta Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17346 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12471 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17347 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:234334881-234336080 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17348 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17349 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:234359341-234359904 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:234376565-234376780 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:234382503-234383102 Neighboring gene PPFIA1 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:234491694-234492284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17350 Neighboring gene UDP glucuronosyltransferase family 1 member A12, pseudogene Neighboring gene UDP glucuronosyltransferase family 1 member A11, pseudogene Neighboring gene UDP glucuronosyltransferase family 1 member A complex locus

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. USP40 promotes hepatocellular carcinoma cell proliferation, migration and stemness by deubiquitinating and stabilizing Claudin1. Wu Q, et al. Biol Direct, 2024 Feb 2. PMID 38308285, Free PMC Article
    2. USP40 promotes hepatocellular carcinoma progression through a YAP/USP40 positive feedback loop. Mo H, et al. Cancer Lett, 2024 May 1. PMID 38537774
    3. Genetic evidence for ubiquitin-specific proteases USP24 and USP40 as candidate genes for late-onset Parkinson disease. Li Y, et al. Hum Mutat, 2006 Oct. PMID 16917932
    4. Association analysis of single-nucleotide polymorphisms of USP24 and USP40 with Parkinson's disease in the Han Chinese population. Zhao B, et al. Eur Neurol, 2012. PMID 22923019
    5. Ubiquitin specific proteases USP24 and USP40 and ubiquitin thiolesterase UCHL1 polymorphisms have synergic effect on the risk of Parkinson's disease among Taiwanese. Wu YR, et al. Clin Chim Acta, 2010 Jul 4. PMID 20302855

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. USP40 promotes hepatocellular carcinoma progression through a YAP/USP40 positive feedback loop.
      Title: USP40 promotes hepatocellular carcinoma progression through a YAP/USP40 positive feedback loop.
    2. USP40 promotes hepatocellular carcinoma cell proliferation, migration and stemness by deubiquitinating and stabilizing Claudin1.
      Title: USP40 promotes hepatocellular carcinoma cell proliferation, migration and stemness by deubiquitinating and stabilizing Claudin1.
    3. Our findings show the de-ubiquitinase USP40 regulates the ubiquitination and degradation of CFLARL; and GMEB1 acts as a bridge protein for USP40 and CFLARL. Mechanistically, we found GMEB1 inhibits the activation of CASP8 by modulating ubiquitination and degradation of CFLARL
      Title: Glucocorticoid modulatory element-binding protein 1 (GMEB1) interacts with the de-ubiquitinase USP40 to stabilize CFLAR(L) and inhibit apoptosis in human non-small cell lung cancer cells.
    4. present study is the first to report a lack of association between SNPs of USP40 and parkinson disease in Han Chinese patients. Other
      Title: Association analysis of single-nucleotide polymorphisms of USP24 and USP40 with Parkinson's disease in the Han Chinese population.
    5. USP24 alone plays a role in PD susceptibility among Taiwanese people >or=60 years of age, or acting synergistically with USP40 and UCHL1 in the total subjects.
      Title: Ubiquitin specific proteases USP24 and USP40 and ubiquitin thiolesterase UCHL1 polymorphisms have synergic effect on the risk of Parkinson's disease among Taiwanese.
    6. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
      Title: Ubiquitin specific proteases USP24 and USP40 and ubiquitin thiolesterase UCHL1 polymorphisms have synergic effect on the risk of Parkinson's disease among Taiwanese.
    7. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic evidence for ubiquitin-specific proteases USP24 and USP40 as candidate genes for late-onset Parkinson disease.
    8. Da suggest that genetic variants in USP40 affect the risk for late-onset Parkinson disease (PD), which is consistent with the predicted role of the ubiquitination pathway in PD etiology.
      Title: Genetic evidence for ubiquitin-specific proteases USP24 and USP40 as candidate genes for late-onset Parkinson disease.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci.
    EBI GWAS Catalog
    Mayo Genome Consortia: a genotype-phenotype resource for genome-wide association studies with an application to the analysis of circulating bilirubin levels.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ10785, FLJ42100

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cysteine-type deubiquitinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in protein deubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of protein stability IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    ubiquitin carboxyl-terminal hydrolase 40
    Names
    deubiquitinating enzyme 40
    ubiquitin specific protease 40
    ubiquitin thioesterase 40
    ubiquitin thiolesterase 40
    ubiquitin-specific-processing protease 40
    NP_001352408.1
    NP_001369224.1
    NP_001369225.1
    NP_001369226.1
    NP_001369227.1
    NP_001369228.1
    NP_001369229.1
    NP_001369230.1
    NP_001369231.1
    NP_001369232.1
    NP_060688.2
    XP_011509699.1
    XP_011509700.2
    XP_011509701.1
    XP_011509703.2
    XP_016859916.1
    XP_047300845.1
    XP_047300846.1
    XP_047300847.1
    XP_047300848.1
    XP_047300849.1
    XP_054198743.1
    XP_054198744.1
    XP_054198745.1
    XP_054198746.1
    XP_054198747.1
    XP_054198748.1
    XP_054198749.1
    XP_054198750.1
    XP_054198751.1
    XP_054198752.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001365479.2 → NP_001352408.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1), as well as variant 3, encodes isoform 1.
      Source sequence(s)
      AC019072, AC019221
      Consensus CDS
      CCDS92972.1
      UniProtKB/TrEMBL
      A0A7I2YQ75
      Related
      ENSP00000502952.1, ENST00000678225.2
      Conserved Domains (1) summary
      cd02659
      Location:39 → 344
      peptidase_C19C; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

    2. NM_001382295.1 → NP_001369224.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3), as well as variant 1, encodes isoform 1.
      Source sequence(s)
      AC019072, AC019221
      Consensus CDS
      CCDS92972.1
      UniProtKB/TrEMBL
      A0A7I2YQ75
      Conserved Domains (1) summary
      cd02659
      Location:39 → 344
      peptidase_C19C; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

    3. NM_001382296.1 → NP_001369225.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) encodes the longest isoform (3).
      Source sequence(s)
      AC019072, AC019221
      Conserved Domains (1) summary
      cd02659
      Location:39 → 344
      peptidase_C19C; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

    4. NM_001382297.1 → NP_001369226.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC019072, AC019221
      Conserved Domains (1) summary
      cd02659
      Location:39 → 344
      peptidase_C19C; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

    5. NM_001382298.1 → NP_001369227.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC019072, AC019221
      Conserved Domains (1) summary
      cl02553
      Location:39 → 392
      Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...

    6. NM_001382299.1 → NP_001369228.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC019072, AC019221
      Conserved Domains (1) summary
      cd02659
      Location:39 → 344
      peptidase_C19C; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

    7. NM_001382300.1 → NP_001369229.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 7

      Status: VALIDATED

      Source sequence(s)
      AC019072, AC019221
      Conserved Domains (1) summary
      cd02659
      Location:39 → 344
      peptidase_C19C; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

    8. NM_001382301.1 → NP_001369230.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 8

      Status: VALIDATED

      Source sequence(s)
      AC019072, AC019221
      Conserved Domains (1) summary
      cd02659
      Location:39 → 344
      peptidase_C19C; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

    9. NM_001382302.1 → NP_001369231.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 9

      Status: VALIDATED

      Source sequence(s)
      AC019221
      Related
      ENST00000483519.5

    10. NM_001382303.1 → NP_001369232.1  ubiquitin carboxyl-terminal hydrolase 40 isoform 10

      Status: VALIDATED

      Source sequence(s)
      AC019072
      Consensus CDS
      CCDS92973.1
      UniProtKB/TrEMBL
      C9JK14
      Related
      ENSP00000394154.2, ENST00000443711.2
      Conserved Domains (1) summary
      cl02553
      Location:39 → 92
      Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...

    11. NM_018218.4 → NP_060688.2  ubiquitin carboxyl-terminal hydrolase 40 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC019072, AC019221
      Consensus CDS
      CCDS46547.2
      UniProtKB/Swiss-Prot
      Q6NX38, Q70EL0, Q9NVE5
      Related
      ENSP00000251722.6, ENST00000251722.10
      Conserved Domains (1) summary
      cd02659
      Location:39 → 344
      peptidase_C19C; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

    RNA

    1. NR_168049.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC019072, AC019221

    2. NR_168050.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC019072, AC019221

    3. NR_168051.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC019072, AC019221

    4. NR_168052.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC019072, AC019221

    5. NR_168053.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC019072, AC019221

    6. NR_168054.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC019072, AC019221

    7. NR_168055.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC019221

    8. NR_168056.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC019221

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      233475526..233566782 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047444889.1 → XP_047300845.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X4

    2. XM_011511399.3 → XP_011509701.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X3

      Conserved Domains (2) summary
      cl02553
      Location:39 → 392
      Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...
      pfam00443
      Location:42 → 389
      UCH; Ubiquitin carboxyl-terminal hydrolase

    3. XM_011511397.3 → XP_011509699.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X1

      Conserved Domains (2) summary
      cd02659
      Location:39 → 344
      peptidase_C19C; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
      pfam13423
      Location:41 → 311
      UCH_1; Ubiquitin carboxyl-terminal hydrolase

    4. XM_047444891.1 → XP_047300847.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X6

    5. XM_047444890.1 → XP_047300846.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X5

    6. XM_017004427.2 → XP_016859916.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X8

      UniProtKB/TrEMBL
      B4DN96

    7. XM_047444893.1 → XP_047300849.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X10

    8. XM_011511398.4 → XP_011509700.2  ubiquitin carboxyl-terminal hydrolase 40 isoform X2

    9. XM_047444892.1 → XP_047300848.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X7

    10. XM_011511401.3 → XP_011509703.2  ubiquitin carboxyl-terminal hydrolase 40 isoform X9

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      233964044..234055315 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054342771.1 → XP_054198746.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X4

    2. XM_054342770.1 → XP_054198745.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X3

    3. XM_054342768.1 → XP_054198743.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X1

    4. XM_054342773.1 → XP_054198748.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X6

    5. XM_054342772.1 → XP_054198747.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X5

    6. XM_054342775.1 → XP_054198750.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X8

      UniProtKB/TrEMBL
      B4DN96

    7. XM_054342777.1 → XP_054198752.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X10

    8. XM_054342769.1 → XP_054198744.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X2

    9. XM_054342774.1 → XP_054198749.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X7

    10. XM_054342776.1 → XP_054198751.1  ubiquitin carboxyl-terminal hydrolase 40 isoform X9

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NVE5.3 GenPept UniProtKB/Swiss-Prot:Q9NVE5

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