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    Usp9x ubiquitin specific peptidase 9, X-linked [ Rattus norvegicus (Norway rat) ]

    Gene ID: 363445, updated on 10-Oct-2024

    Summary

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    Official Symbol
    Usp9xprovided by RGD
    Official Full Name
    ubiquitin specific peptidase 9, X-linkedprovided by RGD
    Primary source
    RGD:1560056
    See related
    EnsemblRapid:ENSRNOG00000003261 AllianceGenome:RGD:1560056
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1560056
    Summary
    Predicted to enable co-SMAD binding activity; cysteine-type peptidase activity; and ubiquitin protein ligase binding activity. Predicted to be involved in several processes, including positive regulation of DNA demethylation; protein deubiquitination involved in ubiquitin-dependent protein catabolic process; and transmembrane receptor protein serine/threonine kinase signaling pathway. Predicted to act upstream of or within several processes, including cellular response to transforming growth factor beta stimulus; in utero embryonic development; and nervous system development. Predicted to be located in apical part of cell; cytoplasm; and growth cone. Predicted to be active in cytosol and nucleus. Human ortholog(s) of this gene implicated in female-restricted syndromic X-linked intellectual disability 99 and non-syndromic X-linked intellectual disability 99. Orthologous to human USP9X (ubiquitin specific peptidase 9 X-linked). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Brain (RPKM 544.8), Muscle (RPKM 539.9) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Usp9x in Genome Data Viewer
    Location:
    Xq12
    Exon count:
    50
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) X NC_086039.1 (12261633..12399780, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) X NC_051356.1 (9588825..9726993, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) X NC_005120.4 (10510033..10660555, complement)

    Chromosome X - NC_086039.1Genomic Context describing neighboring genes Neighboring gene large ribosomal subunit protein eL21 Neighboring gene uncharacterized LOC102547042 Neighboring gene ribosomal protein S19, pseudogene 3 Neighboring gene transfer RNA threonine (anticodon AGU) 31 Neighboring gene peptidylprolyl isomerase A, pseudogene 1 Neighboring gene ubiquitin-conjugating enzyme E2Q family member 2-like

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Mutations in USP9X are associated with X-linked intellectual disability and disrupt neuronal cell migration and growth. Homan CC, et al. Am J Hum Genet, 2014 Mar 6. PMID 24607389, Free PMC Article
    2. Identification of ubiquitin-specific protease 9X (USP9X) as a deubiquitinase acting on ubiquitin-peroxin 5 (PEX5) thioester conjugate. Grou CP, et al. J Biol Chem, 2012 Apr 13. PMID 22371489, Free PMC Article
    3. Identification of a deubiquitinating enzyme as a novel AGS3-interacting protein. Xu Z, et al. PLoS One, 2010 Mar 17. PMID 20305814, Free PMC Article
    4. A close correlation in the expression patterns of Af-6 and Usp9x in Sertoli and granulosa cells of mouse testis and ovary. Sato T, et al. Reproduction, 2004 Nov. PMID 15509704
    5. Rapid Ca2+-dependent decrease of protein ubiquitination at synapses. Chen H, et al. Proc Natl Acad Sci U S A, 2003 Dec 9. PMID 14657369, Free PMC Article

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Usp9x contributes to the development of sepsis-induced acute kidney injury by promoting inflammation and apoptosis in renal tubular epithelial cells via activation of the TLR4/nf-kappab pathway.
      Title: Usp9x contributes to the development of sepsis-induced acute kidney injury by promoting inflammation and apoptosis in renal tubular epithelial cells via activation of the TLR4/nf-κb pathway.
    2. Our results suggest that ubiquitin-specific protease 9X (USP9X) is by far the most active deubiquitinase acting on Ub-PEX5, both in female rat liver and HeLa cells.
      Title: Identification of ubiquitin-specific protease 9X (USP9X) as a deubiquitinase acting on ubiquitin-peroxin 5 (PEX5) thioester conjugate.
    3. Zymophagy, a novel selective autophagy pathway mediated by VMP1-USP9x-p62, prevents pancreatic cell death.
      Title: Zymophagy, a novel selective autophagy pathway mediated by VMP1-USP9x-p62, prevents pancreatic cell death.
    4. levels of AGS3 and USP9x are co-regulated in the prefrontal cortex of rats withdrawn from repeated cocaine treatment
      Title: Identification of a deubiquitinating enzyme as a novel AGS3-interacting protein.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables K11-linked deubiquitinase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables K48-linked deubiquitinase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables K63-linked deubiquitinase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables co-SMAD binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables cysteine-type deubiquitinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables cysteine-type deubiquitinase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables cysteine-type endopeptidase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables deubiquitinase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables molecular sequestering activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ubiquitin protein ligase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in BMP signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in DNA alkylation repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within axon extension ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in axon extension ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within cellular response to transforming growth factor beta stimulus ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within cerebellar cortex structural organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cilium assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cytosolic ciliogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within hippocampus development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within in utero embryonic development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in monoubiquitinated protein deubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of proteasomal ubiquitin-dependent protein catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in neuron migration ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within neuron projection extension ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of TORC2 signaling ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within post-embryonic development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein K63-linked deubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein deubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein deubiquitination involved in ubiquitin-dependent protein catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein import into peroxisome matrix, receptor recycling ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein stabilization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of circadian rhythm ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of postsynapse assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of protein stability IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in transforming growth factor beta receptor signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in apical part of cell ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in centrosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cilium ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in growth cone ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in postsynapse ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    probable ubiquitin carboxyl-terminal hydrolase FAF-X
    Names
    ubiquitin specific peptidase 9, X chromosome
    NP_001129395.1
    XP_038955787.1
    XP_038955788.1
    XP_038955789.1
    XP_038955790.1
    XP_038955791.1
    XP_038955792.1
    XP_038955793.1
    XP_038955795.1
    XP_063136184.1
    XP_063136185.1
    XP_063136186.1

    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_001135923.2 → NP_001129395.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform 2

      See identical proteins and their annotated locations for NP_001129395.1

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000021
      UniProtKB/TrEMBL
      A6JZY9, D3ZC84
      Related
      ENSRNOP00000075990.3, ENSRNOT00000093067.3
      Conserved Domains (3) summary
      cd02659
      Location:1555 → 1958
      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 ...
      pfam12030
      Location:2097 → 2476
      DUF3517; Domain of unknown function (DUF3517)
      cl28922
      Location:900 → 964
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086039.1 Reference GRCr8

      Range
      12261633..12399780 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039099861.2 → XP_038955789.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X1

      UniProtKB/TrEMBL
      A6JZY9, D3ZC84
      Conserved Domains (3) summary
      cd02659
      Location:1560 → 1963
      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 ...
      pfam12030
      Location:2102 → 2481
      DUF3517; Domain of unknown function (DUF3517)
      cl28922
      Location:905 → 969
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold

    2. XM_063280116.1 → XP_063136186.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X2

    3. XM_039099860.2 → XP_038955788.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X1

      UniProtKB/TrEMBL
      A6JZY9, D3ZC84
      Conserved Domains (3) summary
      cd02659
      Location:1560 → 1963
      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 ...
      pfam12030
      Location:2102 → 2481
      DUF3517; Domain of unknown function (DUF3517)
      cl28922
      Location:905 → 969
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold

    4. XM_063280115.1 → XP_063136185.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X1

    5. XM_063280114.1 → XP_063136184.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X1

    6. XM_039099865.2 → XP_038955793.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X4

      UniProtKB/TrEMBL
      A6JZY9, D3ZC84
      Conserved Domains (3) summary
      cd02659
      Location:1555 → 1958
      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 ...
      pfam12030
      Location:2097 → 2476
      DUF3517; Domain of unknown function (DUF3517)
      cl28922
      Location:900 → 964
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold

    7. XM_039099863.2 → XP_038955791.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X2

      UniProtKB/TrEMBL
      A6JZY9, D3ZC84
      Conserved Domains (3) summary
      cd02659
      Location:1555 → 1958
      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 ...
      pfam12030
      Location:2097 → 2476
      DUF3517; Domain of unknown function (DUF3517)
      cl28922
      Location:900 → 964
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold

    8. XM_039099864.2 → XP_038955792.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X3

      UniProtKB/TrEMBL
      A0A0G2K2C7, A6JZY9, D3ZC84
      Related
      ENSRNOP00000072190.2, ENSRNOT00000080651.3
      Conserved Domains (3) summary
      cd02659
      Location:1560 → 1963
      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 ...
      pfam12030
      Location:2102 → 2481
      DUF3517; Domain of unknown function (DUF3517)
      cl28922
      Location:905 → 969
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold

    9. XM_039099859.2 → XP_038955787.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X1

      UniProtKB/TrEMBL
      A6JZY9, D3ZC84
      Conserved Domains (3) summary
      cd02659
      Location:1560 → 1963
      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 ...
      pfam12030
      Location:2102 → 2481
      DUF3517; Domain of unknown function (DUF3517)
      cl28922
      Location:905 → 969
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold

    10. XM_039099862.2 → XP_038955790.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X1

      UniProtKB/TrEMBL
      A6JZY9, D3ZC84
      Conserved Domains (3) summary
      cd02659
      Location:1560 → 1963
      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 ...
      pfam12030
      Location:2102 → 2481
      DUF3517; Domain of unknown function (DUF3517)
      cl28922
      Location:905 → 969
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold

    11. XM_039099867.1 → XP_038955795.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X4

      UniProtKB/TrEMBL
      A6JZY9, D3ZC84
      Conserved Domains (3) summary
      cd02659
      Location:1555 → 1958
      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 ...
      pfam12030
      Location:2097 → 2476
      DUF3517; Domain of unknown function (DUF3517)
      cl28922
      Location:900 → 964
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001135893.1: Suppressed sequence

      Description
      NM_001135893.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

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