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    Usp9x ubiquitin specific peptidase 9, X chromosome [ Mus musculus (house mouse) ]

    Gene ID: 22284, updated on 4-Jan-2025

    Summary

    Official Symbol
    Usp9xprovided by MGI
    Official Full Name
    ubiquitin specific peptidase 9, X chromosomeprovided by MGI
    Primary source
    MGI:MGI:894681
    See related
    Ensembl:ENSMUSG00000031010 AllianceGenome:MGI:894681
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Fafl; Dffrx; FAF-X; 5730589N07Rik
    Summary
    Enables cysteine-type deubiquitinase activity; cysteine-type endopeptidase activity; and ubiquitin protein ligase binding activity. Involved in generation of neurons; protein deubiquitination involved in ubiquitin-dependent protein catabolic process; and regulation of postsynapse assembly. Acts upstream of or within several processes, including cellular response to transforming growth factor beta stimulus; in utero embryonic development; and nervous system development. Located in apical part of cell and cytoplasm. Is active in postsynapse. Is expressed in several structures, including central nervous system; eye; genitourinary system; limb interdigital region; and lung. 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, Jan 2025]
    Expression
    Ubiquitous expression in placenta adult (RPKM 19.5), CNS E18 (RPKM 11.9) and 26 other tissues See more
    Orthologs
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    Genomic context

    See Usp9x in Genome Data Viewer
    Location:
    X A1.1; X 7.95 cM
    Exon count:
    47
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) X NC_000086.8 (12937221..13039567)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) X NC_000086.7 (13070982..13173328)

    Chromosome X - NC_000086.8Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 4930500G05 gene Neighboring gene predicted gene, 41890 Neighboring gene STARR-seq mESC enhancer starr_46774 Neighboring gene RIKEN cDNA 5730405O15 gene Neighboring gene STARR-seq mESC enhancer starr_46778 Neighboring gene STARR-seq mESC enhancer starr_46779 Neighboring gene STARR-seq mESC enhancer starr_46781 Neighboring gene STARR-positive B cell enhancer mm9_chrX:12648426-12648727 Neighboring gene STARR-seq mESC enhancer starr_46782 Neighboring gene ribosomal protein L3, pseudogene 1 Neighboring gene LLP homolog, pseudogene 2

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (3) 
    • Gene trapped (3) 
    • Targeted (3)  1 citation

    Pathways from PubChem

    Interactions

    General gene information

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables K11-linked deubiquitinase activity  
    enables K11-linked deubiquitinase activity  
    enables K48-linked deubiquitinase activity  
    enables K48-linked deubiquitinase activity  
    enables K63-linked deubiquitinase activity  
    enables K63-linked deubiquitinase activity  
    enables co-SMAD binding  
    enables co-SMAD binding  
    enables cysteine-type deubiquitinase activity  
    enables cysteine-type deubiquitinase activity PubMed 
    enables cysteine-type deubiquitinase activity  
    enables cysteine-type deubiquitinase activity  
    enables cysteine-type endopeptidase activity PubMed 
    enables deubiquitinase activity PubMed 
    enables deubiquitinase activity  
    enables metal ion binding  
    enables molecular sequestering activity  
    enables protein binding PubMed 
    enables ubiquitin protein ligase binding PubMed 
    Items 1 - 25 of 49
    Process Evidence Code Pubs
    involved_in BMP signaling pathway  
    involved_in BMP signaling pathway  
    involved_in DNA alkylation repair  
    involved_in DNA alkylation repair  
    acts_upstream_of_or_within axon extension PubMed 
    involved_in axon extension PubMed 
    involved_in axon extension  
    involved_in cell division  
    involved_in cell migration  
    acts_upstream_of_or_within cellular response to transforming growth factor beta stimulus PubMed 
    acts_upstream_of_or_within cerebellar cortex structural organization PubMed 
    involved_in chromosome segregation  
    involved_in cilium assembly  
    involved_in cytosolic ciliogenesis  
    acts_upstream_of_or_within hippocampus development PubMed 
    acts_upstream_of_or_within in utero embryonic development PubMed 
    involved_in monoubiquitinated protein deubiquitination  
    involved_in monoubiquitinated protein deubiquitination  
    involved_in negative regulation of proteasomal ubiquitin-dependent protein catabolic process  
    involved_in negative regulation of proteasomal ubiquitin-dependent protein catabolic process  
    involved_in neuron migration PubMed 
    involved_in neuron migration  
    acts_upstream_of_or_within neuron projection extension PubMed 
    involved_in positive regulation of TORC2 signaling  
    involved_in positive regulation of TORC2 signaling  
    involved_in positive regulation of protein binding  
    involved_in positive regulation of protein binding  
    acts_upstream_of_or_within post-embryonic development PubMed 
    involved_in protein K63-linked deubiquitination  
    involved_in protein K63-linked deubiquitination  
    involved_in protein deubiquitination PubMed 
    involved_in protein deubiquitination  
    involved_in protein deubiquitination  
    involved_in protein deubiquitination involved in ubiquitin-dependent protein catabolic process PubMed 
    involved_in protein deubiquitination involved in ubiquitin-dependent protein catabolic process  
    involved_in protein import into peroxisome matrix, receptor recycling  
    involved_in protein import into peroxisome matrix, receptor recycling  
    involved_in protein stabilization  
    involved_in protein stabilization  
    acts_upstream_of_or_within regulation of T cell receptor signaling pathway PubMed 
    involved_in regulation of circadian rhythm  
    involved_in regulation of circadian rhythm  
    involved_in regulation of postsynapse assembly PubMed 
    involved_in regulation of postsynapse assembly PubMed 
    involved_in regulation of postsynapse assembly PubMed 
    involved_in regulation of protein stability  
    involved_in rhythmic process  
    involved_in transforming growth factor beta receptor signaling pathway  
    involved_in transforming growth factor beta receptor signaling pathway  
    Items 1 - 25 of 49
    Component Evidence Code Pubs
    located_in apical part of cell PubMed 
    is_active_in centrosome  
    located_in cilium  
    located_in cilium  
    located_in cytoplasm PubMed 
    is_active_in cytoplasm  
    located_in cytoplasm  
    located_in cytoplasm  
    located_in cytoskeleton  
    is_active_in cytosol  
    is_active_in cytosol  
    located_in cytosol  
    is_active_in cytosol  
    located_in cytosol  
    located_in growth cone  
    located_in growth cone  
    is_active_in nucleus  
    is_active_in postsynapse PubMed 

    General protein information

    Preferred Names
    ubiquitin carboxyl-terminal hydrolase 9X; probable ubiquitin carboxyl-terminal hydrolase FAF-X
    Names
    deubiquitinating enzyme FAF-X
    fat facets homolog
    fat facets protein-related, X-linked
    fats facets protein related, X
    ubiquitin carboxyl-terminal hydrolase FAM
    ubiquitin thioesterase FAF-X
    ubiquitin thiolesterase FAF-X
    ubiquitin-specific protease 9, X chromosome
    ubiquitin-specific-processing protease FAF-X
    NP_001395646.1
    NP_001395647.1
    NP_001395648.1
    NP_033507.2
    XP_006527649.1
    XP_006527650.1
    XP_006527651.1
    XP_006527652.1
    XP_006527654.1
    XP_011245756.1
    XP_030107164.1
    XP_030107165.1
    XP_030107166.1
    XP_030107167.1
    XP_030107168.1
    XP_036017801.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001408717.1NP_001395646.1  ubiquitin carboxyl-terminal hydrolase 9X isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL669967
      UniProtKB/Swiss-Prot
      E9QLY0, P70398, Q62497
      UniProtKB/TrEMBL
      Q4FE56
    2. NM_001408718.1NP_001395647.1  ubiquitin carboxyl-terminal hydrolase 9X isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL669967
      UniProtKB/Swiss-Prot
      E9QLY0, P70398, Q62497
    3. NM_001408719.1NP_001395648.1  ubiquitin carboxyl-terminal hydrolase 9X isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL669967
      UniProtKB/Swiss-Prot
      E9QLY0, P70398, Q62497
    4. NM_009481.3NP_033507.2  ubiquitin carboxyl-terminal hydrolase 9X isoform 1

      See identical proteins and their annotated locations for NP_033507.2

      Status: VALIDATED

      Source sequence(s)
      AL669967
      Consensus CDS
      CCDS40875.1
      UniProtKB/Swiss-Prot
      E9QLY0, P70398, Q62497
      UniProtKB/TrEMBL
      Q4FE56
      Related
      ENSMUSP00000086716.5, ENSMUST00000089302.11
      Conserved Domains (3) summary
      cd02659
      Location:15551958
      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:20972476
      DUF3517; Domain of unknown function (DUF3517)
      cl28922
      Location:900964
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000086.8 Reference GRCm39 C57BL/6J

      Range
      12937221..13039567
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030251305.1XP_030107165.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X2

      UniProtKB/Swiss-Prot
      E9QLY0, P70398, Q62497
      Conserved Domains (2) summary
      cd02659
      Location:15551958
      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 ...
      cl28922
      Location:900964
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
    2. XM_006527589.5XP_006527652.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X1

      See identical proteins and their annotated locations for XP_006527652.1

      UniProtKB/Swiss-Prot
      E9QLY0, P70398, Q62497
      Conserved Domains (2) summary
      cd02659
      Location:15601963
      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 ...
      cl28922
      Location:905969
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
    3. XM_030251307.2XP_030107167.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X2

      UniProtKB/Swiss-Prot
      E9QLY0, P70398, Q62497
      Conserved Domains (2) summary
      cd02659
      Location:15551958
      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 ...
      cl28922
      Location:900964
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
    4. XM_006527587.5XP_006527650.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X1

      See identical proteins and their annotated locations for XP_006527650.1

      UniProtKB/Swiss-Prot
      E9QLY0, P70398, Q62497
      Conserved Domains (2) summary
      cd02659
      Location:15601963
      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 ...
      cl28922
      Location:905969
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
    5. XM_006527586.4XP_006527649.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X1

      See identical proteins and their annotated locations for XP_006527649.1

      UniProtKB/Swiss-Prot
      E9QLY0, P70398, Q62497
      Conserved Domains (2) summary
      cd02659
      Location:15601963
      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 ...
      cl28922
      Location:905969
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
    6. XM_006527591.4XP_006527654.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X2

      See identical proteins and their annotated locations for XP_006527654.1

      UniProtKB/Swiss-Prot
      E9QLY0, P70398, Q62497
      Conserved Domains (2) summary
      cd02659
      Location:15551958
      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 ...
      cl28922
      Location:900964
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
    7. XM_036161908.1XP_036017801.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X4

      UniProtKB/Swiss-Prot
      E9QLY0, P70398, Q62497
      UniProtKB/TrEMBL
      Q4FE56
      Conserved Domains (3) summary
      cd02659
      Location:15551958
      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:20972476
      DUF3517; Domain of unknown function (DUF3517)
      cl28922
      Location:900964
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
    8. XM_006527588.4XP_006527651.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X1

      See identical proteins and their annotated locations for XP_006527651.1

      UniProtKB/Swiss-Prot
      E9QLY0, P70398, Q62497
      Conserved Domains (2) summary
      cd02659
      Location:15601963
      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 ...
      cl28922
      Location:905969
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
    9. XM_011247454.3XP_011245756.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X1

      See identical proteins and their annotated locations for XP_011245756.1

      UniProtKB/Swiss-Prot
      E9QLY0, P70398, Q62497
      Conserved Domains (2) summary
      cd02659
      Location:15601963
      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 ...
      cl28922
      Location:905969
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
    10. XM_030251306.2XP_030107166.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X2

      UniProtKB/Swiss-Prot
      E9QLY0, P70398, Q62497
      Conserved Domains (2) summary
      cd02659
      Location:15551958
      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 ...
      cl28922
      Location:900964
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
    11. XM_030251304.2XP_030107164.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X1

      UniProtKB/Swiss-Prot
      E9QLY0, P70398, Q62497
      Conserved Domains (2) summary
      cd02659
      Location:15601963
      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 ...
      cl28922
      Location:905969
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
    12. XM_030251308.2XP_030107168.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X2

      UniProtKB/Swiss-Prot
      E9QLY0, P70398, Q62497
      Conserved Domains (2) summary
      cd02659
      Location:15551958
      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 ...
      cl28922
      Location:900964
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
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