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

    Gene ID: 363445, updated on 9-Dec-2024

    Summary

    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
    VALIDATED
    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 several functions, including co-SMAD binding activity; deubiquitinase activity; and ubiquitin protein ligase binding activity. Predicted to be involved in several processes, including DNA alkylation repair; protein deubiquitination; and transforming growth factor beta receptor superfamily 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; cilium; and growth cone. Predicted to be active in several cellular components, including centrosome; cytosol; and postsynapse. 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, Dec 2024]
    Expression
    Biased expression in Brain (RPKM 544.8), Muscle (RPKM 539.9) and 9 other tissues See more
    Orthologs
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    Genomic context

    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

    Expression

    • Project title: 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    General gene information

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables K11-linked deubiquitinase activity  
    enables K48-linked deubiquitinase activity  
    enables K63-linked deubiquitinase activity  
    enables co-SMAD binding  
    enables cysteine-type deubiquitinase activity  
    enables cysteine-type deubiquitinase activity  
    enables cysteine-type endopeptidase activity  
    enables deubiquitinase activity  
    enables molecular sequestering activity  
    enables ubiquitin protein ligase binding  
    Items 1 - 25 of 26
    Process Evidence Code Pubs
    involved_in BMP signaling pathway  
    involved_in DNA alkylation repair  
    acts_upstream_of_or_within axon extension  
    involved_in axon extension  
    involved_in cell migration  
    acts_upstream_of_or_within cellular response to transforming growth factor beta stimulus  
    acts_upstream_of_or_within cerebellar cortex structural organization  
    involved_in cilium assembly  
    involved_in cytosolic ciliogenesis  
    acts_upstream_of_or_within hippocampus development  
    acts_upstream_of_or_within in utero embryonic development  
    involved_in monoubiquitinated protein deubiquitination  
    involved_in negative regulation of proteasomal ubiquitin-dependent protein catabolic process  
    involved_in neuron migration  
    acts_upstream_of_or_within neuron projection extension  
    involved_in positive regulation of TORC2 signaling  
    acts_upstream_of_or_within post-embryonic development  
    involved_in protein K63-linked deubiquitination  
    involved_in protein deubiquitination  
    involved_in protein deubiquitination involved in ubiquitin-dependent protein catabolic process  
    involved_in protein import into peroxisome matrix, receptor recycling  
    involved_in protein stabilization  
    involved_in regulation of circadian rhythm  
    involved_in regulation of postsynapse assembly  
    involved_in regulation of protein stability  
    involved_in transforming growth factor beta receptor signaling pathway  
    Items 1 - 25 of 26
    Component Evidence Code Pubs
    located_in apical part of cell  
    is_active_in centrosome  
    located_in cilium  
    is_active_in cytoplasm  
    located_in cytoplasm  
    is_active_in cytosol  
    is_active_in cytosol  
    located_in cytosol  
    located_in growth cone  
    is_active_in nucleus  
    is_active_in postsynapse  

    General protein information

    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_001135923.2NP_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: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
    2. NM_001434267.1NP_001421196.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000021
      UniProtKB/TrEMBL
      A0A0G2K2C7, A6JZY9, D3ZC84

    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_039099861.2XP_038955789.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X1

      UniProtKB/TrEMBL
      A6JZY9, D3ZC84
      Conserved Domains (3) 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 ...
      pfam12030
      Location:21022481
      DUF3517; Domain of unknown function (DUF3517)
      cl28922
      Location:905969
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
    2. XM_063280116.1XP_063136186.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X2

      UniProtKB/TrEMBL
      A6JZY9, D3ZC84
    3. XM_039099860.2XP_038955788.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X1

      UniProtKB/TrEMBL
      A6JZY9, D3ZC84
      Conserved Domains (3) 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 ...
      pfam12030
      Location:21022481
      DUF3517; Domain of unknown function (DUF3517)
      cl28922
      Location:905969
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
    4. XM_063280115.1XP_063136185.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X1

      UniProtKB/TrEMBL
      A6JZY9, D3ZC84
    5. XM_063280114.1XP_063136184.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X1

      UniProtKB/TrEMBL
      A6JZY9, D3ZC84
    6. XM_039099865.2XP_038955793.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X4

      UniProtKB/TrEMBL
      A6JZY9, D3ZC84
      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
    7. XM_039099863.2XP_038955791.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X2

      UniProtKB/TrEMBL
      A6JZY9, D3ZC84
      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_039099864.2XP_038955792.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X3

      Related
      ENSRNOP00000072190.2, ENSRNOT00000080651.3
      Conserved Domains (3) 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 ...
      pfam12030
      Location:21022481
      DUF3517; Domain of unknown function (DUF3517)
      cl28922
      Location:905969
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
    9. XM_039099859.2XP_038955787.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X1

      UniProtKB/TrEMBL
      A6JZY9, D3ZC84
      Conserved Domains (3) 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 ...
      pfam12030
      Location:21022481
      DUF3517; Domain of unknown function (DUF3517)
      cl28922
      Location:905969
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
    10. XM_039099862.2XP_038955790.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X1

      UniProtKB/TrEMBL
      A6JZY9, D3ZC84
      Conserved Domains (3) 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 ...
      pfam12030
      Location:21022481
      DUF3517; Domain of unknown function (DUF3517)
      cl28922
      Location:905969
      Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
    11. XM_039099867.1XP_038955795.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X4

      UniProtKB/TrEMBL
      A6JZY9, D3ZC84
      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

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