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

Gene ID: 363445, updated on 25-Apr-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
Ensembl: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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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
  • 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. 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.
  2. 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.
  3. 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 IEA
Inferred from Electronic Annotation
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 deubiquitination IBA
Inferred from Biological aspect of Ancestor
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 proteolysis IEA
Inferred from Electronic Annotation
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 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
    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
    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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