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

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: human mouse all
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Genomic context

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_086039.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

px-12d6 (e-PCR)
- UniSTS:258316

USP9X_3261 (e-PCR)
- UniSTS:462609

RH142260 (e-PCR)
- UniSTS:231507

RH125324 (e-PCR)
- UniSTS:162146

RH125670 (e-PCR)
- UniSTS:162451

Usp9x (e-PCR), detects polymorphism
- UniSTS:256412

BG371737 (e-PCR)
- UniSTS:248752

RH127557 (e-PCR)
- UniSTS:210867

RH47975 (e-PCR)
- UniSTS:30142

RH141703 (e-PCR)
- UniSTS:223696

D20S998 (e-PCR)
- UniSTS:154615

BF396338 (e-PCR)
- UniSTS:245752

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

EC 3.1.2.15

XP_038955787.1

EC 3.1.2.15

XP_038955788.1

EC 3.1.2.15

XP_038955789.1

EC 3.1.2.15

XP_038955790.1

EC 3.1.2.15

XP_038955791.1

EC 3.1.2.15

XP_038955792.1

EC 3.1.2.15

XP_038955793.1

EC 3.1.2.15

XP_038955795.1

EC 3.1.2.15

XP_063136184.1

EC 3.1.2.15

XP_063136185.1

EC 3.1.2.15

XP_063136186.1

EC 3.1.2.15

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)

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
NM_001434267.1 → NP_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

NC_086039.1 Reference GRCr8

Range

12261633..12399780 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A6JZY9, D3ZC84
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
XM_063280115.1 → XP_063136185.1 probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X1

UniProtKB/TrEMBL

A6JZY9, D3ZC84
XM_063280114.1 → XP_063136184.1 probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X1

UniProtKB/TrEMBL

A6JZY9, D3ZC84
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
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
XM_039099864.2 → XP_038955792.1 probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X3

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
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
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
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

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.