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

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 deubiquitinase activity and ubiquitin protein ligase binding activity. Involved in neuron migration and protein deubiquitination involved in ubiquitin-dependent protein catabolic process. 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 expressed in several structures, including central nervous system; eye; limb interdigital region; lung; and reproductive system. 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: Ubiquitous expression in placenta adult (RPKM 19.5), CNS E18 (RPKM 11.9) and 26 other tissues See more
Orthologs: human all
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Genomic context

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_000086.8 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

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

USP9X-mediated NRP1 deubiquitination promotes liver fibrosis by activating hepatic stellate cells.
Title: USP9X-mediated NRP1 deubiquitination promotes liver fibrosis by activating hepatic stellate cells.
USP9x promotes CD8 [+] T-cell dysfunction in association with autophagy inhibition in septic liver injury.
Title: USP9x promotes CD8 (+) T-cell dysfunction in association with autophagy inhibition in septic liver injury.
Disruption of USP9X in macrophages promotes foam cell formation and atherosclerosis.
Title: Disruption of USP9X in macrophages promotes foam cell formation and atherosclerosis.
Computationally predicted pathogenic USP9X mutation identified in infertile men does not affect spermatogenesis in mice.
Title: Computationally predicted pathogenic USP9X mutation identified in infertile men does not affect spermatogenesis in mice.
Abnormal Behavior and Cortical Connectivity Deficits in Mice Lacking Usp9x.
Title: Abnormal Behavior and Cortical Connectivity Deficits in Mice Lacking Usp9x.
mTORC2 Assembly Is Regulated by USP9X-Mediated Deubiquitination of RICTOR.
Title: mTORC2 Assembly Is Regulated by USP9X-Mediated Deubiquitination of RICTOR.
USP9X deubiquitinates connexin43 to prevent high glucose-induced epithelial-to-mesenchymal transition in NRK-52E cells.
Title: USP9X deubiquitinates connexin43 to prevent high glucose-induced epithelial-to-mesenchymal transition in NRK-52E cells.
The deubiquitinase Usp9x regulates PRC2-mediated chromatin reprogramming during mouse development.
Title: The deubiquitinase Usp9x regulates PRC2-mediated chromatin reprogramming during mouse development.
USP9X over-expression promoted NF-kappaBp65 activation in acute lung injury and hyperpermeability.
Title: USP9X promotes LPS-induced pulmonary epithelial barrier breakdown and hyperpermeability by activating an NF-κBp65 feedback loop.
In Usp9X knock-out mice there is reduced cortical dendritic spine development.
Title: Usp9X Controls Ankyrin-Repeat Domain Protein Homeostasis during Dendritic Spine Development.

Submit: New GeneRIF Correction See all GeneRIFs (27)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Gene trapped (3)
Targeted (3) 1 citation
Endonuclease-mediated (3)

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

RH125324 (e-PCR)
- UniSTS:162146

RH125670 (e-PCR)
- UniSTS:162451

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

RH125716 (e-PCR)
- UniSTS:162479

BG371737 (e-PCR)
- UniSTS:248752

RH47975 (e-PCR)
- UniSTS:30142

RH141703 (e-PCR)
- UniSTS:223696

D20S998 (e-PCR)
- UniSTS:154615

Gene Ontology Provided by MGI

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	IDA Inferred from Direct Assay more info	PubMed
enables cysteine-type deubiquitinase activity	ISO Inferred from Sequence Orthology more info
enables cysteine-type endopeptidase activity	IDA Inferred from Direct Assay more info	PubMed
enables cysteine-type peptidase activity	IEA Inferred from Electronic Annotation more info
enables deubiquitinase activity	IDA Inferred from Direct Assay more info	PubMed
enables deubiquitinase activity	ISO Inferred from Sequence Orthology more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables molecular sequestering activity	ISO Inferred from Sequence Orthology more info
enables peptidase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin protein ligase binding	IPI Inferred from Physical Interaction more info	PubMed

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	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in axon extension	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in axon extension	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cell cycle	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cell division	IEA Inferred from Electronic Annotation 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	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cerebellar cortex structural organization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within chromosome segregation	IEA Inferred from Electronic Annotation 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	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within in utero embryonic development	IGI Inferred from Genetic Interaction more info	PubMed
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	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron migration	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuron projection extension	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of TORC2 signaling	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein binding	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within post-embryonic development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein K63-linked deubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein deubiquitination	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein deubiquitination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein deubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein deubiquitination involved in ubiquitin-dependent protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
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
acts_upstream_of_or_within proteolysis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of T cell receptor signaling pathway	ISO Inferred from Sequence Orthology more info	PubMed
involved_in regulation of circadian rhythm	ISO Inferred from Sequence Orthology more info
involved_in regulation of postsynapse assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of postsynapse assembly	IEP Inferred from Expression Pattern more info	PubMed
involved_in regulation of postsynapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within rhythmic process	IEA Inferred from Electronic Annotation 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	IDA Inferred from Direct Assay more info	PubMed
located_in cell projection	IEA Inferred from Electronic Annotation more info
is_active_in centrosome	ISO Inferred from Sequence Orthology more info
located_in cilium	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoskeleton	IEA Inferred from Electronic Annotation 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 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	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: 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

EC 3.4.19.12

NP_001395647.1

EC 3.4.19.12

NP_001395648.1

EC 3.4.19.12

NP_033507.2

EC 3.4.19.12

XP_006527649.1

EC 3.4.19.12

XP_006527650.1

EC 3.4.19.12

XP_006527651.1

EC 3.4.19.12

XP_006527652.1

EC 3.4.19.12

XP_006527654.1

EC 3.4.19.12

XP_011245756.1

EC 3.4.19.12

XP_030107164.1

EC 3.4.19.12

XP_030107165.1

EC 3.4.19.12

XP_030107166.1

EC 3.4.19.12

XP_030107167.1

EC 3.4.19.12

XP_030107168.1

EC 3.4.19.12

XP_036017801.1

EC 3.4.19.12

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_001408717.1 → NP_001395646.1 probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform 1

Status: VALIDATED

Source sequence(s)

AL669967

UniProtKB/TrEMBL

Q4FE56
NM_001408718.1 → NP_001395647.1 probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform 2

Status: VALIDATED

Source sequence(s)

AL669967
NM_001408719.1 → NP_001395648.1 probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform 2

Status: VALIDATED

Source sequence(s)

AL669967
NM_009481.3 → NP_033507.2 probable ubiquitin carboxyl-terminal hydrolase FAF-X 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: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_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000086.8 Reference GRCm39 C57BL/6J

Range

12937221..13039567

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

E9QLY0, P70398, Q62497

Conserved Domains (2) 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 ...

cl28922
Location:900 → 964

Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
XM_006527589.5 → XP_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: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 ...

cl28922
Location:905 → 969

Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
XM_030251307.2 → XP_030107167.1 probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X2

UniProtKB/Swiss-Prot

E9QLY0, P70398, Q62497

Conserved Domains (2) 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 ...

cl28922
Location:900 → 964

Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
XM_006527587.5 → XP_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: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 ...

cl28922
Location:905 → 969

Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
XM_006527586.4 → XP_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: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 ...

cl28922
Location:905 → 969

Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
XM_006527591.4 → XP_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: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 ...

cl28922
Location:900 → 964

Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
XM_036161908.1 → XP_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: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_006527588.4 → XP_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: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 ...

cl28922
Location:905 → 969

Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
XM_011247454.3 → XP_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: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 ...

cl28922
Location:905 → 969

Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
XM_030251306.2 → XP_030107166.1 probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X2

UniProtKB/Swiss-Prot

E9QLY0, P70398, Q62497

Conserved Domains (2) 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 ...

cl28922
Location:900 → 964

Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
XM_030251304.2 → XP_030107164.1 probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X1

UniProtKB/Swiss-Prot

E9QLY0, P70398, Q62497

Conserved Domains (2) 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 ...

cl28922
Location:905 → 969

Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
XM_030251308.2 → XP_030107168.1 probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X2

UniProtKB/Swiss-Prot

E9QLY0, P70398, Q62497

Conserved Domains (2) 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 ...

cl28922
Location:900 → 964

Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold