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USP9X ubiquitin specific peptidase 9 X-linked [ Homo sapiens (human) ]

Gene ID: 8239, updated on 1-Jun-2020

Summary

Official Symbol
USP9Xprovided by HGNC
Official Full Name
ubiquitin specific peptidase 9 X-linkedprovided by HGNC
Primary source
HGNC:HGNC:12632
See related
Ensembl:ENSG00000124486 MIM:300072
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
FAF; FAM; DFFRX; MRX99; MRXS99F
Summary
This gene is a member of the peptidase C19 family and encodes a protein that is similar to ubiquitin-specific proteases. Though this gene is located on the X chromosome, it escapes X-inactivation. Mutations in this gene have been associated with Turner syndrome. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in testis (RPKM 14.2), thyroid (RPKM 14.0) and 25 other tissues See more
Orthologs

Genomic context

See USP9X in Genome Data Viewer
Location:
Xp11.4
Exon count:
45
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (41085420..41236579)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (40944727..41095832)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 13807 Neighboring gene chloride intracellular channel 4 pseudogene 3 Neighboring gene uncharacterized LOC105373184 Neighboring gene long intergenic non-protein coding RNA 2601 Neighboring gene RNA, 5S ribosomal pseudogene 502

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Mental retardation, X-linked 99
MedGen: C3806746 OMIM: 300919 GeneReviews: Not available
Compare labs
Mental retardation, X-linked 99, syndromic, female-restricted
MedGen: C4225416 OMIM: 300968 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2018-03-28)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2018-03-28)

ClinGen Genome Curation PagePubMed

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
Lys48-specific deubiquitinase activity IDA
Inferred from Direct Assay
more info
PubMed 
co-SMAD binding IPI
Inferred from Physical Interaction
more info
PubMed 
cysteine-type endopeptidase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cysteine-type peptidase activity TAS
Traceable Author Statement
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
thiol-dependent ubiquitin-specific protease activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
thiol-dependent ubiquitinyl hydrolase activity EXP
Inferred from Experiment
more info
PubMed 
thiol-dependent ubiquitinyl hydrolase activity TAS
Traceable Author Statement
more info
 
ubiquitinyl hydrolase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
BMP signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
axon extension IMP
Inferred from Mutant Phenotype
more info
PubMed 
cell cycle IEA
Inferred from Electronic Annotation
more info
 
cell division IEA
Inferred from Electronic Annotation
more info
 
cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cellular protein metabolic process TAS
Traceable Author Statement
more info
 
chromosome segregation IEA
Inferred from Electronic Annotation
more info
 
female gamete generation TAS
Traceable Author Statement
more info
PubMed 
negative regulation of transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 
neuron migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of DNA demethylation IDA
Inferred from Direct Assay
more info
PubMed 
protein K48-linked deubiquitination IEA
Inferred from Electronic Annotation
more info
 
protein deubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein deubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein deubiquitination ISS
Inferred from Sequence or Structural Similarity
more info
 
protein deubiquitination TAS
Traceable Author Statement
more info
 
protein deubiquitination involved in ubiquitin-dependent protein catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein stabilization IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein targeting to peroxisome TAS
Traceable Author Statement
more info
 
protein ubiquitination TAS
Traceable Author Statement
more info
 
regulation of circadian rhythm IMP
Inferred from Mutant Phenotype
more info
PubMed 
rhythmic process IEA
Inferred from Electronic Annotation
more info
 
transforming growth factor beta receptor signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
growth cone IDA
Inferred from Direct Assay
more info
PubMed 
membrane HDA PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
probable ubiquitin carboxyl-terminal hydrolase FAF-X
Names
Drosophila fat facets related, X-linked
deubiquitinating enzyme FAF-X
fat facets in mammals
fat facets protein related, X-linked
hFAM
ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)
ubiquitin thioesterase FAF-X
ubiquitin thiolesterase FAF-X
ubiquitin-specific processing protease FAF-X
ubiquitin-specific protease 9, X chromosome
NP_001034679.2
NP_001034680.2
XP_005272732.1
XP_005272733.1

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_012547.1 RefSeqGene

    Range
    4811..155945
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001039590.3NP_001034679.2  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform 3

    See identical proteins and their annotated locations for NP_001034679.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) represents the longer transcript and encodes the longer isoform (3).
    Source sequence(s)
    AA261797, AF070645, AL109797, AL391259, AW183065, BC063645, BE925861, BX956755, CD619095, DA854185, X98296
    Consensus CDS
    CCDS43930.1
    UniProtKB/Swiss-Prot
    Q93008
    UniProtKB/TrEMBL
    Q6P468
    Related
    ENSP00000316357.6, ENST00000324545.8
    Conserved Domains (1) 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 ...
  2. NM_001039591.3NP_001034680.2  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform 4

    See identical proteins and their annotated locations for NP_001034680.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate in-frame splice site at the 3' end of an exon compared to variant 3. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 3.
    Source sequence(s)
    AA261797, AL109797, AL391259, AW183065, BC046205, BC063645, BE925861, BX956755, CD619095, DA854185, X98296
    Consensus CDS
    CCDS55403.1
    UniProtKB/Swiss-Prot
    Q93008
    UniProtKB/TrEMBL
    Q6P468, Q86X58
    Related
    ENSP00000367558.2, ENST00000378308.7
    Conserved Domains (1) 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 ...

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

    Range
    41085420..41236579
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005272675.4XP_005272732.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X1

    See identical proteins and their annotated locations for XP_005272732.1

    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 ...
    pfam00443
    Location:15621958
    UCH; Ubiquitin carboxyl-terminal hydrolase
  2. XM_005272676.4XP_005272733.1  probable ubiquitin carboxyl-terminal hydrolase FAF-X isoform X2

    See identical proteins and their annotated locations for XP_005272733.1

    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 ...
    pfam00443
    Location:15621958
    UCH; Ubiquitin carboxyl-terminal hydrolase

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_004652.3: Suppressed sequence

    Description
    NM_004652.3: This RefSeq was temporarily suppressed because currently there is insufficient data to support this transcript.
  2. NM_021906.2: Suppressed sequence

    Description
    NM_021906.2: This RefSeq was temporarily suppressed because currently there is insufficient data to support this transcript.
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