Human Gene USP9X (ENST00000378308.7_11) from GENCODE V47lift37
  Description: ubiquitin specific peptidase 9 X-linked, transcript variant 4 (from RefSeq NM_001039591.3)
Gencode Transcript: ENST00000378308.7_11
Gencode Gene: ENSG00000124486.15_16
Transcript (Including UTRs)
   Position: hg19 chrX:40,944,698-41,095,832 Size: 151,135 Total Exon Count: 45 Strand: +
Coding Region
   Position: hg19 chrX:40,982,882-41,091,777 Size: 108,896 Coding Exon Count: 44 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:40,944,698-41,095,832)mRNA (may differ from genome)Protein (2554 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: USP9X_HUMAN
DESCRIPTION: RecName: Full=Probable ubiquitin carboxyl-terminal hydrolase FAF-X; EC=3.4.19.12; AltName: Full=Deubiquitinating enzyme FAF-X; AltName: Full=Fat facets in mammals; Short=hFAM; AltName: Full=Fat facets protein-related, X-linked; AltName: Full=Ubiquitin thioesterase FAF-X; AltName: Full=Ubiquitin-specific protease 9, X chromosome; AltName: Full=Ubiquitin-specific-processing protease FAF-X;
FUNCTION: Deubiquitinase involved both in the processing of ubiquitin precursors and of ubiquitinated proteins. May therefore play an important role regulatory role at the level of protein turnover by preventing degradation of proteins through the removal of conjugated ubiquitin. Essential component of TGF-beta/BMP signaling cascade. Regulates chromosome alignment and segregation in mitosis by regulating the localization of BIRC5/survivin to mitotic centromeres. Specifically hydrolyzes both 'Lys-29'- and 'Lys-33'-linked polyubiquitins chains. Specifically deubiquitinates monoubiquitinated SMAD4, opposing the activity of E3 ubiquitin-protein ligase TRIM33.
CATALYTIC ACTIVITY: Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C- terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
SUBUNIT: Interacts with SMAD4, MARK4, NUAK1 and BIRC5/survivin.
INTERACTION: Q13485:SMAD4; NbExp=2; IntAct=EBI-302524, EBI-347263;
SUBCELLULAR LOCATION: Cytoplasm.
TISSUE SPECIFICITY: Widely expressed in embryonic and adult tissues.
MISCELLANEOUS: Escapes X-inactivation.
SIMILARITY: Belongs to the peptidase C19 family.
SEQUENCE CAUTION: Sequence=CAD13527.2; Type=Erroneous gene model prediction; Sequence=CAD18900.2; Type=Erroneous gene model prediction;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: USP9X
Diseases sorted by gene-association score: mental retardation, x-linked 99* (1330), mental retardation, x-linked 99, syndromic, female-restricted* (900), x-linked non-specific intellectual disability* (106), mental retsrdation, x-linked syndromic, female restricted* (100), triple-receptor negative breast cancer (11)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 17.35 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 524.90 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -353.90823-0.430 Picture PostScript Text
3' UTR -1018.304055-0.251 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011989 - ARM-like
IPR018200 - Pept_C19ubi-hydrolase_C_CS
IPR001394 - Peptidase_C19

Pfam Domains:
PF00443 - Ubiquitin carboxyl-terminal hydrolase
PF12030 - Domain of unknown function (DUF3517)
PF13423 - Ubiquitin carboxyl-terminal hydrolase

SCOP Domains:
48371 - ARM repeat
48065 - DBL homology domain (DH-domain)
51445 - (Trans)glycosidases
54236 - Ubiquitin-like
54001 - Cysteine proteinases

ModBase Predicted Comparative 3D Structure on Q93008
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004197 cysteine-type endopeptidase activity
GO:0005515 protein binding
GO:0008233 peptidase activity
GO:0008234 cysteine-type peptidase activity
GO:0016787 hydrolase activity
GO:0036459 thiol-dependent ubiquitinyl hydrolase activity
GO:0070410 co-SMAD binding
GO:1990380 Lys48-specific deubiquitinase activity

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001764 neuron migration
GO:0006508 proteolysis
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0006625 protein targeting to peroxisome
GO:0007049 cell cycle
GO:0007059 chromosome segregation
GO:0007179 transforming growth factor beta receptor signaling pathway
GO:0007292 female gamete generation
GO:0016579 protein deubiquitination
GO:0030509 BMP signaling pathway
GO:0044267 cellular protein metabolic process
GO:0048675 axon extension
GO:0051301 cell division
GO:0071108 protein K48-linked deubiquitination
GO:1901537 positive regulation of DNA demethylation

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane
GO:0030426 growth cone
GO:0042995 cell projection


-  Descriptions from all associated GenBank mRNAs
  X98296 - H.sapiens mRNA for ubiquitin hydrolase.
BC172429 - Synthetic construct Homo sapiens clone IMAGE:100069123, MGC:199134 ubiquitin specific peptidase 9, X-linked (USP9X) mRNA, encodes complete protein.
AK294828 - Homo sapiens cDNA FLJ60509 complete cds, highly similar to Probable ubiquitin carboxyl-terminalhydrolase FAF-X (EC 3.1.2.15).
LF329243 - JP 2014500723-A/136746: Polycomb-Associated Non-Coding RNAs.
LF329242 - JP 2014500723-A/136745: Polycomb-Associated Non-Coding RNAs.
LF329241 - JP 2014500723-A/136744: Polycomb-Associated Non-Coding RNAs.
LF383451 - JP 2014500723-A/190954: Polycomb-Associated Non-Coding RNAs.
AB209666 - Homo sapiens mRNA for USP9X protein variant protein.
BC063645 - Homo sapiens ubiquitin specific peptidase 9, X-linked, mRNA (cDNA clone IMAGE:4538919), partial cds.
BC046205 - Homo sapiens ubiquitin specific peptidase 9, X-linked, mRNA (cDNA clone IMAGE:6175281), partial cds.
AF070645 - Homo sapiens clone 24650 ubiquitin hydrolase mRNA, partial cds.
LF211419 - JP 2014500723-A/18922: Polycomb-Associated Non-Coding RNAs.
LF379329 - JP 2014500723-A/186832: Polycomb-Associated Non-Coding RNAs.
JD174810 - Sequence 155834 from Patent EP1572962.
LF379330 - JP 2014500723-A/186833: Polycomb-Associated Non-Coding RNAs.
JD365471 - Sequence 346495 from Patent EP1572962.
LF379331 - JP 2014500723-A/186834: Polycomb-Associated Non-Coding RNAs.
LF379332 - JP 2014500723-A/186835: Polycomb-Associated Non-Coding RNAs.
JD386680 - Sequence 367704 from Patent EP1572962.
AJ012078 - Homo sapiens mRNA for fat facets protein, 3' end.
LF379333 - JP 2014500723-A/186836: Polycomb-Associated Non-Coding RNAs.
BC054861 - Homo sapiens cDNA clone IMAGE:4041327, partial cds.
BC014792 - Homo sapiens, clone IMAGE:3857207, mRNA.
LF379334 - JP 2014500723-A/186837: Polycomb-Associated Non-Coding RNAs.
LF379336 - JP 2014500723-A/186839: Polycomb-Associated Non-Coding RNAs.
LF379337 - JP 2014500723-A/186840: Polycomb-Associated Non-Coding RNAs.
LF379338 - JP 2014500723-A/186841: Polycomb-Associated Non-Coding RNAs.
LF379339 - JP 2014500723-A/186842: Polycomb-Associated Non-Coding RNAs.
LF379342 - JP 2014500723-A/186845: Polycomb-Associated Non-Coding RNAs.
LF379343 - JP 2014500723-A/186846: Polycomb-Associated Non-Coding RNAs.
LF379344 - JP 2014500723-A/186847: Polycomb-Associated Non-Coding RNAs.
LF379345 - JP 2014500723-A/186848: Polycomb-Associated Non-Coding RNAs.
LF379346 - JP 2014500723-A/186849: Polycomb-Associated Non-Coding RNAs.
LF379348 - JP 2014500723-A/186851: Polycomb-Associated Non-Coding RNAs.
LF379349 - JP 2014500723-A/186852: Polycomb-Associated Non-Coding RNAs.
MA564820 - JP 2018138019-A/136746: Polycomb-Associated Non-Coding RNAs.
MA564819 - JP 2018138019-A/136745: Polycomb-Associated Non-Coding RNAs.
MA564818 - JP 2018138019-A/136744: Polycomb-Associated Non-Coding RNAs.
MA619028 - JP 2018138019-A/190954: Polycomb-Associated Non-Coding RNAs.
MA446996 - JP 2018138019-A/18922: Polycomb-Associated Non-Coding RNAs.
MA614906 - JP 2018138019-A/186832: Polycomb-Associated Non-Coding RNAs.
MA614907 - JP 2018138019-A/186833: Polycomb-Associated Non-Coding RNAs.
MA614908 - JP 2018138019-A/186834: Polycomb-Associated Non-Coding RNAs.
MA614909 - JP 2018138019-A/186835: Polycomb-Associated Non-Coding RNAs.
MA614910 - JP 2018138019-A/186836: Polycomb-Associated Non-Coding RNAs.
MA614911 - JP 2018138019-A/186837: Polycomb-Associated Non-Coding RNAs.
MA614913 - JP 2018138019-A/186839: Polycomb-Associated Non-Coding RNAs.
MA614914 - JP 2018138019-A/186840: Polycomb-Associated Non-Coding RNAs.
MA614915 - JP 2018138019-A/186841: Polycomb-Associated Non-Coding RNAs.
MA614916 - JP 2018138019-A/186842: Polycomb-Associated Non-Coding RNAs.
MA614919 - JP 2018138019-A/186845: Polycomb-Associated Non-Coding RNAs.
MA614920 - JP 2018138019-A/186846: Polycomb-Associated Non-Coding RNAs.
MA614921 - JP 2018138019-A/186847: Polycomb-Associated Non-Coding RNAs.
MA614922 - JP 2018138019-A/186848: Polycomb-Associated Non-Coding RNAs.
MA614923 - JP 2018138019-A/186849: Polycomb-Associated Non-Coding RNAs.
MA614925 - JP 2018138019-A/186851: Polycomb-Associated Non-Coding RNAs.
MA614926 - JP 2018138019-A/186852: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q93008 (Reactome details) participates in the following event(s):

R-HSA-870479 USP9X (FAM) binds to ubiquitinated SMAD4
R-HSA-5661157 USP9X binds Ub-SNCA
R-HSA-9033509 USP9X binds Ub:PEX5L
R-HSA-9033526 USP9X binds Ub:PEX5S
R-HSA-870437 USP9X (FAM) deubiquitinates SMAD4
R-HSA-5661161 USP9X:SNCA dissociates
R-HSA-9033478 USP9X hydrolyzes Ub:PEX5S yielding PEX5S and Ubiquitin
R-HSA-9033491 USP9X hydrolyzes Ub:PEX5L yielding PEX5L and Ubiquitin
R-HSA-5660752 USP9X deubiquitinates Ub-SNCA
R-HSA-8853503 UCHL3,USP7,USP9X cleaves RPS27A yielding ubiquitin
R-HSA-8853514 UCHL3,USP7,USP9X cleaves UBA52 yielding ubiquitin
R-HSA-2173795 Downregulation of SMAD2/3:SMAD4 transcriptional activity
R-HSA-5689880 Ub-specific processing proteases
R-HSA-977225 Amyloid fiber formation
R-HSA-9033241 Peroxisomal protein import
R-HSA-2173793 Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer
R-HSA-5688426 Deubiquitination
R-HSA-392499 Metabolism of proteins
R-HSA-8866652 Synthesis of active ubiquitin: roles of E1 and E2 enzymes
R-HSA-170834 Signaling by TGF-beta Receptor Complex
R-HSA-212436 Generic Transcription Pathway
R-HSA-597592 Post-translational protein modification
R-HSA-8852135 Protein ubiquitination
R-HSA-9006936 Signaling by TGF-beta family members
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-162582 Signal Transduction
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: DFFRX, ENST00000378308.1, ENST00000378308.2, ENST00000378308.3, ENST00000378308.4, ENST00000378308.5, ENST00000378308.6, FAM, NM_001039591, O75550, Q8WWT3, Q8WX12, Q93008, uc318ofa.1, uc318ofa.2, USP9, USP9X , USP9X_HUMAN
UCSC ID: ENST00000378308.7_11
RefSeq Accession: NM_001039591.3
Protein: Q93008 (aka USP9X_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.