Human Gene USP25 (ENST00000400183.7_8) from GENCODE V47lift37
  Description: ubiquitin specific peptidase 25, transcript variant 1 (from RefSeq NM_001283041.3)
Gencode Transcript: ENST00000400183.7_8
Gencode Gene: ENSG00000155313.16_11
Transcript (Including UTRs)
   Position: hg19 chr21:17,102,301-17,252,383 Size: 150,083 Total Exon Count: 26 Strand: +
Coding Region
   Position: hg19 chr21:17,102,713-17,250,794 Size: 148,082 Coding Exon Count: 26 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr21:17,102,301-17,252,383)mRNA (may differ from genome)Protein (1125 aa)
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BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: UBP25_HUMAN
DESCRIPTION: RecName: Full=Ubiquitin carboxyl-terminal hydrolase 25; EC=3.4.19.12; AltName: Full=Deubiquitinating enzyme 25; AltName: Full=USP on chromosome 21; AltName: Full=Ubiquitin thioesterase 25; AltName: Full=Ubiquitin-specific-processing protease 25;
FUNCTION: Deubiquitinating enzyme that hydrolyzes ubiquitin moieties conjugated to substrates and thus, functions to process newly synthesized Ubiquitin, to recycle ubiquitin molecules or to edit polyubiquitin chains and prevents proteasomal degradation of substrates. Hydrolyzes both 'Lys-48'- and 'Lys-63'-linked tetraubiquitin chains.
FUNCTION: The muscle-specific isoform (USP25m) may have a role in the regulation of muscular differentiation and function.
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: Homodimer or oligomer. Interacts with ACTA1 (via its C- terminus); the interaction occurs for all isoforms but is strongest for isoform USP25m in muscle differentiating cells. Interacts (isoform USP25m only) with MYBPC1; the interaction prevents proteasomal degradation of MYBPC1. Interacts (isoform USP25m only) with FLNC (via filament repeats 17-18, 20-21 and 24). Interacts with GAPDH. Interacts with SUMO3; the interaction sumoylates efficiently USP25. Interacts with SUMO2; the interaction sumoylates efficiently USP25. Interacts with SUMO1; the interaction only weakly sumoylates USP25. Interacts with SYK; phosphorylates USP25 and regulates USP25 intracellular levels.
SUBCELLULAR LOCATION: Cytoplasm.
SUBCELLULAR LOCATION: Isoform USP25m: Cytoplasm (By similarity). Nucleus (By similarity). Note=Some transient punctuate nuclear location in myotubes during myocyte development (By similarity).
TISSUE SPECIFICITY: Isoform USB25a is found in most adult and fetal tissues; expression is moderately high in testis, pancreas, kidney, skeletal muscle, liver, lung, placenta, brain, heart, but very low in peripheral blood, colon, small intestine, ovary, prostate, thymus and spleen. Isoform USB25b is found in all tissues except heart and skeletal muscle. Isoform USB25m is heart and skeletal muscle specific.
INDUCTION: The muscle-specific isoform (USP25m) is up-regulated during myocyte differentiation. Levels increase up to 100-fold towards completion of differentiation.
PTM: Acetylated.
PTM: Sumoylation impairs binding to and hydrolysis of ubiquitin chains. Sumoylated preferentially with SUMO2 or SUMO3. Desumoylated by SENP1. Regulated by ubiquitination on the same residue.
PTM: Preferentially monoubiquitinated but can also be polyubiquitinated. Autodeubiquitinated. Ubiquitination activates the enzymatic activity either by preventing sumoylation or by allowing novel interactions.
PTM: Phosphorylation in the C-terminal by SYK regulates USP25 cellular levels.
SIMILARITY: Belongs to the peptidase C19 family.
SIMILARITY: Contains 1 UBA-like domain.
SIMILARITY: Contains 2 UIM (ubiquitin-interacting motif) repeats.

-  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


-  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: 33.96 RPKM in Testis
Total median expression: 502.70 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 -228.00412-0.553 Picture PostScript Text
3' UTR -339.401589-0.214 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
IPR018200 - Pept_C19ubi-hydrolase_C_CS
IPR001394 - Peptidase_C19
IPR009060 - UBA-like
IPR003903 - Ubiquitin-int_motif

Pfam Domains:
PF00443 - Ubiquitin carboxyl-terminal hydrolase
PF02809 - Ubiquitin interaction motif

SCOP Domains:
46934 - UBA-like
54001 - Cysteine proteinases

ModBase Predicted Comparative 3D Structure on Q9UHP3
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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 orthologGenome BrowserNo ortholog
Gene DetailsGene Details  Gene Details 
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 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004843 thiol-dependent ubiquitin-specific protease activity
GO:0005515 protein binding
GO:0008233 peptidase activity
GO:0008234 cysteine-type peptidase activity
GO:0016787 hydrolase activity
GO:0031625 ubiquitin protein ligase binding
GO:0036459 thiol-dependent ubiquitinyl hydrolase activity
GO:0043130 ubiquitin binding
GO:0051117 ATPase binding
GO:1904455 ubiquitin-specific protease activity involved in negative regulation of ERAD pathway

Biological Process:
GO:0006464 cellular protein modification process
GO:0006508 proteolysis
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0016579 protein deubiquitination
GO:0070536 protein K63-linked deubiquitination
GO:0071108 protein K48-linked deubiquitination
GO:1904293 negative regulation of ERAD pathway

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  BC075792 - Homo sapiens ubiquitin specific peptidase 25, mRNA (cDNA clone MGC:87147 IMAGE:30346400), complete cds.
AF170562 - Homo sapiens ubiquitin-specific processing protease (USP25) mRNA, complete cds.
AF134213 - Homo sapiens ubiquitin-specific protease (USP21) mRNA, complete cds.
BC015930 - Homo sapiens ubiquitin specific peptidase 25, mRNA (cDNA clone IMAGE:3920963), complete cds.
CU677515 - Synthetic construct Homo sapiens gateway clone IMAGE:100019458 5' read USP25 mRNA.
CU687288 - Synthetic construct Homo sapiens gateway clone IMAGE:100023012 5' read USP25 mRNA.
KJ893694 - Synthetic construct Homo sapiens clone ccsbBroadEn_03088 USP25 gene, encodes complete protein.
KJ902508 - Synthetic construct Homo sapiens clone ccsbBroadEn_11902 USP25 gene, encodes complete protein.
FJ763652 - Homo sapiens ubiquitin-specific protease USP25 muscle isoform mRNA, complete cds, alternatively spliced.
JD458343 - Sequence 439367 from Patent EP1572962.
JD479021 - Sequence 460045 from Patent EP1572962.
JD455554 - Sequence 436578 from Patent EP1572962.
JD458282 - Sequence 439306 from Patent EP1572962.
JD189479 - Sequence 170503 from Patent EP1572962.
JD189480 - Sequence 170504 from Patent EP1572962.
JD189481 - Sequence 170505 from Patent EP1572962.
JD516440 - Sequence 497464 from Patent EP1572962.
JD056228 - Sequence 37252 from Patent EP1572962.
JD056230 - Sequence 37254 from Patent EP1572962.
JD056229 - Sequence 37253 from Patent EP1572962.
AK022574 - Homo sapiens cDNA FLJ12512 fis, clone NT2RM2001730, weakly similar to PROBABLE UBIQUITIN CARBOXYL-TERMINAL HYDROLASE K02C4.3 (EC 3.1.2.15).
HG765100 - Homo Sapiens partial mRNA for Ubiquitin carboxyl-terminal hydrolase 25 (usp25 gene).
AK022447 - Homo sapiens cDNA FLJ12385 fis, clone MAMMA1002619, weakly similar to PROBABLE UBIQUITIN CARBOXYL-TERMINAL HYDROLASE K02C4.3 (EC 3.1.2.15).
AK094083 - Homo sapiens cDNA FLJ36764 fis, clone UTERU2019038, moderately similar to UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 21 (EC 3.1.2.15).
BC018686 - Homo sapiens, clone IMAGE:4696066, mRNA.
JD503679 - Sequence 484703 from Patent EP1572962.
JD350416 - Sequence 331440 from Patent EP1572962.
JD166511 - Sequence 147535 from Patent EP1572962.
JD188361 - Sequence 169385 from Patent EP1572962.
JD303970 - Sequence 284994 from Patent EP1572962.

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

Protein Q9UHP3 (Reactome details) participates in the following event(s):

R-HSA-5696564 USP25 deubiquitinates DDX58
R-HSA-5689880 Ub-specific processing proteases
R-HSA-5688426 Deubiquitination
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: C0LSZ0, ENST00000400183.1, ENST00000400183.2, ENST00000400183.3, ENST00000400183.4, ENST00000400183.5, ENST00000400183.6, NM_001283041, Q6DHZ9, Q9H9W1, Q9UHP3, UBP25_HUMAN, uc319ath.1, uc319ath.2, USP21
UCSC ID: ENST00000400183.7_8
RefSeq Accession: NM_001283041.3
Protein: Q9UHP3 (aka UBP25_HUMAN or UB25_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.