Human Gene USP25 (uc002yjz.1)
  Description: Homo sapiens ubiquitin specific peptidase 25 (USP25), mRNA.
RefSeq Summary (NM_013396): Ubiquitin (MIM 191339) is a highly conserved 76-amino acid protein involved in regulation of intracellular protein breakdown, cell cycle regulation, and stress response. Ubiquitin is released from degraded proteins by disassembly of the polyubiquitin chains, which is mediated by ubiquitin-specific proteases (USPs), such as USP25 (Valero et al., 1999 [PubMed 10644437]).[supplied by OMIM, Mar 2008].
Transcript (Including UTRs)
   Position: hg19 chr21:17,102,496-17,252,377 Size: 149,882 Total Exon Count: 25 Strand: +
Coding Region
   Position: hg19 chr21:17,102,713-17,250,794 Size: 148,082 Coding Exon Count: 25 

Page IndexSequence and LinksPrimersGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr21:17,102,496-17,252,377)mRNA (may differ from genome)Protein (1087 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCLynxMGIOMIMPubMed
ReactomeTreefamUniProtKBBioGrid CRISPR DB

-  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.
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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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): USP25
CDC HuGE Published Literature: USP25
Positive Disease Associations: Hemoglobin A, Glycosylated , panic disorder
Related Studies:
  1. Hemoglobin A, Glycosylated
    Andrew D Paterson et al. Diabetes 2010, A genome-wide association study identifies a novel major locus for glycemic control in type 1 diabetes, as measured by both A1C and glucose., Diabetes. [PubMed 19875614]
    A major locus for A1C and glucose in individuals with diabetes is near SORCS1. This may influence the design and analysis of genetic studies attempting to identify risk factors for long-term diabetic complications.
  2. panic disorder
    Otowa ,et al. 2009, Genome-wide association study of panic disorder in the Japanese population, Journal of human genetics 2009 54- 2 : 122-6. [PubMed 19165232]

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

+  Common Gene Haplotype Alleles
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-  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
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -133.90217-0.617 Picture PostScript Text
3' UTR -359.671583-0.227 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
  Pfam Domains:
PF00443 - Ubiquitin carboxyl-terminal hydrolase
PF02809 - Ubiquitin interaction motif
PF13423 - Ubiquitin carboxyl-terminal hydrolase

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

ModBase Predicted Comparative 3D Structure on Q9UHP3-1
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 orthologGenome BrowserNo ortholog
Gene Details   Gene Details 
Gene Sorter   Gene Sorter 
    WormBase 
    Protein Sequence 
    Alignment 

-  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.
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: AF170562, NM_013396, NP_037528, Q9UHP3-1, USP21
UCSC ID: uc002yjz.1
RefSeq Accession: NM_013396
Protein: Q9UHP3-1, splice isoform of Q9UHP3 CCDS: CCDS33515.1, CCDS63336.1, CCDS63337.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AF170562.1
exon count: 25CDS single in 3' UTR: no RNA size: 5213
ORF size: 3264CDS single in intron: no Alignment % ID: 99.90
txCdsPredict score: 6728.00frame shift in genome: no % Coverage: 97.06
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.