Human Gene USP1 (ENST00000339950.5_4) from GENCODE V47lift37
  Description: ubiquitin specific peptidase 1, transcript variant 1 (from RefSeq NM_003368.5)
Gencode Transcript: ENST00000339950.5_4
Gencode Gene: ENSG00000162607.13_9
Transcript (Including UTRs)
   Position: hg19 chr1:62,902,720-62,917,475 Size: 14,756 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr1:62,905,539-62,916,652 Size: 11,114 Coding Exon Count: 8 

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 (chr1:62,902,720-62,917,475)mRNA (may differ from genome)Protein (785 aa)
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-  Comments and Description Text from UniProtKB
  ID: UBP1_HUMAN
DESCRIPTION: RecName: Full=Ubiquitin carboxyl-terminal hydrolase 1; EC=3.4.19.12; AltName: Full=Deubiquitinating enzyme 1; Short=hUBP; AltName: Full=Ubiquitin thioesterase 1; AltName: Full=Ubiquitin-specific-processing protease 1;
FUNCTION: Negative regulator of DNA damage repair which specifically deubiquitinates monoubiquitinated FANCD2. Also involved in PCNA-mediated translesion synthesis (TLS) by deubiquitinating monoubiquitinated PCNA. Has almost no deubiquitinating activity by itself and requires the interaction with WDR48 to have a high activity.
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).
BIOPHYSICOCHEMICAL PROPERTIES: Kinetic parameters: KM=0.7 uM for ubiquitin vinyl sulfone (in presence of WDR48); KM=1.4 uM for ubiquitin vinyl sulfone (in absence of WDR48);
SUBUNIT: Interacts with FANCD2 and PCNA. Interacts with WDR48.
SUBCELLULAR LOCATION: Nucleus.
DEVELOPMENTAL STAGE: Cell cycle-regulated. Highest level during S phase.
INDUCTION: Down-regulated following DNA damage.
PTM: Autocatalytic cleavage of USP1 following UV irradiation inactivates it leading to an increase in ubiquitinated PCNA, recruitment of POLH and translesion synthesis.
PTM: Ubiquitinated; leading to its subsequent proteasomal degradation (By similarity).
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
MISCELLANEOUS: HEK293T cells expressing reduced levels of USP1 show a higher level of ubiquitinated PCNA and an increase in point mutations upon UV irradiation.
SIMILARITY: Belongs to the peptidase C19 family.
SEQUENCE CAUTION: Sequence=AAH18745.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=AAH32364.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=BAD92130.1; Type=Frameshift; Positions=230;

-  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: USP1
Diseases sorted by gene-association score: fanconi anemia, complementation group a (1)

-  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: 25.59 RPKM in Testis
Total median expression: 425.98 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 -186.90421-0.444 Picture PostScript Text
3' UTR -174.70823-0.212 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

Pfam Domains:
PF00443 - Ubiquitin carboxyl-terminal hydrolase
PF13423 - Ubiquitin carboxyl-terminal hydrolase

SCOP Domains:
54001 - Cysteine proteinases

ModBase Predicted Comparative 3D Structure on O94782
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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 orthologNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004197 cysteine-type endopeptidase activity
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:0036459 thiol-dependent ubiquitinyl hydrolase activity

Biological Process:
GO:0001501 skeletal system development
GO:0006281 DNA repair
GO:0006282 regulation of DNA repair
GO:0006508 proteolysis
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0006974 cellular response to DNA damage stimulus
GO:0009411 response to UV
GO:0016579 protein deubiquitination
GO:0035520 monoubiquitinated protein deubiquitination
GO:0042769 DNA damage response, detection of DNA damage

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm


-  Descriptions from all associated GenBank mRNAs
  BC050525 - Homo sapiens ubiquitin specific peptidase 1, mRNA (cDNA clone MGC:57511 IMAGE:6473568), complete cds.
AK312423 - Homo sapiens cDNA, FLJ92762, highly similar to Homo sapiens ubiquitin specific protease 1 (USP1), mRNA.
AB208893 - Homo sapiens mRNA for ubiquitin specific protease 1 variant protein.
AF117386 - Homo sapiens ubiquitin-specific protease (UBP) mRNA, complete cds.
AB014458 - Homo sapiens hUBP mRNA for ubiquitin specific protease, complete cds.
AL117575 - Homo sapiens mRNA; cDNA DKFZp434A028 (from clone DKFZp434A028).
AB463330 - Synthetic construct DNA, clone: pF1KB8568, Homo sapiens USP1 gene for ubiquitin specific peptidase 1, without stop codon, in Flexi system.
AM392756 - Synthetic construct Homo sapiens clone IMAGE:100001650 for hypothetical protein (USP1 gene).
KJ892366 - Synthetic construct Homo sapiens clone ccsbBroadEn_01760 USP1 gene, encodes complete protein.
BC023216 - Homo sapiens ubiquitin specific peptidase 1, mRNA (cDNA clone IMAGE:4997027).
BC040140 - Homo sapiens ubiquitin specific peptidase 1, mRNA (cDNA clone IMAGE:5114272), with apparent retained intron.
BC018745 - Homo sapiens ubiquitin specific peptidase 1, mRNA (cDNA clone IMAGE:4649027), partial cds.
JD433833 - Sequence 414857 from Patent EP1572962.
BC011881 - Homo sapiens ubiquitin specific peptidase 1, mRNA (cDNA clone IMAGE:3619458), with apparent retained intron.
BC032364 - Homo sapiens ubiquitin specific peptidase 1, mRNA (cDNA clone IMAGE:4524293), partial cds.
JD201947 - Sequence 182971 from Patent EP1572962.
JD218109 - Sequence 199133 from Patent EP1572962.
JD458573 - Sequence 439597 from Patent EP1572962.
JD294404 - Sequence 275428 from Patent EP1572962.
JD154060 - Sequence 135084 from Patent EP1572962.
CU690704 - Synthetic construct Homo sapiens gateway clone IMAGE:100021529 5' read USP1 mRNA.
AK096788 - Homo sapiens cDNA FLJ39469 fis, clone PROST2012550, highly similar to Ubiquitin specific protease 1.
AL117503 - Homo sapiens mRNA; cDNA DKFZp434E0635 (from clone DKFZp434E0635); partial cds.

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

Protein O94782 (Reactome details) participates in the following event(s):

R-HSA-5655483 USP1 autocleavage
R-HSA-5655481 USP1:WDR48 binds monoUb:K164-PCNA
R-HSA-5655466 USP1:WDR48 deubiquitinates monoUb:K164-PCNA
R-HSA-6786171 FANCD2 deubiquitination by USP1:WDR48
R-HSA-110314 Recognition of DNA damage by PCNA-containing replication complex
R-HSA-73893 DNA Damage Bypass
R-HSA-6783310 Fanconi Anemia Pathway
R-HSA-73894 DNA Repair

-  Other Names for This Gene
  Alternate Gene Symbols: A0PJ95, D3DQ57, ENST00000339950.1, ENST00000339950.2, ENST00000339950.3, ENST00000339950.4, NM_003368, O94782, Q05BX7, Q59H66, Q9UFR0, Q9UNJ3, UBP1_HUMAN, uc317vna.1, uc317vna.2
UCSC ID: ENST00000339950.5_4
RefSeq Accession: NM_003368.5
Protein: O94782 (aka UBP1_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.