Human Gene USP47 (ENST00000339865.9) from GENCODE V44
  Description: Homo sapiens ubiquitin specific peptidase 47 (USP47), transcript variant 2, mRNA. (from RefSeq NM_017944)
Gencode Transcript: ENST00000339865.9
Gencode Gene: ENSG00000170242.19
Transcript (Including UTRs)
   Position: hg38 chr11:11,841,423-11,959,323 Size: 117,901 Total Exon Count: 27 Strand: +
Coding Region
   Position: hg38 chr11:11,842,186-11,956,175 Size: 113,990 Coding Exon Count: 27 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:11,841,423-11,959,323)mRNA (may differ from genome)Protein (1287 aa)
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PubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: UBP47_HUMAN
DESCRIPTION: RecName: Full=Ubiquitin carboxyl-terminal hydrolase 47; EC=3.4.19.12; AltName: Full=Deubiquitinating enzyme 47; AltName: Full=Ubiquitin thioesterase 47; AltName: Full=Ubiquitin-specific-processing protease 47;
FUNCTION: Ubiquitin-specific protease that specifically deubiquitinates monoubiquitinated DNA polymerase beta (POLB), stabilizing POLB thereby playing a role in base-excision repair (BER). Acts as a regulator of cell growth and genome integrity. May also indirectly regulates CDC25A expression at a transcriptional level.
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 BTRC and FBXW11. Interacts with POLB.
SUBCELLULAR LOCATION: Cytoplasm.
TISSUE SPECIFICITY: Expressed in skeletal muscle, heart and testis.
SIMILARITY: Belongs to the peptidase C19 family.
CAUTION: Was initially thought to catalytically inactive (PubMed:14715245). However, it was later shown that it is active (PubMed:21362556).
SEQUENCE CAUTION: Sequence=BAA91348.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 25.55 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 687.48 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 -350.30763-0.459 Picture PostScript Text
3' UTR -818.903148-0.260 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

ModBase Predicted Comparative 3D Structure on Q96K76
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
Genome BrowserGenome BrowserNo orthologGenome BrowserNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD Ensembl  
Protein SequenceProtein Sequence Protein Sequence  
AlignmentAlignment 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:0036459 thiol-dependent ubiquitinyl hydrolase activity
GO:0071987 WD40-repeat domain binding
GO:0101005 ubiquitinyl hydrolase activity

Biological Process:
GO:0006281 DNA repair
GO:0006284 base-excision repair
GO:0006508 proteolysis
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0006974 cellular response to DNA damage stimulus
GO:0010972 negative regulation of G2/M transition of mitotic cell cycle
GO:0016579 protein deubiquitination
GO:0030307 positive regulation of cell growth
GO:0034644 cellular response to UV
GO:0035520 monoubiquitinated protein deubiquitination
GO:0042493 response to drug
GO:0043066 negative regulation of apoptotic process
GO:0043154 negative regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0045892 negative regulation of transcription, DNA-templated
GO:0090263 positive regulation of canonical Wnt signaling pathway
GO:1902230 negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage

Cellular Component:
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0019005 SCF ubiquitin ligase complex


-  Descriptions from all associated GenBank mRNAs
  AK127264 - Homo sapiens cDNA FLJ45331 fis, clone BRHIP3007223, highly similar to Ubiquitin carboxyl-terminal hydrolase 47 (EC 3.1.2.15).
LF207854 - JP 2014500723-A/15357: Polycomb-Associated Non-Coding RNAs.
MA443431 - JP 2018138019-A/15357: Polycomb-Associated Non-Coding RNAs.
AK309240 - Homo sapiens cDNA, FLJ99281.
BC071559 - Homo sapiens cDNA clone IMAGE:4815410, containing frame-shift errors.
AK027362 - Homo sapiens cDNA FLJ14456 fis, clone HEMBB1001915, moderately similar to UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 64E (EC 3.1.2.15).
AK092290 - Homo sapiens cDNA FLJ34971 fis, clone NTONG2005373, highly similar to Ubiquitin carboxyl-terminal hydrolase 47 (EC 3.1.2.15).
AX747455 - Sequence 980 from Patent EP1308459.
BC148587 - Synthetic construct Homo sapiens clone IMAGE:100015552, MGC:183092 ubiquitin specific peptidase 47 (USP47) mRNA, encodes complete protein.
AK027283 - Homo sapiens cDNA FLJ14377 fis, clone HEMBA1001750.
LF207852 - JP 2014500723-A/15355: Polycomb-Associated Non-Coding RNAs.
MA443429 - JP 2018138019-A/15355: Polycomb-Associated Non-Coding RNAs.
LF369477 - JP 2014500723-A/176980: Polycomb-Associated Non-Coding RNAs.
MA605054 - JP 2018138019-A/176980: Polycomb-Associated Non-Coding RNAs.
CR749502 - Homo sapiens mRNA; cDNA DKFZp686C13257 (from clone DKFZp686C13257).
JD279306 - Sequence 260330 from Patent EP1572962.
LF369479 - JP 2014500723-A/176982: Polycomb-Associated Non-Coding RNAs.
MA605056 - JP 2018138019-A/176982: Polycomb-Associated Non-Coding RNAs.
LF369495 - JP 2014500723-A/176998: Polycomb-Associated Non-Coding RNAs.
MA605072 - JP 2018138019-A/176998: Polycomb-Associated Non-Coding RNAs.
LF369496 - JP 2014500723-A/176999: Polycomb-Associated Non-Coding RNAs.
MA605073 - JP 2018138019-A/176999: Polycomb-Associated Non-Coding RNAs.
LF369497 - JP 2014500723-A/177000: Polycomb-Associated Non-Coding RNAs.
MA605074 - JP 2018138019-A/177000: Polycomb-Associated Non-Coding RNAs.
LF369498 - JP 2014500723-A/177001: Polycomb-Associated Non-Coding RNAs.
MA605075 - JP 2018138019-A/177001: Polycomb-Associated Non-Coding RNAs.
AK074076 - Homo sapiens mRNA for FLJ00147 protein.
LF369499 - JP 2014500723-A/177002: Polycomb-Associated Non-Coding RNAs.
MA605076 - JP 2018138019-A/177002: Polycomb-Associated Non-Coding RNAs.
AL832991 - Homo sapiens mRNA; cDNA DKFZp666K033 (from clone DKFZp666K033).
LF369500 - JP 2014500723-A/177003: Polycomb-Associated Non-Coding RNAs.
MA605077 - JP 2018138019-A/177003: Polycomb-Associated Non-Coding RNAs.
LF369501 - JP 2014500723-A/177004: Polycomb-Associated Non-Coding RNAs.
MA605078 - JP 2018138019-A/177004: Polycomb-Associated Non-Coding RNAs.
AF059318 - Homo sapiens My002 protein mRNA, complete cds.
LF369503 - JP 2014500723-A/177006: Polycomb-Associated Non-Coding RNAs.
MA605080 - JP 2018138019-A/177006: Polycomb-Associated Non-Coding RNAs.
BC030562 - Homo sapiens ubiquitin specific peptidase 47, mRNA (cDNA clone IMAGE:4499200).
LF369504 - JP 2014500723-A/177007: Polycomb-Associated Non-Coding RNAs.
MA605081 - JP 2018138019-A/177007: Polycomb-Associated Non-Coding RNAs.
LF369505 - JP 2014500723-A/177008: Polycomb-Associated Non-Coding RNAs.
MA605082 - JP 2018138019-A/177008: Polycomb-Associated Non-Coding RNAs.
AK000734 - Homo sapiens cDNA FLJ20727 fis, clone HEP13238.
AK225358 - Homo sapiens mRNA for ubiquitin specific protease 47 variant, clone: HEP13238.
BC047044 - Homo sapiens ubiquitin specific peptidase 47, mRNA (cDNA clone IMAGE:5575723), partial cds.
LF369506 - JP 2014500723-A/177009: Polycomb-Associated Non-Coding RNAs.
MA605083 - JP 2018138019-A/177009: Polycomb-Associated Non-Coding RNAs.
LF369507 - JP 2014500723-A/177010: Polycomb-Associated Non-Coding RNAs.
MA605084 - JP 2018138019-A/177010: Polycomb-Associated Non-Coding RNAs.
JD512404 - Sequence 493428 from Patent EP1572962.
BC017795 - Homo sapiens ubiquitin specific peptidase 47, mRNA (cDNA clone IMAGE:4672711), partial cds.
LF369508 - JP 2014500723-A/177011: Polycomb-Associated Non-Coding RNAs.
MA605085 - JP 2018138019-A/177011: Polycomb-Associated Non-Coding RNAs.
LF369511 - JP 2014500723-A/177014: Polycomb-Associated Non-Coding RNAs.
MA605088 - JP 2018138019-A/177014: Polycomb-Associated Non-Coding RNAs.
LF369512 - JP 2014500723-A/177015: Polycomb-Associated Non-Coding RNAs.
MA605089 - JP 2018138019-A/177015: Polycomb-Associated Non-Coding RNAs.
LF369514 - JP 2014500723-A/177017: Polycomb-Associated Non-Coding RNAs.
MA605091 - JP 2018138019-A/177017: Polycomb-Associated Non-Coding RNAs.
LF369516 - JP 2014500723-A/177019: Polycomb-Associated Non-Coding RNAs.
MA605093 - JP 2018138019-A/177019: Polycomb-Associated Non-Coding RNAs.
LF369517 - JP 2014500723-A/177020: Polycomb-Associated Non-Coding RNAs.
MA605094 - JP 2018138019-A/177020: Polycomb-Associated Non-Coding RNAs.
BC000226 - Homo sapiens ubiquitin specific peptidase 47, mRNA (cDNA clone IMAGE:3350895), complete cds.
AK093714 - Homo sapiens cDNA FLJ36395 fis, clone THYMU2009338.
KJ902746 - Synthetic construct Homo sapiens clone ccsbBroadEn_12140 USP47 gene, encodes complete protein.
LF369519 - JP 2014500723-A/177022: Polycomb-Associated Non-Coding RNAs.
MA605096 - JP 2018138019-A/177022: Polycomb-Associated Non-Coding RNAs.
LF369520 - JP 2014500723-A/177023: Polycomb-Associated Non-Coding RNAs.
MA605097 - JP 2018138019-A/177023: Polycomb-Associated Non-Coding RNAs.
LF369521 - JP 2014500723-A/177024: Polycomb-Associated Non-Coding RNAs.
MA605098 - JP 2018138019-A/177024: Polycomb-Associated Non-Coding RNAs.
LF369522 - JP 2014500723-A/177025: Polycomb-Associated Non-Coding RNAs.
MA605099 - JP 2018138019-A/177025: Polycomb-Associated Non-Coding RNAs.
LF369523 - JP 2014500723-A/177026: Polycomb-Associated Non-Coding RNAs.
MA605100 - JP 2018138019-A/177026: Polycomb-Associated Non-Coding RNAs.
JD155088 - Sequence 136112 from Patent EP1572962.
JD318930 - Sequence 299954 from Patent EP1572962.
JD225820 - Sequence 206844 from Patent EP1572962.
JD155365 - Sequence 136389 from Patent EP1572962.
JD130227 - Sequence 111251 from Patent EP1572962.
LF369524 - JP 2014500723-A/177027: Polycomb-Associated Non-Coding RNAs.
MA605101 - JP 2018138019-A/177027: Polycomb-Associated Non-Coding RNAs.
JD027017 - Sequence 8041 from Patent EP1572962.
JD028610 - Sequence 9634 from Patent EP1572962.
JD026522 - Sequence 7546 from Patent EP1572962.
JD031692 - Sequence 12716 from Patent EP1572962.
JD022323 - Sequence 3347 from Patent EP1572962.
JD032238 - Sequence 13262 from Patent EP1572962.

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

Protein Q96K76 (Reactome details) participates in the following event(s):

R-HSA-5696947 USP47 deubiquitinates POLB
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: B3KXF5, ENST00000339865.1, ENST00000339865.2, ENST00000339865.3, ENST00000339865.4, ENST00000339865.5, ENST00000339865.6, ENST00000339865.7, ENST00000339865.8, NM_017944, Q658U0, Q86Y73, Q8TEP6, Q96K76, Q9BWI0, Q9NWN1, UBP47_HUMAN, uc001mjr.1, uc001mjr.2, uc001mjr.3, uc001mjr.4
UCSC ID: ENST00000339865.9
RefSeq Accession: NM_017944
Protein: Q96K76 (aka UBP47_HUMAN)
CCDS: CCDS41619.1

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