Human Gene USP46 (uc003gzn.3)
  Description: Homo sapiens ubiquitin specific peptidase 46 (USP46), transcript variant 1, mRNA.
RefSeq Summary (NM_022832): Modification of cellular proteins by ubiquitin is an essential regulatory mechanism controlled by the coordinated action of multiple ubiquitin-conjugating and deubiquitinating enzymes. USP46 belongs to a large family of cysteine proteases that function as deubiquitinating enzymes (Quesada et al., 2004 [PubMed 14715245]).[supplied by OMIM, Jun 2009].
Transcript (Including UTRs)
   Position: hg19 chr4:53,457,127-53,525,502 Size: 68,376 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr4:53,463,806-53,525,317 Size: 61,512 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:53,457,127-53,525,502)mRNA (may differ from genome)Protein (366 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: UBP46_HUMAN
DESCRIPTION: RecName: Full=Ubiquitin carboxyl-terminal hydrolase 46; EC=3.4.19.12; AltName: Full=Deubiquitinating enzyme 46; AltName: Full=Ubiquitin thioesterase 46; AltName: Full=Ubiquitin-specific-processing protease 46;
FUNCTION: Deubiquitinating enzyme that plays a role in behavior, possibly by regulating GABA action. May act by mediating the deubiquitination of GAD1/GAD67. Has almost no deubiquitinating activity by itself and requires the interaction with WDR48 to have a high activity. Not involved in deubiquitination of monoubiquitinated FANCD2.
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 WDR48.
TISSUE SPECIFICITY: Broadly expressed.
SIMILARITY: Belongs to the peptidase C19 family. USP12/USP46 subfamily.

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): USP46
CDC HuGE Published Literature: USP46
Positive Disease Associations: Biochemical measures
Related Studies:
  1. Biochemical measures
    Zemunik ,et al. 2009, Genome-wide association study of biochemical traits in Korcula Island, Croatia, Croatian medical journal 2009 50- 1 : 23-33. [PubMed 19260141]

-  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: 14.24 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 253.25 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 -62.50185-0.338 Picture PostScript Text
3' UTR -1972.806679-0.295 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 P62068
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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 orthologGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details  Gene DetailsGene Details 
Gene Sorter  Gene SorterGene Sorter 
  EnsemblFlyBaseWormBase 
  Protein SequenceProtein SequenceProtein Sequence 
  AlignmentAlignmentAlignment 

-  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:0046872 metal ion binding
GO:0101005 ubiquitinyl hydrolase activity

Biological Process:
GO:0001662 behavioral fear response
GO:0006508 proteolysis
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0007610 behavior
GO:0008343 adult feeding behavior
GO:0016579 protein deubiquitination
GO:0032228 regulation of synaptic transmission, GABAergic
GO:0048149 behavioral response to ethanol
GO:0060013 righting reflex


-  Descriptions from all associated GenBank mRNAs
  BC037574 - Homo sapiens ubiquitin specific peptidase 46, mRNA (cDNA clone MGC:44970 IMAGE:5529667), complete cds.
AK024318 - Homo sapiens cDNA FLJ14256 fis, clone PLACE1000007, weakly similar to PROBABLE UBIQUITIN CARBOXYL-TERMINAL HYDROLASE R10E11.3 (EC 3.1.2.15).
AK022614 - Homo sapiens cDNA FLJ12552 fis, clone NT2RM4000712, moderately similar to Homo sapiens ubiquitin hydrolyzing enzyme I (UBH1) mRNA.
AK299883 - Homo sapiens cDNA FLJ52275 complete cds, highly similar to Ubiquitin carboxyl-terminal hydrolase 46 (EC 3.1.2.15).
AK296493 - Homo sapiens cDNA FLJ58777 complete cds, highly similar to Ubiquitin carboxyl-terminal hydrolase 46 (EC 3.1.2.15).
AK302438 - Homo sapiens cDNA FLJ52415 complete cds, highly similar to Ubiquitin carboxyl-terminal hydrolase 46 (EC 3.1.2.15).
GU455414 - Homo sapiens ubiquitin specific protease 46 (USP46) mRNA, complete cds.
DQ896764 - Synthetic construct Homo sapiens clone IMAGE:100011224; FLH196434.01L; RZPDo839D04155D ubiquitin specific peptidase 46 (USP46) gene, encodes complete protein.
EU176797 - Synthetic construct Homo sapiens clone IMAGE:100011609; FLH263879.01L; RZPDo839F01247D ubiquitin specific peptidase 46 (USP46) gene, encodes complete protein.
KJ899482 - Synthetic construct Homo sapiens clone ccsbBroadEn_08876 USP46 gene, encodes complete protein.
AK021912 - Homo sapiens cDNA FLJ11850 fis, clone HEMBA1006717.
AK096712 - Homo sapiens cDNA FLJ39393 fis, clone PLACE6007798.
AK024345 - Homo sapiens cDNA FLJ14283 fis, clone PLACE1005850.
JD346383 - Sequence 327407 from Patent EP1572962.
JD311900 - Sequence 292924 from Patent EP1572962.
JD213116 - Sequence 194140 from Patent EP1572962.
JD533869 - Sequence 514893 from Patent EP1572962.
JD407587 - Sequence 388611 from Patent EP1572962.
AF070557 - Homo sapiens clone 24422 mRNA sequence.
AK021861 - Homo sapiens cDNA FLJ11799 fis, clone HEMBA1006235, highly similar to Homo sapiens clone 24422 mRNA sequence.
JD026708 - Sequence 7732 from Patent EP1572962.
JD028931 - Sequence 9955 from Patent EP1572962.
JD026168 - Sequence 7192 from Patent EP1572962.
JD034711 - Sequence 15735 from Patent EP1572962.
JD031804 - Sequence 12828 from Patent EP1572962.
JD520841 - Sequence 501865 from Patent EP1572962.
JD490683 - Sequence 471707 from Patent EP1572962.
JD348799 - Sequence 329823 from Patent EP1572962.
JD326692 - Sequence 307716 from Patent EP1572962.
JD097929 - Sequence 78953 from Patent EP1572962.
JD301593 - Sequence 282617 from Patent EP1572962.
JD036532 - Sequence 17556 from Patent EP1572962.
JD313591 - Sequence 294615 from Patent EP1572962.
JD565353 - Sequence 546377 from Patent EP1572962.
JD092405 - Sequence 73429 from Patent EP1572962.
JD350049 - Sequence 331073 from Patent EP1572962.
JD088934 - Sequence 69958 from Patent EP1572962.
JD048907 - Sequence 29931 from Patent EP1572962.
JD410962 - Sequence 391986 from Patent EP1572962.
JD266712 - Sequence 247736 from Patent EP1572962.
JD565894 - Sequence 546918 from Patent EP1572962.
JD232533 - Sequence 213557 from Patent EP1572962.
JD181336 - Sequence 162360 from Patent EP1572962.
JD083673 - Sequence 64697 from Patent EP1572962.
JD313429 - Sequence 294453 from Patent EP1572962.
JD379153 - Sequence 360177 from Patent EP1572962.
JD480114 - Sequence 461138 from Patent EP1572962.
JD547351 - Sequence 528375 from Patent EP1572962.
JD467100 - Sequence 448124 from Patent EP1572962.
JD372203 - Sequence 353227 from Patent EP1572962.
JD239758 - Sequence 220782 from Patent EP1572962.
JD538604 - Sequence 519628 from Patent EP1572962.
JD309883 - Sequence 290907 from Patent EP1572962.
JD528348 - Sequence 509372 from Patent EP1572962.
JD543925 - Sequence 524949 from Patent EP1572962.
JD125496 - Sequence 106520 from Patent EP1572962.
JD346139 - Sequence 327163 from Patent EP1572962.
JD533911 - Sequence 514935 from Patent EP1572962.
JD124703 - Sequence 105727 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B7Z3Y7, B7Z675, B7Z7S3, G8ACC7, NM_022832, NP_073743, P62068, Q80V95, Q9H7U4, Q9H9T8, UBP46_HUMAN
UCSC ID: uc003gzn.3
RefSeq Accession: NM_022832
Protein: P62068 (aka UBP46_HUMAN or UB46_HUMAN)
CCDS: CCDS47053.1, CCDS47054.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_022832.3
exon count: 9CDS single in 3' UTR: no RNA size: 7981
ORF size: 1101CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2262.50frame shift in genome: no % Coverage: 99.80
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.