Human Gene OTUD4 (ENST00000509620.6) from GENCODE V44
  Description: Homo sapiens OTU deubiquitinase 4 (OTUD4), transcript variant 2, mRNA. (from RefSeq NM_017493)
RefSeq Summary (NM_017493): Alternatively spliced transcript variants have been found for this gene. The smaller protein isoform encoded by the shorter transcript variant is found only in HIV-1 infected cells. [provided by RefSeq, Jul 2010].
Gencode Transcript: ENST00000509620.6
Gencode Gene: ENSG00000164164.17
Transcript (Including UTRs)
   Position: hg38 chr4:145,159,137-145,178,155 Size: 19,019 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg38 chr4:145,159,499-145,174,708 Size: 15,210 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:145,159,137-145,178,155)mRNA (may differ from genome)Protein (145 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: OTUD4_HUMAN
DESCRIPTION: RecName: Full=OTU domain-containing protein 4; AltName: Full=HIV-1-induced protein HIN-1;
INDUCTION: By HIV-1 insertion.
SIMILARITY: Contains 1 OTU domain.
SEQUENCE CAUTION: Sequence=AAI18573.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAI18654.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=ABD72605.1; Type=Erroneous gene model prediction; Sequence=BAA82998.2; Type=Miscellaneous discrepancy; Note=Intron retention; Sequence=BAB71229.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=CAA48313.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Originates from a chimeric transcript in HIV-1-infected cells. The premature stop may be due to intron retention;
WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/otud4/";

-  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: OTUD4
Diseases sorted by gene-association score: hypogonadotropism (10), hiv-1 (5)

-  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: 20.01 RPKM in Testis
Total median expression: 364.20 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 -4.2064-0.066 Picture PostScript Text
3' UTR -70.60362-0.195 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
IPR003323 - OTU

Pfam Domains:
PF02338 - OTU-like cysteine protease

ModBase Predicted Comparative 3D Structure on Q01804
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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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
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:0032947 protein complex scaffold
GO:0036459 thiol-dependent ubiquitinyl hydrolase activity
GO:0061578 Lys63-specific deubiquitinase activity

Biological Process:
GO:0002376 immune system process
GO:0006508 proteolysis
GO:0034122 negative regulation of toll-like receptor signaling pathway
GO:0045087 innate immune response
GO:0070536 protein K63-linked deubiquitination
GO:0071108 protein K48-linked deubiquitination
GO:1901537 positive regulation of DNA demethylation
GO:1903093 regulation of protein K48-linked deubiquitination
GO:2000660 negative regulation of interleukin-1-mediated signaling pathway

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  AK302581 - Homo sapiens cDNA FLJ56410 complete cds, highly similar to Homo sapiens OTU domain containing 4 (OTUD4), transcript variant 1, mRNA.
BC118572 - Homo sapiens OTU domain containing 4, mRNA (cDNA clone MGC:126484 IMAGE:40036249), complete cds.
BC118653 - Homo sapiens OTU domain containing 4, mRNA (cDNA clone MGC:126483 IMAGE:40036248), complete cds.
X68242 - H.sapiens mRNA for Hin-1.
JD561921 - Sequence 542945 from Patent EP1572962.
JD304253 - Sequence 285277 from Patent EP1572962.
JD504450 - Sequence 485474 from Patent EP1572962.
JD110132 - Sequence 91156 from Patent EP1572962.
JD112940 - Sequence 93964 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B4DYS4, ENST00000509620.1, ENST00000509620.2, ENST00000509620.3, ENST00000509620.4, ENST00000509620.5, HIN1, KIAA1046, NM_017493, OTUD4_HUMAN, Q01804, Q147U2, Q1ZYK1, Q6PG39, Q96MQ5, Q9NT94, Q9UPV6, uc021xsl.1, uc021xsl.2
UCSC ID: ENST00000509620.6
RefSeq Accession: NM_017493
Protein: Q01804 (aka OTUD4_HUMAN)
CCDS: CCDS3764.1

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