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Aliases for OTUD6B Gene

Aliases for OTUD6B Gene

  • OTU Domain Containing 6B 2 3 5
  • OTU Domain-Containing Protein 6B 3 4
  • DUBA-5 3 4
  • DUBA5 3 4
  • EC 3.4.19.12 4
  • IDDFSDA 3
  • CGI-77 3

External Ids for OTUD6B Gene

Previous GeneCards Identifiers for OTUD6B Gene

  • GC08P092152
  • GC08P092153
  • GC08P092082
  • GC08P087293

Summaries for OTUD6B Gene

Entrez Gene Summary for OTUD6B Gene

  • This gene encodes a member of the ovarian tumor domain (OTU)-containing subfamily of deubiquitinating enzymes. Deubiquitinating enzymes are primarily involved in removing ubiquitin from proteins targeted for degradation. This protein may function as a negative regulator of the cell cycle in B cells. [provided by RefSeq, Nov 2013]

GeneCards Summary for OTUD6B Gene

OTUD6B (OTU Domain Containing 6B) is a Protein Coding gene. Diseases associated with OTUD6B include Intellectual Developmental Disorder With Dysmorphic Facies, Seizures, And Distal Limb Anomalies and Alacrima, Achalasia, And Mental Retardation Syndrome. Gene Ontology (GO) annotations related to this gene include cysteine-type peptidase activity. An important paralog of this gene is OTUD6A.

UniProtKB/Swiss-Prot for OTUD6B Gene

  • Isoform 1: Deubiquitinating enzyme that may play a role in the ubiquitin-dependent regulation of protein synthesis, downstream of mTORC1 (PubMed:21267069, PubMed:27864334). May associate with the protein synthesis initiation complex and modify its ubiquitination to repress translation (PubMed:27864334). May also repress DNA synthesis and modify different cellular targets thereby regulating cell growth and proliferation (PubMed:27864334). May also play a role in proteasome assembly and function (PubMed:28343629).

  • Isoform 2: Stimulates protein synthesis. Influences the expression of CCND1/cyclin D1 by promoting its translation and regulates MYC/c-Myc protein stability.

Gene Wiki entry for OTUD6B Gene

Additional gene information for OTUD6B Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for OTUD6B Gene

Genomics for OTUD6B Gene

GeneHancer (GH) Regulatory Elements for OTUD6B Gene

Promoters and enhancers for OTUD6B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH08J091068 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 650.7 -0.2 -157 2.7 HDGF PKNOX1 FOXA2 SMAD1 ARNT ARID4B NEUROD1 SIN3A DMAP1 ZBTB7B OTUD6B-AS1 OTUD6B PIP4P2 C8orf88 SLC26A7 LOC102724670 LRRC69 ENSG00000254219
GH08J092058 Promoter/Enhancer 2 VISTA Ensembl ENCODE dbSUPER 11.8 +990.8 990820 5.9 MXI1 MAX SIN3A COPS2 ZNF366 POLR2A PRDM10 RCOR1 ZNF600 CHD2 OTUD6B RUNX1T1 GC08P092008
GH08J090983 Promoter/Enhancer 1.5 Ensembl ENCODE 10.8 -85.1 -85113 2.2 HDGF PKNOX1 ATF1 ZNF2 POLR2B ZNF766 GLIS2 E2F8 ZNF143 ATF7 C8orf88 LOC102724670 OTUD6B OTUD6B-AS1 LOC105375634 TMEM64
GH08J090625 Enhancer 0.8 ENCODE 12.6 -442.1 -442104 5.1 HDGF PKNOX1 FOXA2 STAT5A BATF IRF4 ATF7 ETV6 BCLAF1 IKZF2 OTUD6B LINC01030 LOC105375634 ENSG00000254180 LOC102724670 TMEM64
GH08J090675 Enhancer 1 Ensembl ENCODE dbSUPER 9.6 -393.9 -393885 1 ZNF217 CTCF CTBP1 NFIB POLR2A RCOR1 CHD2 FOXA1 OTUD6B OTUD6B-AS1 TMEM64 LRRC69 ENSG00000254182 LOC102724670
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around OTUD6B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the OTUD6B gene promoter:
  • Hand1
  • E47
  • POU3F2 (N-Oct-5b)
  • POU3F2 (N-Oct-5a)
  • POU3F2
  • CUTL1
  • HOXA9
  • HOXA9B
  • Meis-1b
  • FOXO3

Genomic Locations for OTUD6B Gene

Genomic Locations for OTUD6B Gene
chr8:91,070,196-91,087,095
(GRCh38/hg38)
Size:
16,900 bases
Orientation:
Plus strand
chr8:92,082,424-92,099,323
(GRCh37/hg19)
Size:
16,900 bases
Orientation:
Plus strand

Genomic View for OTUD6B Gene

Genes around OTUD6B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
OTUD6B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for OTUD6B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for OTUD6B Gene

Proteins for OTUD6B Gene

  • Protein details for OTUD6B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N6M0-OTU6B_HUMAN
    Recommended name:
    Deubiquitinase OTUD6B
    Protein Accession:
    Q8N6M0
    Secondary Accessions:
    • A8K6I1
    • B4DEY0
    • Q9NTA4
    • Q9Y387

    Protein attributes for OTUD6B Gene

    Size:
    293 amino acids
    Molecular mass:
    33813 Da
    Quaternary structure:
    • Interacts with the eukaryotic translation initiation factor 4F complex.

    Alternative splice isoforms for OTUD6B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for OTUD6B Gene

Post-translational modifications for OTUD6B Gene

  • Ubiquitination at isoforms=24
  • Modification sites at PhosphoSitePlus

Other Protein References for OTUD6B Gene

No data available for DME Specific Peptides for OTUD6B Gene

Domains & Families for OTUD6B Gene

Gene Families for OTUD6B Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for OTUD6B Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for OTUD6B Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with OTUD6B: view

No data available for UniProtKB/Swiss-Prot for OTUD6B Gene

Function for OTUD6B Gene

Molecular function for OTUD6B Gene

UniProtKB/Swiss-Prot Function:
Isoform 1: Deubiquitinating enzyme that may play a role in the ubiquitin-dependent regulation of protein synthesis, downstream of mTORC1 (PubMed:21267069, PubMed:27864334). May associate with the protein synthesis initiation complex and modify its ubiquitination to repress translation (PubMed:27864334). May also repress DNA synthesis and modify different cellular targets thereby regulating cell growth and proliferation (PubMed:27864334). May also play a role in proteasome assembly and function (PubMed:28343629).
UniProtKB/Swiss-Prot Function:
Isoform 2: Stimulates protein synthesis. Influences the expression of CCND1/cyclin D1 by promoting its translation and regulates MYC/c-Myc protein stability.
UniProtKB/Swiss-Prot CatalyticActivity:
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).

Enzyme Numbers (IUBMB) for OTUD6B Gene

Gene Ontology (GO) - Molecular Function for OTUD6B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008233 peptidase activity IEA --
GO:0008234 cysteine-type peptidase activity IEA --
GO:0016787 hydrolase activity IEA --
GO:0036459 thiol-dependent ubiquitinyl hydrolase activity IEA,IDA 21267069
genes like me logo Genes that share ontologies with OTUD6B: view
genes like me logo Genes that share phenotypes with OTUD6B: view

Human Phenotype Ontology for OTUD6B Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for OTUD6B Gene

MGI Knock Outs for OTUD6B:
  • Otud6b Otud6b<tm1b(EUCOMM)Wtsi>

Animal Model Products

  • Taconic Biosciences Mouse Models for OTUD6B

CRISPR Products

miRNA for OTUD6B Gene

miRTarBase miRNAs that target OTUD6B

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for OTUD6B

No data available for Phenotypes From GWAS Catalog , Transcription Factor Targets and HOMER Transcription for OTUD6B Gene

Localization for OTUD6B Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for OTUD6B gene
Compartment Confidence
cytosol 3
extracellular 2
nucleus 2
endoplasmic reticulum 2
golgi apparatus 2
plasma membrane 1
mitochondrion 1
peroxisome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Golgi apparatus (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for OTUD6B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016281 colocalizes_with eukaryotic translation initiation factor 4F complex IDA 27864334
genes like me logo Genes that share ontologies with OTUD6B: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for OTUD6B Gene

Pathways & Interactions for OTUD6B Gene

SuperPathways for OTUD6B Gene

No Data Available

Gene Ontology (GO) - Biological Process for OTUD6B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008283 cell proliferation IDA 27864334
GO:0016579 protein deubiquitination IDA,IMP 27864334
GO:0043248 proteasome assembly IMP 28343629
GO:0097010 eukaryotic translation initiation factor 4F complex assembly IDA --
genes like me logo Genes that share ontologies with OTUD6B: view

No data available for Pathways by source and SIGNOR curated interactions for OTUD6B Gene

Drugs & Compounds for OTUD6B Gene

No Compound Related Data Available

Transcripts for OTUD6B Gene

mRNA/cDNA for OTUD6B Gene

Unigene Clusters for OTUD6B Gene

OTU domain containing 6B:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for OTUD6B

Alternative Splicing Database (ASD) splice patterns (SP) for OTUD6B Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b · 5c ^ 6 ^ 7
SP1: -
SP2:
SP3:

Relevant External Links for OTUD6B Gene

GeneLoc Exon Structure for
OTUD6B
ECgene alternative splicing isoforms for
OTUD6B

Expression for OTUD6B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for OTUD6B Gene

Protein differential expression in normal tissues from HIPED for OTUD6B Gene

This gene is overexpressed in Breast (26.3) and Stomach (8.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for OTUD6B Gene



Protein tissue co-expression partners for OTUD6B Gene

NURSA nuclear receptor signaling pathways regulating expression of OTUD6B Gene:

OTUD6B

SOURCE GeneReport for Unigene cluster for OTUD6B Gene:

Hs.30532

Evidence on tissue expression from TISSUES for OTUD6B Gene

  • Nervous system(4.5)
genes like me logo Genes that share expression patterns with OTUD6B: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for OTUD6B Gene

Orthologs for OTUD6B Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for OTUD6B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia OTUD6B 34 33
  • 99.28 (n)
OneToOne
cow
(Bos Taurus)
Mammalia OTUD6B 34 33
  • 87.77 (n)
OneToOne
dog
(Canis familiaris)
Mammalia OTUD6B 34 33
  • 87.41 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Otud6b 16 34 33
  • 85.45 (n)
rat
(Rattus norvegicus)
Mammalia Otud6b 33
  • 83.8 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 83 (a)
OneToMany
-- 34
  • 81 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia OTUD6B 34
  • 79 (a)
OneToOne
chicken
(Gallus gallus)
Aves OTUD6B 34 33
  • 75.93 (n)
OneToMany
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 66 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia otud6b 33
  • 67.64 (n)
Str.11832 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.15114 33
zebrafish
(Danio rerio)
Actinopterygii otud6b 34 33
  • 64.23 (n)
OneToMany
zgc56305 33
fruit fly
(Drosophila melanogaster)
Insecta CG7857 34 33
  • 52.16 (n)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006160 33
  • 48.22 (n)
worm
(Caenorhabditis elegans)
Secernentea F21D5.2 33
  • 49.11 (n)
otub-3 34
  • 27 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes OTU2 36 34
  • 29 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G62940 33
  • 46.91 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.7595 33
rice
(Oryza sativa)
Liliopsida Os04g0619500 33
  • 47.91 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 50 (a)
ManyToMany
-- 34
  • 43 (a)
ManyToMany
-- 34
  • 38 (a)
ManyToMany
Species where no ortholog for OTUD6B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for OTUD6B Gene

ENSEMBL:
Gene Tree for OTUD6B (if available)
TreeFam:
Gene Tree for OTUD6B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for OTUD6B: view image

Paralogs for OTUD6B Gene

Paralogs for OTUD6B Gene

(1) SIMAP similar genes for OTUD6B Gene using alignment to 2 proteins:

  • OTU6B_HUMAN
  • H0YB21_HUMAN
genes like me logo Genes that share paralogs with OTUD6B: view

Variants for OTUD6B Gene

Sequence variations from dbSNP and Humsavar for OTUD6B Gene

SNP ID Clin Chr 08 pos Variation AA Info Type
rs1064797102 pathogenic, Intellectual developmental disorder with dysmorphic facies, seizures, and distal limb anomalies, Dysmorphic features, Intellectual disability, Seizure Disorders 91,071,136(+) A/G splice_acceptor_variant
rs1064797103 pathogenic, likely-pathogenic, Intellectual developmental disorder with dysmorphic facies, seizures, and distal limb anomalies, Dysmorphic features, Intellectual disability, Seizure Disorders 91,078,597(+) A/G coding_sequence_variant, missense_variant
rs368313959 pathogenic, Intellectual developmental disorder with dysmorphic facies, seizures, and distal limb anomalies, Dysmorphic features, Intellectual disability, Seizure Disorders, not provided 91,078,383(+) C/T coding_sequence_variant, stop_gained
rs759317757 pathogenic, Intellectual developmental disorder with dysmorphic facies, seizures, and distal limb anomalies, Dysmorphic features, Intellectual disability, Seizure Disorders 91,078,416(+) AACTTAAC/AAC coding_sequence_variant, frameshift
VAR_080404 Intellectual developmental disorder with dysmorphic facies, seizures, and distal limb anomalies (IDDFSDA) [MIM:617452] p.Tyr186Cys

Structural Variations from Database of Genomic Variants (DGV) for OTUD6B Gene

Variant ID Type Subtype PubMed ID
esv2669421 CNV deletion 23128226
esv2759629 CNV loss 17122850
esv3543832 CNV deletion 23714750
esv3618013 CNV loss 21293372
nsv831390 CNV gain 17160897
nsv957656 CNV deletion 24416366

Variation tolerance for OTUD6B Gene

Residual Variation Intolerance Score: 88.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.90; 48.70% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for OTUD6B Gene

Human Gene Mutation Database (HGMD)
OTUD6B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
OTUD6B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for OTUD6B Gene

Disorders for OTUD6B Gene

MalaCards: The human disease database

(3) MalaCards diseases for OTUD6B Gene - From: HGMD, OMIM, ClinVar, Orphanet, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

OTU6B_HUMAN
  • Intellectual developmental disorder with dysmorphic facies, seizures, and distal limb anomalies (IDDFSDA) [MIM:617452]: An autosomal recessive severe multisystem disorder characterized by poor overall growth, developmental delay, early-onset seizures, intellectual disability, and dysmorphic features. Additional features include microcephaly, absent speech, hypotonia, feeding difficulties, structural brain abnormalities, congenital malformations including congenital heart disease, and musculoskeletal features. {ECO:0000269 PubMed:28343629}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for OTUD6B

genes like me logo Genes that share disorders with OTUD6B: view

No data available for Genatlas for OTUD6B Gene

Publications for OTUD6B Gene

  1. Biallelic Variants in OTUD6B Cause an Intellectual Disability Syndrome Associated with Seizures and Dysmorphic Features. (PMID: 28343629) Santiago-Sim T … Walkiewicz MA (American journal of human genetics 2017) 3 4 58
  2. Deubiquitinase OTUD6B Isoforms Are Important Regulators of Growth and Proliferation. (PMID: 27864334) Sobol A … Bocchetta M (Molecular cancer research : MCR 2017) 3 4 58
  3. Evidence for OTUD-6B participation in B lymphocytes cell cycle after cytokine stimulation. (PMID: 21267069) Xu Z … Hu L (PloS one 2011) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics. (PMID: 10810093) Lai CH … Lin W (Genome research 2000) 3 4 58

Products for OTUD6B Gene

Sources for OTUD6B Gene

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