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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

UBXN6 Gene

protein-coding   GIFtS: 51
GCID: GC19M004444

UBX domain protein 6

(Previous names: UBX domain-containing 1, UBX domain containing 1 )
(Previous symbol: UBXD1)
  Search for UBXN6
in our new
 Human Malady Compendium 
Biological research products
for UBXN6
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
UBX Domain Protein 61 2     UBX Domain-Containing 11 2
UBXD11 2 3 5     UBX Domain-Containing Protein 12 3
UBXDC21 2 3     UBX Domain-Containing 22
UBX Domain Containing 11 2     UBX Domain-Containing Protein 62

External Ids:    HGNC: 149281   Entrez Gene: 807002   Ensembl: ENSG000001676717   OMIM: 6119465   UniProtKB: Q9BZV13   

Export aliases for UBXN6 gene to outside databases

Previous GC identifers: GC19M004397 GC19M004207


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: UBXN6_HUMAN, Q9BZV1
Function: Acts in a complex with VCP and cooperates with USP7 in promoting MDM2 deubiquitination and stabilization.
MDM2 stabilization leads to MDM2-dependent TP53 degradation




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000019.9  NC_018930.1  NT_011255.14  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the UBXN6 gene promoter:
         c-Fos   AP-1   AP-4   C/EBPalpha   ARP-1   c-Jun   NF-Y   Pax-4a   CBF(2)   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidUBXN6 promoter sequence
   Search SABiosciences Chromatin IP Primers for UBXN6

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat UBXN6


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 19p13   Ensembl cytogenetic band:  19p13.3   HGNC cytogenetic band: 19p13

UBXN6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
UBXN6 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M004444:  view genomic region     (about GC identifiers)

Start:
4,444,996 bp from pter      End:
4,457,819 bp from pter
Size:
12,824 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: UBXN6_HUMAN, Q9BZV1 (See protein sequence)
Recommended Name: UBX domain-containing protein 6  
Size: 441 amino acids; 49754 Da
Subunit: Interacts with VCP through the PUB domain. Interacts with SYVN1, HERPUD1, MDM2 and USP7
Subcellular location: Cytoplasm. Nucleus. Cytoplasm, cytoskeleton, centrosome. Note=Localizes at the centrosome both in
interphase and during mitosis
Secondary accessions: D6W626 Q96AH1 Q96IK9 Q9BZV0
Alternative splicing: 2 isoforms:  Q9BZV1-1   Q9BZV1-2   

Explore the universe of human proteins at neXtProt for UBXN6: NX_Q9BZV1

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9BZV1

  • UBXN6 Protein expression data from MOPED and PaxDb:    About this image 
    UBXN6 Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_001164562.1  NP_079517.1  

    ENSEMBL proteins: 
     ENSP00000467206   ENSP00000301281   ENSP00000378246   ENSP00000466148   ENSP00000464967  

    Human Recombinant Protein Products for UBXN6: 
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    Browse ProSpec Recombinant Proteins
    Uscn Proteins for UBXN6

    Gene Ontology (GO): 5 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575cellular_component ND--
    GO:0005634nucleus IDA--
    GO:0005730nucleolus IDA--
    GO:0005737cytoplasm IEA--
    GO:0005815microtubule organizing center IEA--

    UBXN6 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    UBXN6 for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR018997 PUB_domain
     IPR001012 UBX
     IPR006567 PUG-dom

    Graphical View of Domain Structure for InterPro Entry Q9BZV1

    ProtoNet protein and cluster: Q9BZV1

    1 Blocks protein family: IPB001012 UBX domain

    UniProtKB/Swiss-Prot: UBXN6_HUMAN, Q9BZV1
    Similarity: Contains 1 PUB (PUG) domain
    Similarity: Contains 1 UBX domain


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, Sirion Biotech, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, Sirion Biotech, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: UBXN6_HUMAN, Q9BZV1
    Function: Acts in a complex with VCP and cooperates with USP7 in promoting MDM2 deubiquitination and stabilization.
    MDM2 stabilization leads to MDM2-dependent TP53 degradation

         Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
    GO:0005515protein binding IPI18775313
         
    UBXN6 for ontologies           About GeneDecksing


    Animal Models:
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    miRNA
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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for UBXN6


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Protein processing in endoplasmic reticulum
    Protein processing in endoplasmic reticulum1.00

    Pathway sources
    See GeneCards unified pathways
    Show all pathways



    1         Kegg Pathway  (Kegg details for UBXN6):
        Protein processing in endoplasmic reticulum


    UBXN6 for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for UBXN6

    STRING Interaction Network Preview (showing 5 interactants - click image to see 10)

    5/12 Interacting proteins for UBXN6 (Q9BZV11, 2, 3 ENSP000003012814) via UniProtKB, MINT, STRING, and/or I2D (see all 12)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    VCPP550721, 3, ENSP000003517774EBI-1993899,EBI-1046421 I2D: score=3 STRING: ENSP00000351777
    GSK3BP498412, 3MINT-8257790 I2D: score=2 
    VCPIP1Q96JH73, ENSP000003090314I2D: score=2 STRING: ENSP00000309031
    ALPPP051873, ENSP000003758814I2D: score=1 STRING: ENSP00000375881
    HERPUD1Q150113, ENSP000003003024I2D: score=1 STRING: ENSP00000300302
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008150biological_process ND--

    UBXN6 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for UBXN6
    Search CenterWatch for drugs/clinical trials and news about UBXN6 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for UBXN6 gene (2 alternative transcripts): 
    NM_001171091.1  NM_025241.2  

    Unigene Cluster for UBXN6:

    UBX domain protein 6
    Hs.435255  [show with all ESTs]
    Unigene Representative Sequence: NM_025241
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000591919 ENST00000301281(uc002man.2) ENST00000588238 ENST00000587009
    ENST00000394765(uc002mam.2) ENST00000590466 ENST00000587324 ENST00000593024
    ENST00000592358 ENST00000592515

    miRNA
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    Additional cDNA sequence: 

    AF272893.1 AF272894.1 BC007414.2 BC008288.1 BC017113.1 

    14 DOTS entries:

    DT.448407  DT.95173506  DT.92437292  DT.95173512  DT.100780561  DT.40199374  DT.86995579  DT.121498103 
    DT.100773996  DT.100774115  DT.121498161  DT.100728395  DT.95334761  DT.95089981 

    24/418 AceView cDNA sequences (see all 418):

    BM909721 BM753199 BG030981 CA309386 BE882202 CN484529 BM006830 AI358862 
    BM982341 BG680372 BM562398 BM720633 BX355003 AA323826 CR598178 BQ668871 
    AI620464 CA454006 BM696364 BM545154 BI907665 BM766033 BM909229 BE614753 

    GeneLoc Exon Structure

    5/7 Alternative Splicing Database (ASD) splice patterns (SP) for UBXN6 (see all 7)    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13a · 13b · 13c
    SP1:        -                                               -                                   -                           
    SP2:                                                        -                                   -                           
    SP3:                                                        -                             -     -                           
    SP4:                                                        -                                                               
    SP5:                                                                                                                        


    ECgene alternative splicing isoforms for UBXN6

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    UBXN6 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GGTCCTGTTC
    UBXN6 Expression
    About this image
    See UBXN6 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for UBXN6

    SOURCE GeneReport for Unigene cluster: Hs.435255

    UniProtKB/Swiss-Prot: UBXN6_HUMAN, Q9BZV1
    Tissue specificity: Enhanced expression in testis

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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for UBXN6 gene from 8/22 species (see all 22)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ubxn61 , 5 UBX domain protein 61, 5 79.39(n)1
    81.14(a)1
      17 (29.14 cM)5
    665301  NM_024432.21  NP_077752.11 
     560670455 
    chicken
    (Gallus gallus)
    Aves UBXN61 UBX domain protein 6 63.61(n)
    64.22(a)
      428329  XM_001232669.2  XP_001232670.1 
    lizard
    (Anolis carolinensis)
    Reptilia UBXN66
    --
    66(a)
    1 ↔ 1
    GL343757.1(168202-181315)
    zebrafish
    (Danio rerio)
    Actinopterygii BC055680.12   -- 72.03(n)   327469  BC055680.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG423061 CG42306 49.01(n)
    37.35(a)
      7354425  NM_137512.2  NP_611356.1 
    worm
    (Caenorhabditis elegans)
    Secernentea ubxn-61 Protein UBXN-6 42.93(n)
    33.93(a)
      177253  NM_068247.4  NP_500648.2 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons PUX26
    UBX domain-containing protein 2
    22(a)
    1 ↔ 1
    2(284672-286493)
    rice
    (Oryza sativa)
    Liliopsida --
    --
    UBX domain containing protein, expressed
    28(a)
    22(a)
    many → 1
    many → 1
    3(24339310-24342864)
    9(14082858-14086561)


    ENSEMBL Gene Tree for UBXN6 (if available)
    TreeFam Gene Tree for UBXN6 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
      --

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/355 NCBI SNPs in UBXN6 are shown (see all 355    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1995623741,2
    Cother4446362(+) TTCTCC/G/TCGCAT 7 R syn1 ds50010--------
    rs1390003301,2
    C--4444654(+) CATAC-/CCGCCAAG 3 -- us2k1 int10--------
    rs48075891,2
    F--4444683(+) GTTGCG/ACATCT 3 -- int1 us2k11Minor allele frequency- A:0.10EA 120
    rs1925161751,2
    --4444698(+) GTTCCA/CGGAAT 3 -- int1 us2k10--------
    rs1845273291,2
    --4444715(+) TGGCCA/GTCTCA 3 -- us2k1 int10--------
    rs788690601,2
    C--4444742(+) TGGCCA/GCAGGG 3 -- us2k1 int14Minor allele frequency- G:0.13NA WA EA 360
    rs22939301,2
    C,F,A,H--4444856(+) CTCATC/TGGGCA 3 -- int1 us2k119Minor allele frequency- T:0.32EA NS NA CSA WA 3825
    rs2433851,2
    C,F,A,H--4444950(+) GCTCTG/TCAGCA 3 -- us2k1 int125Minor allele frequency- T:0.34EA NS NA WA CSA 3846
    rs775712671,2
    --4444959(+) CAGGTG/AGGCCT 3 -- int1 us2k11Minor allele frequency- A:0.01EA 120
    rs1501127261,2
    --4444996(+) GAACCA/GAGAAA 3 -- us2k1 int10--------

    HapMap Linkage Disequilibrium report for UBXN6 (4444996 - 4457819 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for UBXN6: --

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    UBXN6 for disorders           About MalaCards

    UBXN6 for disorders           About GeneDecksing

    OMIM gene information: 611946    OMIM disorders: --


    Export disorders for UBXN6 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for UBXN6 gene, integrated from 9 sources (see all 27):
    (articles sorted by number of sources associating them with UBXN6)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification and characterization of UBXD1, a novel UBX domain- containing gene on human chromosome 19p13, and its mouse ortholog. (PubMed id 11342112)1, 2, 3 Carim-Todd L.... Sumoy L. (2001)
    2. Ubxd1 is a novel co-factor of the human p97 ATPase. (PubMed id 18656546)1, 2 Madsen L....Hartmann-Petersen R. (2008)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    4. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    5. Exploring the role of p97 and its UBX-domain cofactors through identification of their interacting proteins. (PubMed id 22350894)1 Alexandru G. (2012)
    6. Methods for quantification of in vivo changes in prote in ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (2012)
    7. Protein interaction profiling of the p97 adaptor UBXD1 points to a role for the complex in modulating ERGIC-53 trafficking. (PubMed id 22337587)1 Haines D.S....Deshaies R.J. (2012)
    8. The general definition of the p97/valosin-containing protein (VCP)-interacting motif (VIM) delineates a new family of p97 cofactors. (PubMed id 21896481)1 Stapf C....Buchberger A. (2011)
    9. The structural and functional basis of the p97/valosi n-containing protein (VCP)-interacting motif (VIM): mutually exclusive binding of cofactors to the N-terminal domain of p97. (PubMed id 21914798)1 HAonzelmann P. and Schindelin H. (2011)
    10. Endolysosomal sorting of ubiquitylated caveolin-1 is regulated by VCP and UBXD1 and impaired by VCP disease mutations. (PubMed id 21822278)1 Ritz D....Meyer H. (2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 80700 HGNC: 14928 AceView: UBXD1 Ensembl:ENSG00000167671 euGenes: HUgn80700
    ECgene: UBXN6 Kegg: 80700 H-InvDB: UBXN6

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for UBXN6 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for UBXN6 gene:
    Search GeneIP for patents involving UBXN6

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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