U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Ubxn6 UBX domain protein 6 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 363332, updated on 3-Apr-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Ubxn6provided by RGD
    Official Full Name
    UBX domain protein 6provided by RGD
    Primary source
    RGD:1590866
    See related
    Ensembl:ENSRNOG00000048509 AllianceGenome:RGD:1590866
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Ubxd1
    Summary
    Predicted to be involved in ERAD pathway; endosome to lysosome transport via multivesicular body sorting pathway; and macroautophagy. Predicted to be located in bounding membrane of organelle and cytosol. Predicted to be extrinsic component of membrane. Predicted to be part of protein-containing complex. Orthologous to human UBXN6 (UBX domain protein 6). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Testes (RPKM 432.1), Heart (RPKM 169.0) and 9 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    Location:
    9q11
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (988051..993221, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (900883..906047, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (10995516..11000643)

    Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene SH3 domain containing GRB2 like 1, endophilin A2 Neighboring gene MPN domain containing Neighboring gene chromatin assembly factor 1 subunit A Neighboring gene HDGF like 2 Neighboring gene perilipin 4 Neighboring gene perilipin 5

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. The N-terminal Region of the Ubiquitin Regulatory X (UBX) Domain-containing Protein 1 (UBXD1) Modulates Interdomain Communication within the Valosin-containing Protein p97. Trusch F, et al. J Biol Chem, 2015 Dec 4. PMID 26475856, Free PMC Article
    2. UBXD1 is a VCP-interacting protein that is involved in ER-associated degradation. Nagahama M, et al. Biochem Biophys Res Commun, 2009 May 1. PMID 19275885
    3. Endolysosomal sorting of ubiquitylated caveolin-1 is regulated by VCP and UBXD1 and impaired by VCP disease mutations. Ritz D, et al. Nat Cell Biol, 2011 Aug 7. PMID 21822278, Free PMC Article
    4. VCP/p97 cooperates with YOD1, UBXD1 and PLAA to drive clearance of ruptured lysosomes by autophagy. Papadopoulos C, et al. EMBO J, 2017 Jan 17. PMID 27753622, Free PMC Article
    5. Large-scale proteomics and phosphoproteomics of urinary exosomes. Gonzales PA, et al. J Am Soc Nephrol, 2009 Feb. PMID 19056867, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    involved_in ERAD pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in endosome to lysosome transport via multivesicular body sorting pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in macroautophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in early endosome membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in endosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in late endosome membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in lysosomal membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of protein-containing complex ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    UBX domain-containing protein 6
    Names
    UBX domain containing 1

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001399140.1 → NP_001386069.1  UBX domain-containing protein 6 isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      Conserved Domains (2) summary
      cd10460
      Location:171 → 275
      PUB_UBXD1; PNGase/UBA or UBX (PUB) domain of UBXD1
      cd16119
      Location:348 → 421
      UBX_UBXN6; Ubiquitin regulatory domain X (UBX) found in UBX domain protein 6 (UBXN6) and similar proteins

    2. NM_001399141.1 → NP_001386070.1  UBX domain-containing protein 6 isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/TrEMBL
      A6KR06
      Related
      ENSRNOP00000071261.2, ENSRNOT00000089071.2
      Conserved Domains (2) summary
      cd10460
      Location:158 → 262
      PUB_UBXD1; PNGase/UBA or UBX (PUB) domain of UBXD1
      cd16119
      Location:335 → 408
      UBX_UBXN6; Ubiquitin regulatory domain X (UBX) found in UBX domain protein 6 (UBXN6) and similar proteins

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086027.1 Reference GRCr8

      Range
      988051..993221 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063267481.1 → XP_063123551.1  UBX domain-containing protein 6 isoform X2

    2. XM_039083941.1 → XP_038939869.1  UBX domain-containing protein 6 isoform X1

      Conserved Domains (1) summary
      cl15262
      Location:224 → 271
      PUB; PNGase/UBA or UBX (PUB) domain of p97 adaptor proteins

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001108812.1: Suppressed sequence

      Description
      NM_001108812.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous