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

Gene ID: 363332, updated on 17-Aug-2024

Summary

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Official Symbol
Ubxn6provided by RGD
Official Full Name
UBX domain protein 6provided by RGD
Primary source
RGD:1590866
See related
EnsemblRapid: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
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Genomic context

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See Ubxn6 in Genome Data Viewer
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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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

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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

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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

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Preferred Names
UBX domain-containing protein 6
Names
UBX domain containing 1

NCBI Reference Sequences (RefSeq)

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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
    UniProtKB/TrEMBL
    A6KR07, M0RAE4
    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, A6KR07, M0RAE4
    Related
    ENSRNOP00000071261.3, ENSRNOT00000089071.3
    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

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