Human Gene UBXN1 (ENST00000301935.10_10) from GENCODE V47lift37
  Description: UBX domain protein 1, transcript variant 2 (from RefSeq NM_001286077.2)
Gencode Transcript: ENST00000301935.10_10
Gencode Gene: ENSG00000162191.14_15
Transcript (Including UTRs)
   Position: hg19 chr11:62,443,972-62,446,545 Size: 2,574 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr11:62,444,062-62,446,395 Size: 2,334 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:62,443,972-62,446,545)mRNA (may differ from genome)Protein (297 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMGIOMIMPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: UBXN1_HUMAN
DESCRIPTION: RecName: Full=UBX domain-containing protein 1; AltName: Full=SAPK substrate protein 1; AltName: Full=UBA/UBX 33.3 kDa protein;
FUNCTION: Ubiquitin-binding protein that interacts with the BRCA1- BARD1 heterodimer, and regulates its activity. Specifically binds 'Lys-6'-linked polyubiquitin chains. Interaction with autoubiquitinated BRCA1, leads to inhibit the E3 ubiquitin-protein ligase activity of the BRCA1-BARD1 heterodimer. Component of a complex required to couple deglycosylation and proteasome-mediated degradation of misfolded proteins in the endoplasmic reticulum that are retrotranslocated in the cytosol.
SUBUNIT: Component of a complex required to couple retrotranslocation, ubiquitination and deglycosylation composed of NGLY1, SAKS1, AMFR, VCP and RAD23B. Interacts with HOMER2 (By similarity). Interacts directly with VCP. Interacts with BRCA1 and BARD1; interaction takes place when BRCA1 is not autoubiquitinated but is strongly enhanced in the presence of autoubiquitinated BRCA1.
SUBCELLULAR LOCATION: Cytoplasm (By similarity).
DOMAIN: The UBA domain specifically recognizes and binds 'Lys-6'- linked polyubiquitin chains.
SIMILARITY: Contains 1 UBA domain.
SIMILARITY: Contains 1 UBX domain.

-  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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 107.73 RPKM in Ovary
Total median expression: 3603.98 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 -69.40150-0.463 Picture PostScript Text
3' UTR -10.1090-0.112 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
IPR009060 - UBA-like
IPR000449 - UBA/transl_elong_EF1B_N
IPR015940 - UBA/transl_elong_EF1B_N_euk
IPR001012 - UBX

Pfam Domains:
PF00627 - UBA/TS-N domain
PF00789 - UBX domain

SCOP Domains:
46934 - UBA-like
54236 - Ubiquitin-like

ModBase Predicted Comparative 3D Structure on Q04323
FrontTopSide
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
No orthologNo orthologNo orthologNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
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 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0031593 polyubiquitin binding
GO:0031625 ubiquitin protein ligase binding
GO:0036435 K48-linked polyubiquitin binding
GO:0043130 ubiquitin binding
GO:0051117 ATPase binding
GO:0071796 K6-linked polyubiquitin binding

Biological Process:
GO:0006457 protein folding
GO:0031397 negative regulation of protein ubiquitination
GO:0032435 negative regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:1903094 negative regulation of protein K48-linked deubiquitination
GO:1904293 negative regulation of ERAD pathway
GO:2000157 negative regulation of ubiquitin-specific protease activity

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005829 cytosol
GO:0030425 dendrite
GO:0034098 VCP-NPL4-UFD1 AAA ATPase complex
GO:0043025 neuronal cell body
GO:0000502 proteasome complex


-  Descriptions from all associated GenBank mRNAs
  BC001372 - Homo sapiens UBX domain protein 1, mRNA (cDNA clone MGC:2274 IMAGE:3051213), complete cds.
BC000902 - Homo sapiens UBX domain protein 1, mRNA (cDNA clone MGC:5321 IMAGE:2900493), complete cds.
BC032689 - Homo sapiens UBX domain protein 1, mRNA (cDNA clone IMAGE:5241425), complete cds.
BC040129 - Homo sapiens UBX domain protein 1, mRNA (cDNA clone MGC:48785 IMAGE:6065505), complete cds.
M68864 - Human ORF mRNA, complete cds.
AK054832 - Homo sapiens cDNA FLJ30270 fis, clone BRACE2002661, highly similar to UBA/UBX 33.3 kDa protein.
AK303471 - Homo sapiens cDNA FLJ53007 complete cds, highly similar to UBA/UBX 33.3 kDa protein.
JD380452 - Sequence 361476 from Patent EP1572962.
GQ129328 - Synthetic construct Homo sapiens clone HAIB:100068582; DKFZo008D0535 SAPK substrate protein 1 protein (LOC51035) gene, complete cds.
KJ902543 - Synthetic construct Homo sapiens clone ccsbBroadEn_11937 UBXN1 gene, encodes complete protein.
JD377105 - Sequence 358129 from Patent EP1572962.
HQ448734 - Synthetic construct Homo sapiens clone IMAGE:100072180; CCSB006778_02 SAPK substrate protein 1 (LOC51035) gene, encodes complete protein.
KJ898807 - Synthetic construct Homo sapiens clone ccsbBroadEn_08201 UBXN1 gene, encodes complete protein.
JD022124 - Sequence 3148 from Patent EP1572962.
JD031346 - Sequence 12370 from Patent EP1572962.
AK316012 - Homo sapiens cDNA, FLJ78911 complete cds, highly similar to UBA/UBX 33.3 kDa protein.
AK297856 - Homo sapiens cDNA FLJ58850 complete cds, highly similar to UBA/UBX 33.3 kDa protein.
AK300542 - Homo sapiens cDNA FLJ58945 complete cds, highly similar to UBA/UBX 33.3 kDa protein.
CU674676 - Synthetic construct Homo sapiens gateway clone IMAGE:100017009 5' read LOC51035 mRNA.
JD129557 - Sequence 110581 from Patent EP1572962.
JD197409 - Sequence 178433 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q04323 (Reactome details) participates in the following event(s):

R-HSA-8850594 Deglycosylation complex hydrolyses N-glycans from unfolded glycoproteins
R-HSA-532668 N-glycan trimming in the ER and Calnexin/Calreticulin cycle
R-HSA-446203 Asparagine N-linked glycosylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000301935.1, ENST00000301935.2, ENST00000301935.3, ENST00000301935.4, ENST00000301935.5, ENST00000301935.6, ENST00000301935.7, ENST00000301935.8, ENST00000301935.9, NM_001286077, Q04323, Q9BV93, Q9BVV5, SAKS1, UBXN1_HUMAN, uc317mxp.1, uc317mxp.2
UCSC ID: ENST00000301935.10_10
RefSeq Accession: NM_001286077.2
Protein: Q04323 (aka UBXN1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

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