Human Gene UBQLN4 (ENST00000368309.4) from GENCODE V44
  Description: Homo sapiens ubiquilin 4 (UBQLN4), transcript variant 1, mRNA. (from RefSeq NM_020131)
Gencode Transcript: ENST00000368309.4
Gencode Gene: ENSG00000160803.8
Transcript (Including UTRs)
   Position: hg38 chr1:156,035,299-156,053,798 Size: 18,500 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg38 chr1:156,036,978-156,053,701 Size: 16,724 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:156,035,299-156,053,798)mRNA (may differ from genome)Protein (601 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: UBQL4_HUMAN
DESCRIPTION: RecName: Full=Ubiquilin-4; AltName: Full=Ataxin-1 interacting ubiquitin-like protein; Short=A1Up; AltName: Full=Ataxin-1 ubiquitin-like-interacting protein A1U; AltName: Full=Connexin43-interacting protein of 75 kDa; Short=CIP75;
FUNCTION: Plays a role in the regulation of proteasomal protein degradation. Depending on the case, may promote or inhibit proteasomal protein degradation.
SUBUNIT: Binds signal sequences of proteins that are targeted to the endoplasmic reticulum. Interacts (via UBA domain) with GJA1 (not ubiquitinated) and with ubiquitin; both compete for the same binding site (By similarity). Homodimer. Interacts (via UBA domain) with ubiquitin and with polyubiquitin chains. Interacts (via ubiquitin-like domain) with PSMD4, a regulatory subunit of the 26S proteasome. Interacts with ATXN1/SCA1. Interaction with ATXN1 inhibits polyubiquitination of UBQLN4 and interferes with PSMD4 binding.
INTERACTION: P54253:ATXN1; NbExp=6; IntAct=EBI-711226, EBI-930964; P26885:FKBP2; NbExp=2; IntAct=EBI-711226, EBI-719873; P55198:MLLT6; NbExp=2; IntAct=EBI-711226, EBI-740216; Q9NR12:PDLIM7; NbExp=2; IntAct=EBI-711226, EBI-350517; Q9Y5P3:RAI2; NbExp=3; IntAct=EBI-711226, EBI-746228; Q13049:TRIM32; NbExp=3; IntAct=EBI-711226, EBI-742790; O95201:ZNF205; NbExp=2; IntAct=EBI-711226, EBI-747343;
SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Endoplasmic reticulum (Probable). Cytoplasm, perinuclear region (By similarity). Note=Colocalizes with the proteasome, both in nucleus and cytoplasm. May associate with the endoplasmic reticulum.
TISSUE SPECIFICITY: Highly expressed in pancreas, kidney, skeletal muscle, heart and throughout the brain, and at lower levels in placenta, lung and liver.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
PTM: Ubiquitinated; this does not lead to proteasomal degradation. May undergo both 'Lys-48'- and 'Lys-63'-linked polyubiquitination.
SIMILARITY: Contains 1 UBA domain.
SIMILARITY: Contains 1 ubiquitin-like domain.
SEQUENCE CAUTION: Sequence=AAF19084.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=AAH06410.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: UBQLN4
Diseases sorted by gene-association score: spinocerebellar ataxia 1 (5)

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 33.23 RPKM in Brain - Cortex
Total median expression: 974.15 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 -47.3097-0.488 Picture PostScript Text
3' UTR -579.601679-0.345 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
IPR006636 - STI1_HS-bd
IPR009060 - UBA-like
IPR000449 - UBA/transl_elong_EF1B_N
IPR015940 - UBA/transl_elong_EF1B_N_euk
IPR015496 - Ubiquilin
IPR000626 - Ubiquitin
IPR019955 - Ubiquitin_supergroup

Pfam Domains:
PF00627 - UBA/TS-N domain
PF00240 - Ubiquitin family

ModBase Predicted Comparative 3D Structure on Q9NRR5
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
Genome BrowserGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0031593 polyubiquitin binding
GO:0042802 identical protein binding

Biological Process:
GO:0006914 autophagy
GO:0032434 regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:1901097 negative regulation of autophagosome maturation

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005776 autophagosome
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005829 cytosol
GO:0031410 cytoplasmic vesicle
GO:0048471 perinuclear region of cytoplasm
GO:0031595 nuclear proteasome complex
GO:0031597 cytosolic proteasome complex


-  Descriptions from all associated GenBank mRNAs
  AK023354 - Homo sapiens cDNA FLJ13292 fis, clone OVARC1001180, weakly similar to UBIQUITIN-LIKE PROTEIN DSK2.
BC006410 - Homo sapiens ubiquilin 4, mRNA (cDNA clone IMAGE:2988342), complete cds.
BC063841 - Homo sapiens ubiquilin 4, mRNA (cDNA clone MGC:74959 IMAGE:6183942), complete cds.
AF113544 - Homo sapiens HRIHFB2157-like protein mRNA, partial cds.
AB209566 - Homo sapiens mRNA for ataxin-1 ubiquitin-like interacting protein variant protein.
AK098368 - Homo sapiens cDNA FLJ25502 fis, clone CBR04190, highly similar to Homo sapiens A1U mRNA.
BC018403 - Homo sapiens ubiquilin 4, mRNA (cDNA clone MGC:16849 IMAGE:4214386), complete cds.
JD555013 - Sequence 536037 from Patent EP1572962.
JD548492 - Sequence 529516 from Patent EP1572962.
JD132720 - Sequence 113744 from Patent EP1572962.
JD559313 - Sequence 540337 from Patent EP1572962.
JD532823 - Sequence 513847 from Patent EP1572962.
JD307856 - Sequence 288880 from Patent EP1572962.
JD366108 - Sequence 347132 from Patent EP1572962.
JD507976 - Sequence 489000 from Patent EP1572962.
JD090575 - Sequence 71599 from Patent EP1572962.
JD338332 - Sequence 319356 from Patent EP1572962.
JD427354 - Sequence 408378 from Patent EP1572962.
AF188240 - Homo sapiens A1U mRNA, complete cds.
JD102633 - Sequence 83657 from Patent EP1572962.
JD063966 - Sequence 44990 from Patent EP1572962.
JD316092 - Sequence 297116 from Patent EP1572962.
JD548297 - Sequence 529321 from Patent EP1572962.
JD500731 - Sequence 481755 from Patent EP1572962.
JD131197 - Sequence 112221 from Patent EP1572962.
JD523587 - Sequence 504611 from Patent EP1572962.
JD559292 - Sequence 540316 from Patent EP1572962.
JD486158 - Sequence 467182 from Patent EP1572962.
JD545389 - Sequence 526413 from Patent EP1572962.
JD227486 - Sequence 208510 from Patent EP1572962.
JD051928 - Sequence 32952 from Patent EP1572962.
JD299767 - Sequence 280791 from Patent EP1572962.
JD526031 - Sequence 507055 from Patent EP1572962.
JD394039 - Sequence 375063 from Patent EP1572962.
JD165952 - Sequence 146976 from Patent EP1572962.
JD201888 - Sequence 182912 from Patent EP1572962.
JD285865 - Sequence 266889 from Patent EP1572962.
AK302895 - Homo sapiens cDNA FLJ54206 complete cds, highly similar to Ubiquilin-4.
AK314413 - Homo sapiens cDNA, FLJ95194.
KJ902914 - Synthetic construct Homo sapiens clone ccsbBroadEn_12308 UBQLN4 gene, encodes complete protein.
AB587408 - Synthetic construct DNA, clone: pF1KB6163, Homo sapiens UBQLN4 gene for ubiquilin 4, without stop codon, in Flexi system.

-  Other Names for This Gene
  Alternate Gene Symbols: A6ND44, B2RAY7, C1orf6, CIP75, ENST00000368309.1, ENST00000368309.2, ENST00000368309.3, NM_020131, Q5VYA0, Q5VYA1, Q9BR98, Q9NRR5, Q9UHX4, UBIN, UBQL4_HUMAN, uc001fna.1, uc001fna.2, uc001fna.3, uc001fna.4, uc001fna.5
UCSC ID: ENST00000368309.4
RefSeq Accession: NM_020131
Protein: Q9NRR5 (aka UBQL4_HUMAN or A1UP_HUMAN)
CCDS: CCDS1127.1

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