Human Gene PSMD6 (uc003dmb.2)
  Description: Homo sapiens proteasome (prosome, macropain) 26S subunit, non-ATPase, 6 (PSMD6), transcript variant 1, mRNA.
RefSeq Summary (NM_001271779): This gene encodes a member of the protease subunit S10 family. The encoded protein is a subunit of the 26S proteasome which colocalizes with DNA damage foci and is involved in the ATP-dependent degradation of ubiquinated proteins. Alternative splicing results in multiple transcript variants [provided by RefSeq, Nov 2012].
Transcript (Including UTRs)
   Position: hg19 chr3:63,996,225-64,009,282 Size: 13,058 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr3:63,996,344-64,009,095 Size: 12,752 Coding Exon Count: 9 

Page IndexSequence and LinksPrimersGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:63,996,225-64,009,282)mRNA (may differ from genome)Protein (442 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMGIOMIMPubMed
UniProtKBWikipediaBioGrid CRISPR DB

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PSMD6
CDC HuGE Published Literature: PSMD6
Positive Disease Associations: Diabetes Mellitus, Type 2 , Folic Acid , Stroke
Related Studies:
  1. Diabetes Mellitus, Type 2
    Yoon Shin Cho et al. Nature genetics 2012, Meta-analysis of genome-wide association studies identifies eight new loci for type 2 diabetes in east Asians., Nature genetics. [PubMed 22158537]
  2. Folic Acid
    Toshiko Tanaka et al. American journal of human genetics 2009, Genome-wide association study of vitamin B6, vitamin B12, folate, and homocysteine blood concentrations., American journal of human genetics. [PubMed 19303062]
  3. Stroke
    , , . [PubMed 0]
           more ... click here to view the complete list

-  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: 96.70 RPKM in Testis
Total median expression: 1513.75 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 -94.00187-0.503 Picture PostScript Text
3' UTR -19.61119-0.165 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
IPR019585 - 26S_proteasome_reg_su-Rpn7
IPR000717 - PCI_dom
IPR011991 - WHTH_trsnscrt_rep_DNA-bd

Pfam Domains:
PF01399 - PCI domain
PF10602 - 26S proteasome subunit RPN7

SCOP Domains:
81901 - HCP-like
48452 - TPR-like
46785 - "Winged helix" DNA-binding domain

ModBase Predicted Comparative 3D Structure on C9IZE4
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 orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AK290205 - Homo sapiens cDNA FLJ76777 complete cds, highly similar to Homo sapiens proteasome (prosome, macropain) 26S subunit, non-ATPase, 6 (PSMD6), mRNA.
AL832109 - Homo sapiens mRNA; cDNA DKFZp313H118 (from clone DKFZp313H118).
AK054730 - Homo sapiens cDNA FLJ30168 fis, clone BRACE2000750.
BC000630 - Homo sapiens proteasome (prosome, macropain) 26S subunit, non-ATPase, 6, mRNA (cDNA clone MGC:809 IMAGE:3344973), complete cds.
AK095059 - Homo sapiens cDNA FLJ37740 fis, clone BRHIP2021870, highly similar to 26S proteasome non-ATPase regulatory subunit 6.
AY568086 - Homo sapiens breast cancer associated protein SGA-113M mRNA, complete cds.
D14663 - Homo sapiens KIAA0107 mRNA, complete cds.
BC012369 - Homo sapiens proteasome (prosome, macropain) 26S subunit, non-ATPase, 6, mRNA (cDNA clone MGC:9794 IMAGE:3858094), complete cds.
BX647742 - Homo sapiens mRNA; cDNA DKFZp686D02286 (from clone DKFZp686D02286).
AF215935 - Homo sapiens proteasome regulatory particle subunit p44S10 mRNA, complete cds.
AY359879 - Homo sapiens KIAA0107 isoform mRNA, complete cds.
AK055210 - Homo sapiens cDNA FLJ30648 fis, clone CTONG2006449, moderately similar to Drosophila melanogaster 26S proteasome regulatory complex subunit p42A mRNA.
BC000904 - Homo sapiens proteasome (prosome, macropain) 26S subunit, non-ATPase, 6, mRNA (cDNA clone MGC:5202 IMAGE:2900971), complete cds.
JD287140 - Sequence 268164 from Patent EP1572962.
JD241364 - Sequence 222388 from Patent EP1572962.
JD307685 - Sequence 288709 from Patent EP1572962.
AF530062 - Homo sapiens phosphonoformate immuno-associated protein 4 (PFAAP4) mRNA, complete cds.
KJ892868 - Synthetic construct Homo sapiens clone ccsbBroadEn_02262 PSMD6 gene, encodes complete protein.
AB463196 - Synthetic construct DNA, clone: pF1KA0107, Homo sapiens PSMD6 gene for proteasome (prosome, macropain) 26S subunit, non-ATPase, 6, without stop codon, in Flexi system.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03050 - Proteasome

BioCyc Knowledge Library
PWY3DJ-213 - Targeted protein degradation

-  Other Names for This Gene
  Alternate Gene Symbols: C9IZE4, C9IZE4_HUMAN, hCG_23509, NM_001271779, NP_001258708, uc003dmb.1
UCSC ID: uc003dmb.2
RefSeq Accession: NM_001271779
Protein: C9IZE4 CCDS: CCDS63677.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001271779.1
exon count: 9CDS single in 3' UTR: no RNA size: 1652
ORF size: 1329CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2564.00frame shift in genome: no % Coverage: 98.97
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.