Human Gene PSMD13 (uc001lol.2) Description and Page Index
  Description: Homo sapiens proteasome (prosome, macropain) 26S subunit, non-ATPase, 13 (PSMD13), transcript variant 1, mRNA.
RefSeq Summary (NM_002817): The 26S proteasome is a multicatalytic proteinase complex with a highly ordered structure composed of 2 complexes, a 20S core and a 19S regulator. The 20S core is composed of 4 rings of 28 non-identical subunits; 2 rings are composed of 7 alpha subunits and 2 rings are composed of 7 beta subunits. The 19S regulator is composed of a base, which contains 6 ATPase subunits and 2 non-ATPase subunits, and a lid, which contains up to 10 non-ATPase subunits. Proteasomes are distributed throughout eukaryotic cells at a high concentration and cleave peptides in an ATP/ubiquitin-dependent process in a non-lysosomal pathway. An essential function of a modified proteasome, the immunoproteasome, is the processing of class I MHC peptides. This gene encodes a non-ATPase subunit of the 19S regulator. Two transcripts encoding different isoforms have been described. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr11:236,808-252,984 Size: 16,177 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg19 chr11:237,050-252,600 Size: 15,551 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:236,808-252,984)mRNA (may differ from genome)Protein (376 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: PSD13_HUMAN
DESCRIPTION: RecName: Full=26S proteasome non-ATPase regulatory subunit 13; AltName: Full=26S proteasome regulatory subunit RPN9; AltName: Full=26S proteasome regulatory subunit S11; AltName: Full=26S proteasome regulatory subunit p40.5;
FUNCTION: Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.
SUBUNIT: Component of the PA700 complex.
SIMILARITY: Belongs to the proteasome subunit S11 family.
SIMILARITY: Contains 1 PCI domain.

-  MalaCards Disease Associations
  MalaCards Gene Search: PSMD13
Diseases sorted by gene-association score: leber congenital amaurosis (1)

-  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: 76.26 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 2284.48 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 -116.60242-0.482 Picture PostScript Text
3' UTR -148.10384-0.386 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
IPR000717 - PCI_dom

Pfam Domains:
PF01399 - PCI domain

SCOP Domains:
46785 - "Winged helix" DNA-binding domain

ModBase Predicted Comparative 3D Structure on Q9UNM6
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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsemblFlyBaseWormBaseSGD
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005198 structural molecule activity

Biological Process:
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0007127 meiosis I
GO:0016579 protein deubiquitination
GO:0043248 proteasome assembly
GO:0043312 neutrophil degranulation
GO:0043687 post-translational protein modification

Cellular Component:
GO:0000502 proteasome complex
GO:0005576 extracellular region
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005829 cytosol
GO:0005838 proteasome regulatory particle
GO:0008541 proteasome regulatory particle, lid subcomplex
GO:0016020 membrane
GO:0022624 proteasome accessory complex
GO:0034774 secretory granule lumen
GO:1904813 ficolin-1-rich granule lumen


-  Descriptions from all associated GenBank mRNAs
  AK314733 - Homo sapiens cDNA, FLJ95595, highly similar to Homo sapiens proteasome (prosome, macropain) 26S subunit, non-ATPase, 13 (PSMD13), mRNA.
AK295944 - Homo sapiens cDNA FLJ53046 complete cds, highly similar to 26S proteasome non-ATPase regulatory subunit 13.
AK222895 - Homo sapiens mRNA for proteasome 26S non-ATPase subunit 13 isoform 1 variant, clone: HRC01339.
AK094775 - Homo sapiens cDNA FLJ37456 fis, clone BRAWH2011096, highly similar to 26S proteasome non-ATPase regulatory subunit 13.
AB009398 - Homo sapiens mRNA for 26S proteasome subunit p40.5, complete cds.
BC001100 - Homo sapiens proteasome (prosome, macropain) 26S subunit, non-ATPase, 13, mRNA (cDNA clone MGC:734 IMAGE:3506530), complete cds.
AF083245 - Homo sapiens HSPC027 mRNA, complete cds.
AK307447 - Homo sapiens cDNA, FLJ97395.
AF107837 - Homo sapiens clone AS0053 26S proteasome subunit p40.5 mRNA, complete cds.
BC001747 - Homo sapiens proteasome (prosome, macropain) 26S subunit, non-ATPase, 13, mRNA (cDNA clone MGC:672 IMAGE:3535807), complete cds.
BX647314 - Homo sapiens mRNA; cDNA DKFZp686H16220 (from clone DKFZp686H16220).
KJ897414 - Synthetic construct Homo sapiens clone ccsbBroadEn_06808 PSMD13 gene, encodes complete protein.
AB528493 - Synthetic construct DNA, clone: pF1KB5349, Homo sapiens PSMD13 gene for proteasome (prosome, macropain) 26S subunit, non-ATPase, 13, without stop codon, in Flexi system.
DQ892171 - Synthetic construct clone IMAGE:100004801; FLH183662.01X; RZPDo839F02142D proteasome (prosome, macropain) 26S subunit, non-ATPase, 13 (PSMD13) gene, encodes complete protein.
DQ895365 - Synthetic construct Homo sapiens clone IMAGE:100009825; FLH183658.01L; RZPDo839F02141D proteasome (prosome, macropain) 26S subunit, non-ATPase, 13 (PSMD13) gene, encodes complete protein.
AF086708 - Homo sapiens 26S proteasome subunit 11 (S11) mRNA, partial cds.
BT007307 - Homo sapiens proteasome (prosome, macropain) 26S subunit, non-ATPase, 13 mRNA, complete cds.
JD203677 - Sequence 184701 from Patent EP1572962.
JD130249 - Sequence 111273 from Patent EP1572962.
AF107836 - Homo sapiens clone PFTGT1-2 26S proteasome subunit p40.5 mRNA, partial cds.
JD023740 - Sequence 4764 from Patent EP1572962.
JD022003 - Sequence 3027 from Patent EP1572962.
JD029184 - Sequence 10208 from Patent EP1572962.
JD026405 - Sequence 7429 from Patent EP1572962.
AK092845 - Homo sapiens cDNA FLJ35526 fis, clone SPLEN2001761.
AX747762 - Sequence 1287 from Patent EP1308459.
JD409984 - Sequence 391008 from Patent EP1572962.
JD392582 - Sequence 373606 from Patent EP1572962.
JD355874 - Sequence 336898 from Patent EP1572962.
JD355875 - Sequence 336899 from Patent EP1572962.
JD277164 - Sequence 258188 from Patent EP1572962.
JD455366 - Sequence 436390 from Patent EP1572962.
JD283134 - Sequence 264158 from Patent EP1572962.
JD181989 - Sequence 163013 from Patent EP1572962.
JD042555 - Sequence 23579 from Patent EP1572962.
JD307623 - Sequence 288647 from Patent EP1572962.

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

Reactome (by CSHL, EBI, and GO)

Protein Q9UNM6 (Reactome details) participates in the following event(s):

R-HSA-5665871 ADRM1 binds 26S proteasome
R-HSA-8956140 NEDD8 and UBD bind NUB1 and the 26S proteasome
R-HSA-6800434 Exocytosis of ficolin-rich granule lumen proteins
R-HSA-6798748 Exocytosis of secretory granule lumen proteins
R-HSA-5665854 ADRM1:26S proteaseome binds UCHL5
R-HSA-5689539 ADRM1:26S proteaseome binds USP14
R-HSA-5689603 UCH proteinases
R-HSA-8951664 Neddylation
R-HSA-6798695 Neutrophil degranulation
R-HSA-5689880 Ub-specific processing proteases
R-HSA-5688426 Deubiquitination
R-HSA-597592 Post-translational protein modification
R-HSA-68827 CDT1 association with the CDC6:ORC:origin complex
R-HSA-68949 Orc1 removal from chromatin
R-HSA-69017 CDK-mediated phosphorylation and removal of Cdc6
R-HSA-69601 Ubiquitin Mediated Degradation of Phosphorylated Cdc25A
R-HSA-69229 Ubiquitin-dependent degradation of Cyclin D1
R-HSA-174178 APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1
R-HSA-174154 APC/C:Cdc20 mediated degradation of Securin
R-HSA-2467813 Separation of Sister Chromatids
R-HSA-174113 SCF-beta-TrCP mediated degradation of Emi1
R-HSA-174184 Cdc20:Phospho-APC/C mediated degradation of Cyclin A
R-HSA-180534 Vpu mediated degradation of CD4
R-HSA-180585 Vif-mediated degradation of APOBEC3G
R-HSA-9020702 Interleukin-1 signaling
R-HSA-211733 Regulation of activated PAK-2p34 by proteasome mediated degradation
R-HSA-349425 Autodegradation of the E3 ubiquitin ligase COP1
R-HSA-350562 Regulation of ornithine decarboxylase (ODC)
R-HSA-450408 AUF1 (hnRNP D0) binds and destabilizes mRNA
R-HSA-983168 Antigen processing: Ubiquitination & Proteasome degradation
R-HSA-1169091 Activation of NF-kappaB in B cells
R-HSA-1234176 Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha
R-HSA-1236974 ER-Phagosome pathway
R-HSA-1236978 Cross-presentation of soluble exogenous antigens (endosomes)
R-HSA-4641258 Degradation of DVL
R-HSA-195253 Degradation of beta-catenin by the destruction complex
R-HSA-4641257 Degradation of AXIN
R-HSA-4608870 Asymmetric localization of PCP proteins
R-HSA-5358346 Hedgehog ligand biogenesis
R-HSA-5362768 Hh mutants that don't undergo autocatalytic processing are degraded by ERAD
R-HSA-202424 Downstream TCR signaling
R-HSA-2871837 FCERI mediated NF-kB activation
R-HSA-5607764 CLEC7A (Dectin-1) signaling
R-HSA-5607761 Dectin-1 mediated noncanonical NF-kB signaling
R-HSA-5676590 NIK-->noncanonical NF-kB signaling
R-HSA-5610785 GLI3 is processed to GLI3R by the proteasome
R-HSA-5610783 Degradation of GLI2 by the proteasome
R-HSA-5610780 Degradation of GLI1 by the proteasome
R-HSA-5632684 Hedgehog 'on' state
R-HSA-5658442 Regulation of RAS by GAPs
R-HSA-5668541 TNFR2 non-canonical NF-kB pathway
R-HSA-5687128 MAPK6/MAPK4 signaling
R-HSA-8948751 Regulation of PTEN stability and activity
R-HSA-69481 G2/M Checkpoints
R-HSA-8852276 The role of GTSE1 in G2/M progression after G2 checkpoint
R-HSA-8854050 FBXL7 down-regulates AURKA during mitotic entry and in early mitosis
R-HSA-382556 ABC-family proteins mediated transport
R-HSA-5678895 Defective CFTR causes cystic fibrosis
R-HSA-8939236 RUNX1 regulates transcription of genes involved in differentiation of HSCs
R-HSA-8939902 Regulation of RUNX2 expression and activity
R-HSA-9010553 Regulation of expression of SLITs and ROBOs
R-HSA-174084 Autodegradation of Cdh1 by Cdh1:APC/C
R-HSA-187577 SCF(Skp2)-mediated degradation of p27/p21
R-HSA-8941858 Regulation of RUNX3 expression and activity
R-HSA-168249 Innate Immune System
R-HSA-392499 Metabolism of proteins
R-HSA-68867 Assembly of the pre-replicative complex
R-HSA-69052 Switching of origins to a post-replicative state
R-HSA-69610 p53-Independent DNA Damage Response
R-HSA-75815 Ubiquitin-dependent degradation of Cyclin D
R-HSA-174143 APC/C-mediated degradation of cell cycle proteins
R-HSA-176409 APC/C:Cdc20 mediated degradation of mitotic proteins
R-HSA-68882 Mitotic Anaphase
R-HSA-176408 Regulation of APC/C activators between G1/S and early anaphase
R-HSA-179419 APC:Cdc20 mediated degradation of cell cycle proteins prior to satisfation of the cell cycle checkpoint
R-HSA-162909 Host Interactions of HIV factors
R-HSA-446652 Interleukin-1 family signaling
R-HSA-169911 Regulation of Apoptosis
R-HSA-69541 Stabilization of p53
R-HSA-351202 Metabolism of polyamines
R-HSA-450531 Regulation of mRNA stability by proteins that bind AU-rich elements
R-HSA-983169 Class I MHC mediated antigen processing & presentation
R-HSA-1168372 Downstream signaling events of B Cell Receptor (BCR)
R-HSA-1234174 Regulation of Hypoxia-inducible Factor (HIF) by oxygen
R-HSA-1236975 Antigen processing-Cross presentation
R-HSA-201681 TCF dependent signaling in response to WNT
R-HSA-195721 Signaling by WNT
R-HSA-4086400 PCP/CE pathway
R-HSA-5358351 Signaling by Hedgehog
R-HSA-5387390 Hh mutants abrogate ligand secretion
R-HSA-202403 TCR signaling
R-HSA-2454202 Fc epsilon receptor (FCERI) signaling
R-HSA-5621481 C-type lectin receptors (CLRs)
R-HSA-5610787 Hedgehog 'off' state
R-HSA-5673001 RAF/MAP kinase cascade
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-5683057 MAPK family signaling cascades
R-HSA-6807070 PTEN Regulation
R-HSA-69620 Cell Cycle Checkpoints
R-HSA-69275 G2/M Transition
R-HSA-382551 Transport of small molecules
R-HSA-5619084 ABC transporter disorders
R-HSA-8878171 Transcriptional regulation by RUNX1
R-HSA-8878166 Transcriptional regulation by RUNX2
R-HSA-376176 Signaling by ROBO receptors
R-HSA-69202 Cyclin E associated events during G1/S transition
R-HSA-69656 Cyclin A:Cdk2-associated events at S phase entry
R-HSA-8878159 Transcriptional regulation by RUNX3
R-HSA-168256 Immune System
R-HSA-69002 DNA Replication Pre-Initiation
R-HSA-69239 Synthesis of DNA
R-HSA-69613 p53-Independent G1/S DNA damage checkpoint
R-HSA-69242 S Phase
R-HSA-453276 Regulation of mitotic cell cycle
R-HSA-176814 Activation of APC/C and APC/C:Cdc20 mediated degradation of mitotic proteins
R-HSA-2555396 Mitotic Metaphase and Anaphase
R-HSA-162906 HIV Infection
R-HSA-449147 Signaling by Interleukins
R-HSA-109581 Apoptosis
R-HSA-69563 p53-Dependent G1 DNA Damage Response
R-HSA-71291 Metabolism of nitrogenous molecules
R-HSA-8953854 Metabolism of RNA
R-HSA-1280218 Adaptive Immune System
R-HSA-983705 Signaling by the B Cell Receptor (BCR)
R-HSA-2262749 Cellular response to hypoxia
R-HSA-162582 Signal Transduction
R-HSA-3858494 Beta-catenin independent WNT signaling
R-HSA-5663202 Diseases of signal transduction
R-HSA-5684996 MAPK1/MAPK3 signaling
R-HSA-1257604 PIP3 activates AKT signaling
R-HSA-1640170 Cell Cycle
R-HSA-453274 Mitotic G2-G2/M phases
R-HSA-5619115 Disorders of transmembrane transporters
R-HSA-212436 Generic Transcription Pathway
R-HSA-422475 Axon guidance
R-HSA-69206 G1/S Transition
R-HSA-68874 M/G1 Transition
R-HSA-69306 DNA Replication
R-HSA-69615 G1/S DNA Damage Checkpoints
R-HSA-69278 Cell Cycle (Mitotic)
R-HSA-68886 M Phase
R-HSA-5663205 Infectious disease
R-HSA-5357801 Programmed Cell Death
R-HSA-69580 p53-Dependent G1/S DNA damage checkpoint
R-HSA-1430728 Metabolism
R-HSA-2262752 Cellular responses to stress
R-HSA-1643685 Disease
R-HSA-9006925 Intracellular signaling by second messengers
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-1266738 Developmental Biology
R-HSA-453279 Mitotic G1-G1/S phases
R-HSA-8953897 Cellular responses to external stimuli
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: B3KT15, NM_002817, NP_002808, O75831, PSD13_HUMAN, Q53XU2, Q9UNM6, Q9UNV3
UCSC ID: uc001lol.2
RefSeq Accession: NM_002817
Protein: Q9UNM6 (aka PSD13_HUMAN or PSDD_HUMAN)
CCDS: CCDS7692.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_002817.3
exon count: 13CDS single in 3' UTR: no RNA size: 1757
ORF size: 1131CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1895.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 287# 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.