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Aliases for PSMD13 Gene

Aliases for PSMD13 Gene

  • Proteasome 26S Subunit, Non-ATPase 13 2 3 5
  • Proteasome (Prosome, Macropain) 26S Subunit, Non-ATPase, 13 2 3
  • 26S Proteasome Regulatory Subunit P40.5 3 4
  • 26S Proteasome Regulatory Subunit RPN9 3 4
  • 26S Proteasome Regulatory Subunit S11 3 4
  • 26S Proteasome Non-ATPase Regulatory Subunit 13 3
  • 26S Proteasome Subunit P40.5 3
  • HSPC027 3
  • P40.5 3
  • Rpn9 3
  • S11 3

External Ids for PSMD13 Gene

Previous GeneCards Identifiers for PSMD13 Gene

  • GC11P000459
  • GC11P000281
  • GC11M000945
  • GC11P000056

Summaries for PSMD13 Gene

Entrez Gene Summary for PSMD13 Gene

  • 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]

GeneCards Summary for PSMD13 Gene

PSMD13 (Proteasome 26S Subunit, Non-ATPase 13) is a Protein Coding gene. Diseases associated with PSMD13 include Leber Congenital Amaurosis. Among its related pathways are RET signaling and CDK-mediated phosphorylation and removal of Cdc6.

UniProtKB/Swiss-Prot for PSMD13 Gene

  • Component of the 26S proteasome, a multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins. This complex plays a key role in the maintenance of protein homeostasis by removing misfolded or damaged proteins, which could impair cellular functions, and by removing proteins whose functions are no longer required. Therefore, the proteasome participates in numerous cellular processes, including cell cycle progression, apoptosis, or DNA damage repair.

Gene Wiki entry for PSMD13 Gene

Additional gene information for PSMD13 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PSMD13 Gene

Genomics for PSMD13 Gene

GeneHancer (GH) Regulatory Elements for PSMD13 Gene

Promoters and enhancers for PSMD13 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11I000234 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 594.4 +0.0 4 3.5 HDGF HNRNPUL1 PKNOX1 FOXA2 ARNT ZFP64 ARID4B SIN3A DMAP1 YY1 PSMD13 SIRT3 RIC8A BET1L SNORA52 RNH1 GATD1 TMEM80 ENSG00000255237 RPLP2
GH11I000205 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 32.6 -27.8 -27834 6 HDGF PKNOX1 SMAD1 MLX ARID4B SIN3A DMAP1 YY1 SLC30A9 POLR2B RIC8A BET1L MIR6743 GC11P000208 PSMD13 PIR57925
GH11I000266 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 24.7 +33.5 33506 6.8 HDGF PKNOX1 FOXA2 SMAD1 ARNT IRF4 YY1 POLR2B ZNF766 CBX5 PIR53591 IFITM2 RIC8A PSMD13 BET1L SIRT3 PGGHG TMEM80 ENSG00000254559 ODF3
GH11I000574 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE 14.5 +341.8 341835 6.9 HDGF PKNOX1 FOXA2 SMAD1 MLX ARNT ARID4B SIN3A FEZF1 DMAP1 PHRF1 TMEM80 SNORA52 ENSG00000255237 BET1L TSPAN4 PSMD13 RIC8A RPLP2 HRAS
GH11I000276 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE dbSUPER 14.8 +43.4 43401 6.7 ATF1 PKNOX1 ARNT NFRKB SIN3A ZBTB40 YY1 POLR2B EGR1 SCRT2 NLRP6 PSMD13 RIC8A BET1L ENSG00000255026 GC11P000259 GC11M000282
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PSMD13 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PSMD13 gene promoter:

Genomic Locations for PSMD13 Gene

Genomic Locations for PSMD13 Gene
chr11:236,546-252,984
(GRCh38/hg38)
Size:
16,439 bases
Orientation:
Plus strand
chr11:236,546-252,984
(GRCh37/hg19)

Genomic View for PSMD13 Gene

Genes around PSMD13 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PSMD13 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PSMD13 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PSMD13 Gene

Proteins for PSMD13 Gene

  • Protein details for PSMD13 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UNM6-PSD13_HUMAN
    Recommended name:
    26S proteasome non-ATPase regulatory subunit 13
    Protein Accession:
    Q9UNM6
    Secondary Accessions:
    • B3KT15
    • O75831
    • Q53XU2
    • Q9UNV3

    Protein attributes for PSMD13 Gene

    Size:
    376 amino acids
    Molecular mass:
    42945 Da
    Quaternary structure:
    • Component of the 19S proteasome regulatory particle complex. The 26S proteasome consists of a 20S core particle (CP) and two 19S regulatory subunits (RP). The regulatory particle is made of a lid composed of 9 subunits including PSMD13, a base containing 6 ATPases and few additional components.

    Three dimensional structures from OCA and Proteopedia for PSMD13 Gene

    Alternative splice isoforms for PSMD13 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PSMD13 Gene

Post-translational modifications for PSMD13 Gene

  • Ubiquitination at isoforms=22, Lys99, Lys115, isoforms=2122, isoforms=2161, isoforms=2174, isoforms=2186, isoforms=2252, isoforms=2313, isoforms=2321, and Lys347
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PSMD13 Gene

Domains & Families for PSMD13 Gene

Gene Families for PSMD13 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for PSMD13 Gene

Graphical View of Domain Structure for InterPro Entry

Q9UNM6

UniProtKB/Swiss-Prot:

PSD13_HUMAN :
  • Belongs to the proteasome subunit S11 family.
Family:
  • Belongs to the proteasome subunit S11 family.
genes like me logo Genes that share domains with PSMD13: view

Function for PSMD13 Gene

Molecular function for PSMD13 Gene

UniProtKB/Swiss-Prot Function:
Component of the 26S proteasome, a multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins. This complex plays a key role in the maintenance of protein homeostasis by removing misfolded or damaged proteins, which could impair cellular functions, and by removing proteins whose functions are no longer required. Therefore, the proteasome participates in numerous cellular processes, including cell cycle progression, apoptosis, or DNA damage repair.

Phenotypes From GWAS Catalog for PSMD13 Gene

Gene Ontology (GO) - Molecular Function for PSMD13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005198 structural molecule activity IBA --
genes like me logo Genes that share ontologies with PSMD13: view
genes like me logo Genes that share phenotypes with PSMD13: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PSMD13 Gene

Localization for PSMD13 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PSMD13 gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 5
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nuclear speckles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PSMD13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000502 proteasome complex TAS,IDA 17323924
GO:0005576 extracellular region TAS --
GO:0005634 nucleus IDA,HDA 21630459
GO:0005654 nucleoplasm TAS --
GO:0005829 cytosol TAS,IBA --
genes like me logo Genes that share ontologies with PSMD13: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for PSMD13 Gene

Pathways & Interactions for PSMD13 Gene

SuperPathways for PSMD13 Gene

SuperPathway Contained pathways
1 CDK-mediated phosphorylation and removal of Cdc6
.78
.31
2 RET signaling
3 HIV Life Cycle
.45
4 Class I MHC mediated antigen processing and presentation
5 Antigen processing-Cross presentation
genes like me logo Genes that share pathways with PSMD13: view

Gene Ontology (GO) - Biological Process for PSMD13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000165 MAPK cascade TAS --
GO:0000209 protein polyubiquitination TAS --
GO:0002223 stimulatory C-type lectin receptor signaling pathway TAS --
GO:0002479 antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent TAS --
GO:0006511 ubiquitin-dependent protein catabolic process IBA --
genes like me logo Genes that share ontologies with PSMD13: view

No data available for SIGNOR curated interactions for PSMD13 Gene

Drugs & Compounds for PSMD13 Gene

(2) Drugs for PSMD13 Gene - From: DGIdb

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Bortezomib Approved, Investigational Pharma inhibitor, other Proteosome and NF-kappaB inhibitor, Other, Proteasome inhibitors 826
carfilzomib Approved, Investigational Pharma other, Inhibitor Other, 20S Proteasome Inhibitor 0
genes like me logo Genes that share compounds with PSMD13: view

Transcripts for PSMD13 Gene

Unigene Clusters for PSMD13 Gene

Proteasome (prosome, macropain) 26S subunit, non-ATPase, 13:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for PSMD13 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b · 14c · 14d
SP1: - - -
SP2: - - - -
SP3: - -
SP4: -
SP5: - - - -
SP6:
SP7:
SP8:

Relevant External Links for PSMD13 Gene

GeneLoc Exon Structure for
PSMD13
ECgene alternative splicing isoforms for
PSMD13

Expression for PSMD13 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PSMD13 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PSMD13 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (7.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PSMD13 Gene



Protein tissue co-expression partners for PSMD13 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PSMD13 Gene:

PSMD13

SOURCE GeneReport for Unigene cluster for PSMD13 Gene:

Hs.134688

Evidence on tissue expression from TISSUES for PSMD13 Gene

  • Nervous system(4.8)
  • Lung(4.7)
  • Kidney(4.4)
  • Liver(4.4)
  • Skin(3.7)
  • Eye(2.6)
  • Adrenal gland(2.4)
  • Intestine(2.3)
  • Pancreas(2.3)
genes like me logo Genes that share expression patterns with PSMD13: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PSMD13 Gene

Orthologs for PSMD13 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PSMD13 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PSMD13 33 34
  • 99.56 (n)
dog
(Canis familiaris)
Mammalia PSMD13 33 34
  • 92.82 (n)
cow
(Bos Taurus)
Mammalia PSMD13 33 34
  • 91.22 (n)
rat
(Rattus norvegicus)
Mammalia Psmd13 33
  • 90.07 (n)
mouse
(Mus musculus)
Mammalia Psmd13 33 16 34
  • 89.98 (n)
oppossum
(Monodelphis domestica)
Mammalia PSMD13 34
  • 51 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PSMD13 34
  • 50 (a)
OneToOne
chicken
(Gallus gallus)
Aves PSMD13 33 34
  • 82.89 (n)
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 85 (a)
OneToMany
-- 34
  • 84 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia psmd13 33
  • 76.06 (n)
Str.1435 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.3428 33
zebrafish
(Danio rerio)
Actinopterygii psmd13 33 34
  • 73.67 (n)
zgc56377 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9211 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001651 33
  • 55.14 (n)
fruit fly
(Drosophila melanogaster)
Insecta Rpn9 35 33 34
  • 52.99 (n)
worm
(Caenorhabditis elegans)
Secernentea rpn-9 33 34
  • 48.92 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RPN9 33 34 36
  • 44.85 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0B00825g 33
  • 44.83 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ADR191C 33
  • 44.13 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT4G19006 33
  • 51.8 (n)
rice
(Oryza sativa)
Liliopsida Os01g0511300 33
  • 50.27 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 59 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU02374 33
  • 51.54 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes rpn9 33
  • 45.76 (n)
Species where no ortholog for PSMD13 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PSMD13 Gene

ENSEMBL:
Gene Tree for PSMD13 (if available)
TreeFam:
Gene Tree for PSMD13 (if available)

Paralogs for PSMD13 Gene

(1) SIMAP similar genes for PSMD13 Gene using alignment to 8 proteins:

genes like me logo Genes that share paralogs with PSMD13: view

No data available for Paralogs for PSMD13 Gene

Variants for PSMD13 Gene

Sequence variations from dbSNP and Humsavar for PSMD13 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs1000284075 -- 247,264(+) TT/T intron_variant
rs1000510473 -- 252,308(+) T/C intron_variant
rs1000529982 -- 247,871(+) T/A intron_variant
rs1000756257 -- 236,526(+) G/A upstream_transcript_variant
rs1001129383 -- 252,777(+) A/T 3_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for PSMD13 Gene

Variant ID Type Subtype PubMed ID
dgv1010n100 CNV gain 25217958
dgv1011n100 CNV gain 25217958
dgv1012n100 CNV gain 25217958
dgv1505n54 CNV gain 21841781
esv32593 CNV loss 17666407
esv3625060 CNV gain 21293372
esv3625064 CNV gain 21293372
nsv1052484 CNV gain 25217958
nsv1069987 CNV deletion 25765185
nsv467631 CNV gain 19166990
nsv469921 CNV gain 18288195
nsv516439 CNV loss 19592680
nsv522596 CNV gain 19592680
nsv527533 CNV gain 19592680
nsv552762 CNV gain 21841781
nsv552765 CNV gain 21841781
nsv552766 CNV loss 21841781
nsv552767 CNV loss 21841781
nsv7632 CNV insertion 18451855

Variation tolerance for PSMD13 Gene

Residual Variation Intolerance Score: 53% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.46; 28.56% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PSMD13 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PSMD13

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PSMD13 Gene

Disorders for PSMD13 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PSMD13 Gene - From: DISEASES

Disorder Aliases PubMed IDs
leber congenital amaurosis
  • lca
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PSMD13

genes like me logo Genes that share disorders with PSMD13: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PSMD13 Gene

Publications for PSMD13 Gene

  1. cDNA cloning and functional analysis of p28 (Nas6p) and p40.5 (Nas7p), two novel regulatory subunits of the 26S proteasome. (PMID: 9714768) Hori T … Tanaka K (Gene 1998) 2 3 4 22 58
  2. Mass spectrometric characterization of the affinity-purified human 26S proteasome complex. (PMID: 17323924) Wang X … Huang L (Biochemistry 2007) 3 4 58
  3. Characterization of a bidirectional promoter shared between two human genes related to aging: SIRT3 and PSMD13. (PMID: 17059877) Bellizzi D … De Benedictis G (Genomics 2007) 3 22 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for PSMD13 Gene