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    PSMD13 proteasome 26S subunit, non-ATPase 13 [ Homo sapiens (human) ]

    Gene ID: 5719, updated on 3-Nov-2024

    Summary

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    Official Symbol
    PSMD13provided by HGNC
    Official Full Name
    proteasome 26S subunit, non-ATPase 13provided by HGNC
    Primary source
    HGNC:HGNC:9558
    See related
    Ensembl:ENSG00000185627 MIM:603481; AllianceGenome:HGNC:9558
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    S11; Rpn9; p40.5; HSPC027
    Summary
    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]
    Expression
    Ubiquitous expression in appendix (RPKM 33.3), lymph node (RPKM 32.2) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See PSMD13 in Genome Data Viewer
    Location:
    11p15.5
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (236976..252984)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (277982..293919)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (236976..252984)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:208989-209576 Neighboring gene microRNA 6743 Neighboring gene RIC8 guanine nucleotide exchange factor A Neighboring gene sirtuin 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2989 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4255 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4256 Neighboring gene signal recognition particle 19kDa pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:257568-258068 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2990 Neighboring gene cytochrome c oxidase subunit 8B, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4257 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:279707-280257 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4258 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2991 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:283867-284636 Neighboring gene NLR family pyrin domain containing 6

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Alternative splicing of PSMD13 mediated by genetic variants is significantly associated with endometrial cancer risk. He S, et al. J Gynecol Oncol, 2023 May. PMID 36731897, Free PMC Article
    2. Characterization of a bidirectional promoter shared between two human genes related to aging: SIRT3 and PSMD13. Bellizzi D, et al. Genomics, 2007 Jan. PMID 17059877
    3. Identification, molecular cloning, and characterization of subunit 11 of the human 26S proteasome. Hoffman L, et al. FEBS Lett, 1999 Apr 16. PMID 10225435
    4. Proteasome system dysregulation and treatment resistance mechanisms in major depressive disorder. Minelli A, et al. Transl Psychiatry, 2015 Dec 1. PMID 26624926, Free PMC Article
    5. Rescue of enzymatic function for disease-associated RPE65 proteins containing various missense mutations in non-active sites. Li S, et al. J Biol Chem, 2014 Jul 4. PMID 24849605, Free PMC Article

    See all (209) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Alternative splicing of PSMD13 mediated by genetic variants is significantly associated with endometrial cancer risk.
      Title: Alternative splicing of PSMD13 mediated by genetic variants is significantly associated with endometrial cancer risk.
    2. Data show that UBLCP1 selectively binds to the 26S proteasome non-ATPase regulatory subunit 13 (19S regulatory particle) in regulating proteasome assembly.
      Title: Phosphatase UBLCP1 controls proteasome assembly.
    3. Studies have found significant associations of the treatment response with the 26S proteasome non-ATPase subunit 9 (PSMD9), proteasome alpha type 7 subunit (PSMA7) and PSMD13 genes.
      Title: Proteasome system dysregulation and treatment resistance mechanisms in major depressive disorder.
    4. The SIRT3 5' flanking region encompasses the PSMD13 gene encoding the p40.5 regulator subunit of the 26S proteasome.
      Title: Characterization of a bidirectional promoter shared between two human genes related to aging: SIRT3 and PSMD13.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects.
    EBI GWAS Catalog
    New gene functions in megakaryopoiesis and platelet formation.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 interacts with PSMD13 PubMed
    Tat tat Expression of HIV-1 Tat downregulates the abundance of proteasome (prosome, macropain) 26S subunit, non-ATPase, 13 (PSMD13) in the nucleoli of Jurkat T-cells PubMed
    tat HIV-1 Tat slightly enhances the activity of the purified 26 S proteasome PubMed
    tat Amino acids Lys51, Arg52, and Asp67 of HIV-1 Tat represent the proteasome binding site of Tat, and Tat amino acids 37-72 are necessary for proteasomal interaction and suppression of 11 S regulator-mediated antigen presentation PubMed
    tat HIV-1 Tat inhibits the peptidase activity of the 20 S proteasome and interferes with the formation of the 20 S proteasome-11 S regulator complex PubMed
    tat HIV-1 Tat binds to the alpha2, alpha4, alpha6, alpha7, beta1, beta2, beta3, beta5, beta6, beta7, LMP7/beta5i, and MECL1/beta2i subunits of the proteasome 20 S core structure and can inhibit cellular proteasome function PubMed
    Vif vif HIV-1 Vif binds to the cellular cytidine deaminase APOBEC3G and targets it for degradation through an interaction with the proteasome, thereby inhibiting APOBEC3G mediated restriction of HIV-1 replication PubMed
    integrase gag-pol Proteasomal degradation of HIV-1 integrase in mammalian cells occurs by the N-end rule pathway PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables structural molecule activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in meiosis I IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in ubiquitin-dependent protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  
    located_in ficolin-1-rich granule lumen TAS
    Traceable Author Statement
    more info
    		  
    located_in membrane HDA PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus HDA PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of proteasome accessory complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of proteasome complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of proteasome complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of proteasome regulatory particle TAS
    Traceable Author Statement
    more info
    		 PubMed 
    part_of proteasome regulatory particle, lid subcomplex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in secretory granule lumen TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    26S proteasome non-ATPase regulatory subunit 13
    Names
    26S proteasome regulatory subunit RPN9
    26S proteasome regulatory subunit S11
    26S proteasome regulatory subunit p40.5
    26S proteasome subunit p40.5
    proteasome (prosome, macropain) 26S subunit, non-ATPase, 13

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_002817.4 → NP_002808.3  26S proteasome non-ATPase regulatory subunit 13 isoform 1

      See identical proteins and their annotated locations for NP_002808.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AA931044, AB009398, AC136475
      Consensus CDS
      CCDS7692.1
      UniProtKB/Swiss-Prot
      B3KT15, O75831, Q53XU2, Q9UNM6, Q9UNV3
      UniProtKB/TrEMBL
      B2RBM7, Q53GN6
      Related
      ENSP00000436186.1, ENST00000532097.6
      Conserved Domains (1) summary
      pfam01399
      Location:231 → 335
      PCI; PCI domain

    2. NM_175932.3 → NP_787128.2  26S proteasome non-ATPase regulatory subunit 13 isoform 2

      See identical proteins and their annotated locations for NP_787128.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate segment and uses a different splice site in the 5' coding region, compared to variant 1. These differences cause a frameshift and then a restoration in the reading frame. Isoform 2 has a slightly shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AA931044, AC136475, AK094775, AL556906
      Consensus CDS
      CCDS44504.1
      UniProtKB/TrEMBL
      B2RBM7
      Related
      ENSP00000396937.2, ENST00000431206.6
      Conserved Domains (1) summary
      pfam01399
      Location:233 → 337
      PCI; PCI domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      236976..252984
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011520235.4 → XP_011518537.1  26S proteasome non-ATPase regulatory subunit 13 isoform X1

      UniProtKB/TrEMBL
      J3KNQ3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      277982..293919
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054369445.1 → XP_054225420.1  26S proteasome non-ATPase regulatory subunit 13 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UNM6.2 GenPept UniProtKB/Swiss-Prot:Q9UNM6

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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