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PSMD9 proteasome 26S subunit, non-ATPase 9 [ Homo sapiens (human) ]

Gene ID: 5715, updated on 17-Jun-2024

Summary

Official Symbol
PSMD9provided by HGNC
Official Full Name
proteasome 26S subunit, non-ATPase 9provided by HGNC
Primary source
HGNC:HGNC:9567
See related
Ensembl:ENSG00000110801 MIM:603146; AllianceGenome:HGNC:9567
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
p27; Rpn4
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. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, May 2012]
Expression
Ubiquitous expression in bone marrow (RPKM 16.1), kidney (RPKM 11.1) and 25 other tissues See more
Orthologs
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Genomic context

See PSMD9 in Genome Data Viewer
Location:
12q24.31
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (121888790..121918297)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (121885089..121914595)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (122326696..122356203)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7187 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122235825-122236366 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122236367-122236906 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122236907-122237446 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122237447-122237986 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4992 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4993 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7188 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7189 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7190 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4994 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4995 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4996 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4997 Neighboring gene long intergenic non-protein coding RNA 1089 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122248237-122249046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122249091-122249703 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4998 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4999 Neighboring gene SET domain containing 1B, histone lysine methyltransferase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122252006-122252512 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122276754-122277424 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5000 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122278096-122278765 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:122293687-122294886 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122297907-122298424 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122298425-122298941 Neighboring gene Sharpr-MPRA regulatory region 2080 Neighboring gene 4-hydroxyphenylpyruvate dioxygenase Neighboring gene Sharpr-MPRA regulatory region 2229 Neighboring gene transcript inducer of AURKA lysosomal degradation Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:122326353-122326966 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:122326967-122327580 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:122349577-122349733 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5001 Neighboring gene RNA, U7 small nuclear 170 pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122362388-122363066 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5002 Neighboring gene cilia and flagella associated protein 251 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122396110-122396629 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122396630-122397148 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122409067-122409566 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7192 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7193 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7194 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7195 Neighboring gene Sharpr-MPRA regulatory region 10891 Neighboring gene uncharacterized LOC124903038 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5003 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5004 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122460343-122461158 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5006 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7196 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7197 Neighboring gene BAF chromatin remodeling complex subunit BCL7A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122492684-122493298

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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
Genome-wide association study of metabolic traits reveals novel gene-metabolite-disease links.
EBI GWAS Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Tat 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
tat HIV-1 Tat slightly enhances the activity of the purified 26 S proteasome 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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC8644

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables bHLH transcription factor binding ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables transcription coactivator activity ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
Process Evidence Code Pubs
involved_in negative regulation of insulin secretion ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
involved_in positive regulation of DNA-templated transcription ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
involved_in positive regulation of insulin secretion ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
involved_in proteasome regulatory particle assembly IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in proteasome regulatory particle assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in ubiquitin-dependent protein catabolic process NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in cytosol TAS
Traceable Author Statement
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
part_of proteasome regulatory particle NAS
Non-traceable Author Statement
more info
PubMed 
part_of proteasome regulatory particle, base subcomplex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
26S proteasome non-ATPase regulatory subunit 9
Names
26S proteasome regulatory subunit p27
homolog of rat Bridge 1
proteasome (prosome, macropain) 26S subunit, non-ATPase, 9
proteasome 26S non-ATPase regulatory subunit 9

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_001261400.3NP_001248329.1  26S proteasome non-ATPase regulatory subunit 9 isoform 2

    See identical proteins and their annotated locations for NP_001248329.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks two alternate in-frame exons compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC069503, BC002383, BU726372, CB111716, KF459562
    Consensus CDS
    CCDS58284.1
    UniProtKB/Swiss-Prot
    O00233
    Related
    ENSP00000443772.1, ENST00000542602.1
    Conserved Domains (1) summary
    cl00117
    Location:45100
    PDZ; PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. ...
  2. NM_002813.7NP_002804.2  26S proteasome non-ATPase regulatory subunit 9 isoform 1

    See identical proteins and their annotated locations for NP_002804.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC069503, BC002383, BU726372, KF459562
    Consensus CDS
    CCDS9225.1
    UniProtKB/Swiss-Prot
    B2RD35, G3V1Q6, O00233, Q9BQ42
    UniProtKB/TrEMBL
    J3KN29
    Related
    ENSP00000440485.1, ENST00000541212.6
    Conserved Domains (1) summary
    cd00989
    Location:129205
    PDZ_metalloprotease; PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ ...

RNA

  1. NR_048555.3 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate coding exon compared to variant 1, that causes a frameshift. The resulting transcript is not thought to be protein-coding.
    Source sequence(s)
    AC069503, BC002383, BM850893, BU726372, KF459562

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    121888790..121918297
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    121885089..121914595
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)