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PSMD6 proteasome 26S subunit, non-ATPase 6 [ Homo sapiens (human) ]

Gene ID: 9861, updated on 13-Mar-2020

Summary

Official Symbol
PSMD6provided by HGNC
Official Full Name
proteasome 26S subunit, non-ATPase 6provided by HGNC
Primary source
HGNC:HGNC:9564
See related
Ensembl:ENSG00000163636 MIM:617857
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
S10; Rpn7; p42A; p44S10; SGA-113M
Summary
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]
Expression
Ubiquitous expression in testis (RPKM 47.2), bone marrow (RPKM 29.6) and 25 other tissues See more
Orthologs

Genomic context

See PSMD6 in Genome Data Viewer
Location:
3p14.1
Exon count:
11
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (64010549..64024010, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (63996225..64009686, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ataxin 7 Neighboring gene ataxin 7 repeat instability region Neighboring gene SCA7/ATXN7 antisense RNA 1 Neighboring gene PSMD6 antisense RNA 2 Neighboring gene uncharacterized LOC105377121 Neighboring gene uncharacterized LOC107986093 Neighboring gene PRICKLE2 antisense RNA 1 Neighboring gene long intergenic non-protein coding RNA 994

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

NHGRI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci.
NHGRI GWA Catalog
Genome-wide association study of a heart failure related metabolomic profile among African Americans in the Atherosclerosis Risk in Communities (ARIC) study.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies identifies eight new loci for type 2 diabetes in east Asians.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of proteasome (prosome, macropain) 26S subunit, non-ATPase, 6 (PSMD6) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Protein interactions

Protein Gene Interaction Pubs
Tat 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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ30168, KIAA0107

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATPase activity NAS
Non-traceable Author Statement
more info
PubMed 
enzyme regulator activity IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
Fc-epsilon receptor signaling pathway TAS
Traceable Author Statement
more info
 
MAPK cascade TAS
Traceable Author Statement
more info
 
NIK/NF-kappaB signaling TAS
Traceable Author Statement
more info
 
SCF-dependent proteasomal ubiquitin-dependent protein catabolic process TAS
Traceable Author Statement
more info
 
T cell receptor signaling pathway TAS
Traceable Author Statement
more info
 
Wnt signaling pathway, planar cell polarity pathway TAS
Traceable Author Statement
more info
 
anaphase-promoting complex-dependent catabolic process TAS
Traceable Author Statement
more info
 
antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent TAS
Traceable Author Statement
more info
 
interleukin-1-mediated signaling pathway TAS
Traceable Author Statement
more info
 
negative regulation of G2/M transition of mitotic cell cycle TAS
Traceable Author Statement
more info
 
negative regulation of canonical Wnt signaling pathway TAS
Traceable Author Statement
more info
 
neutrophil degranulation TAS
Traceable Author Statement
more info
 
positive regulation of canonical Wnt signaling pathway TAS
Traceable Author Statement
more info
 
post-translational protein modification TAS
Traceable Author Statement
more info
 
proteasome-mediated ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
proteasome-mediated ubiquitin-dependent protein catabolic process TAS
Traceable Author Statement
more info
 
protein deubiquitination TAS
Traceable Author Statement
more info
 
protein polyubiquitination TAS
Traceable Author Statement
more info
 
proteolysis NAS
Non-traceable Author Statement
more info
PubMed 
regulation of catalytic activity IEA
Inferred from Electronic Annotation
more info
 
regulation of cellular amino acid metabolic process TAS
Traceable Author Statement
more info
 
regulation of hematopoietic stem cell differentiation TAS
Traceable Author Statement
more info
 
regulation of mRNA stability TAS
Traceable Author Statement
more info
 
regulation of mitotic cell cycle phase transition TAS
Traceable Author Statement
more info
 
regulation of transcription from RNA polymerase II promoter in response to hypoxia TAS
Traceable Author Statement
more info
 
stimulatory C-type lectin receptor signaling pathway TAS
Traceable Author Statement
more info
 
transmembrane transport TAS
Traceable Author Statement
more info
 
tumor necrosis factor-mediated signaling pathway TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
cytosol TAS
Traceable Author Statement
more info
 
extracellular region TAS
Traceable Author Statement
more info
 
ficolin-1-rich granule lumen TAS
Traceable Author Statement
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
proteasome accessory complex ISS
Inferred from Sequence or Structural Similarity
more info
 
proteasome complex IDA
Inferred from Direct Assay
more info
PubMed 
proteasome regulatory particle IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
secretory granule lumen TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
26S proteasome non-ATPase regulatory subunit 6
Names
breast cancer-associated protein SGA-113M
phosphonoformate immuno-associated protein 4
proteasome (prosome, macropain) 26S subunit, non-ATPase, 6
proteasome regulatory particle subunit p44S10

NCBI Reference Sequences (RefSeq)

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_001271779.1NP_001258708.1  26S proteasome non-ATPase regulatory subunit 6 isoform 1

    See identical proteins and their annotated locations for NP_001258708.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    BC000904, BM681873, BX647742, CD692691, HY010377
    Consensus CDS
    CCDS63677.1
    UniProtKB/Swiss-Prot
    Q15008
    Related
    ENSP00000418695.1, ENST00000492933.5
    Conserved Domains (2) summary
    pfam01399
    Location:307411
    PCI; PCI domain
    pfam10602
    Location:119292
    RPN7; 26S proteasome subunit RPN7
  2. NM_001271780.1NP_001258709.1  26S proteasome non-ATPase regulatory subunit 6 isoform 3

    See identical proteins and their annotated locations for NP_001258709.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate 5' exon, lacks an exon in the coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AC012557, AY359879, BC000904, BG723464, BM681873
    Consensus CDS
    CCDS63679.1
    UniProtKB/Swiss-Prot
    Q15008
    Related
    ENSP00000377952.2, ENST00000394431.6
    Conserved Domains (1) summary
    cl26505
    Location:11344
    RPN7; 26S proteasome subunit RPN7
  3. NM_001271781.1NP_001258710.1  26S proteasome non-ATPase regulatory subunit 6 isoform 4

    See identical proteins and their annotated locations for NP_001258710.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and uses an alternate in-frame splice site in the 5' coding region compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
    Source sequence(s)
    AL529900, AU105740, BC000904, BM681873, CD110455, DA633802
    Consensus CDS
    CCDS63678.1
    UniProtKB/Swiss-Prot
    Q15008
    Related
    ENSP00000419227.1, ENST00000482510.5
    Conserved Domains (1) summary
    cl26505
    Location:6343
    RPN7; 26S proteasome subunit RPN7
  4. NM_014814.3NP_055629.1  26S proteasome non-ATPase regulatory subunit 6 isoform 2

    See identical proteins and their annotated locations for NP_055629.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon in the coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    BC000904, BC012369, CD678025, HY010377
    Consensus CDS
    CCDS2901.1
    UniProtKB/Swiss-Prot
    Q15008
    Related
    ENSP00000295901.4, ENST00000295901.8
    Conserved Domains (1) summary
    cl26505
    Location:15382
    RPN7; 26S proteasome subunit RPN7

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    64010549..64024010 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024453841.1XP_024309609.1  26S proteasome non-ATPase regulatory subunit 6 isoform X3

    Conserved Domains (1) summary
    pfam10602
    Location:28201
    RPN7; 26S proteasome subunit RPN7
  2. XM_011534288.1XP_011532590.1  26S proteasome non-ATPase regulatory subunit 6 isoform X1

    Conserved Domains (1) summary
    pfam10602
    Location:119292
    RPN7; 26S proteasome subunit RPN7
  3. XM_005265619.1XP_005265676.1  26S proteasome non-ATPase regulatory subunit 6 isoform X2

    See identical proteins and their annotated locations for XP_005265676.1

    Conserved Domains (2) summary
    pfam01399
    Location:205309
    PCI; PCI domain
    pfam10602
    Location:17190
    RPN7; 26S proteasome subunit RPN7
  4. XM_017007569.1XP_016863058.1  26S proteasome non-ATPase regulatory subunit 6 isoform X4

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