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

Gene ID: 9861, updated on 3-Nov-2024

Summary

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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; AllianceGenome:HGNC:9564
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
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Genomic context

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See PSMD6 in Genome Data Viewer
Location:
3p14.1
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (64010551..64024007, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (64054166..64067621, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (63996227..64009683, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene THO complex subunit 7 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14498 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14499 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14500 Neighboring gene THOC7 antisense RNA 1 Neighboring gene ataxin 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20031 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14501 Neighboring gene ataxin 7 repeat instability region Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20032 Neighboring gene SCA7/ATXN7 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:63946089-63946588 Neighboring gene NANOG hESC enhancer GRCh37_chr3:63950216-63950720 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20033 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20034 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20035 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:63956153-63956804 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:63958786-63959286 Neighboring gene NANOG hESC enhancer GRCh37_chr3:63986120-63986621 Neighboring gene PSMD6 antisense RNA 2 Neighboring gene PSMD6 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:64008472-64009094 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:64009095-64009716 Neighboring gene uncharacterized LOC105377121 Neighboring gene Sharpr-MPRA regulatory region 15028 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:64048916-64050115 Neighboring gene PRICKLE2 antisense RNA 1 Neighboring gene small nucleolar RNA U3

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. A variant of PSMD6 is associated with the therapeutic efficacy of oral antidiabetic drugs in Chinese type 2 diabetes patients. Chen M, et al. Sci Rep, 2015 May 29. PMID 26024304, Free PMC Article
  2. The 19S proteasome subunit Rpn7 stabilizes DNA damage foci upon genotoxic insult. Tsolou A, et al. IUBMB Life, 2012 May. PMID 22473755
  3. Increased New lncRNA-mRNA Gene Pair Levels in Human Cumulus Cells Correlate With Oocyte Maturation and Embryo Development. Li J, et al. Reprod Sci, 2015 Aug. PMID 25670720
  4. Prognostic Value and Molecular Mechanisms of Proteasome 26S Subunit, Non-ATPase Family Genes for Pancreatic Ductal Adenocarcinoma Patients after Pancreaticoduodenectomy. Zhou C, et al. J Invest Surg, 2022 Feb. PMID 33525943
  5. The p44S10 locus, encoding a subunit of the proteasome regulatory particle, is amplified during progression of cutaneous malignant melanoma. Ren S, et al. Oncogene, 2000 Mar 9. PMID 10723133

See all (204) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Prognostic Value and Molecular Mechanisms of Proteasome 26S Subunit, Non-ATPase Family Genes for Pancreatic Ductal Adenocarcinoma Patients after Pancreaticoduodenectomy.
    Title: Prognostic Value and Molecular Mechanisms of Proteasome 26S Subunit, Non-ATPase Family Genes for Pancreatic Ductal Adenocarcinoma Patients after Pancreaticoduodenectomy.
  2. Suggest AK124742 and PSMD6 as a new lncRNA-messenger RNA gene pair in human cumulus cells that may be considered as potential biomarkers to aid embryo selection.
    Title: Increased New lncRNA-mRNA Gene Pair Levels in Human Cumulus Cells Correlate With Oocyte Maturation and Embryo Development.
  3. we observed that the PSMD6 variant rs831571 might be associated with the therapeutic efficacy of rosiglitazone and repaglinide in Chinese patients with type 2 diabetes.
    Title: A variant of PSMD6 is associated with the therapeutic efficacy of oral antidiabetic drugs in Chinese type 2 diabetes patients.
  4. interaction of Rpn7 with DNA damage response foci in situ mediates the protection of DNA damage foci from premature resolution.
    Title: The 19S proteasome subunit Rpn7 stabilizes DNA damage foci upon genotoxic insult.
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
Biological insights from 108 schizophrenia-associated genetic loci.
EBI GWAS Catalog
Genome-wide association study of a heart failure related metabolomic profile among African Americans in the Atherosclerosis Risk in Communities (ARIC) study.
EBI GWAS Catalog
Meta-analysis of genome-wide association studies identifies eight new loci for type 2 diabetes in east Asians.
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)

HIV-1 interactions

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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

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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

Clone Names

  • FLJ30168, KIAA0107

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
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 nucleoplasm TAS
Traceable Author Statement
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 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 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)

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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_001271779.2 → NP_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 (1) summary
    COG5187
    Location:103 → 435
    RPN7; 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]

  2. NM_001271780.2 → NP_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/TrEMBL
    B3KT66
    Related
    ENSP00000377952.2, ENST00000394431.6
    Conserved Domains (1) summary
    cl26505
    Location:11 → 344
    RPN7; 26S proteasome subunit RPN7

  3. NM_001271781.2 → NP_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)
    AC012557, AL529900, AU105740, BC000904, CD110455, DA633802
    Consensus CDS
    CCDS63678.1
    UniProtKB/TrEMBL
    B3KT66
    Related
    ENSP00000419227.1, ENST00000482510.5
    Conserved Domains (1) summary
    cl26505
    Location:6 → 343
    RPN7; 26S proteasome subunit RPN7

  4. NM_014814.3 → NP_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
    A8K2E0, E9PHI9, Q15008, Q6UV22
    UniProtKB/TrEMBL
    B3KT66
    Related
    ENSP00000295901.4, ENST00000295901.9
    Conserved Domains (1) summary
    COG5187
    Location:15 → 382
    RPN7; 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    64010551..64024007 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011534288.2 → XP_011532590.1  26S proteasome non-ATPase regulatory subunit 6 isoform X1

    Conserved Domains (1) summary
    pfam10602
    Location:119 → 292
    RPN7; 26S proteasome subunit RPN7

  2. XM_005265619.2 → XP_005265676.1  26S proteasome non-ATPase regulatory subunit 6 isoform X3

    See identical proteins and their annotated locations for XP_005265676.1

    UniProtKB/TrEMBL
    B3KT66
    Conserved Domains (2) summary
    pfam01399
    Location:205 → 309
    PCI; PCI domain
    pfam10602
    Location:17 → 190
    RPN7; 26S proteasome subunit RPN7

  3. XM_017007569.1 → XP_016863058.1  26S proteasome non-ATPase regulatory subunit 6 isoform X2

    UniProtKB/TrEMBL
    B3KT66

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    64054166..64067621 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054348585.1 → XP_054204560.1  26S proteasome non-ATPase regulatory subunit 6 isoform X1

  2. XM_054348587.1 → XP_054204562.1  26S proteasome non-ATPase regulatory subunit 6 isoform X3

  3. XM_054348586.1 → XP_054204561.1  26S proteasome non-ATPase regulatory subunit 6 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q15008.1 GenPept UniProtKB/Swiss-Prot:Q15008

Gene LinkOut

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

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