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

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; 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: mouse all
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Genomic context

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_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.

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Phenotypes

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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 EBI GWAS CatalogPubMed
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 EBI GWAS CatalogPubMed
Meta-analysis of genome-wide association studies identifies eight new loci for type 2 diabetes in east Asians. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-77025 (e-PCR)
- UniSTS:11789

D8S2279 (e-PCR)
- UniSTS:473907

STS-N50805 (e-PCR)
- UniSTS:77536

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)

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]
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
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
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

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

64010551..64024007 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

B3KT66

Alternate T2T-CHM13v2.0

Genomic

NC_060927.1 Alternate T2T-CHM13v2.0

Range

64054166..64067621 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054348585.1 → XP_054204560.1 26S proteasome non-ATPase regulatory subunit 6 isoform X1
XM_054348587.1 → XP_054204562.1 26S proteasome non-ATPase regulatory subunit 6 isoform X3

UniProtKB/TrEMBL

B3KT66
XM_054348586.1 → XP_054204561.1 26S proteasome non-ATPase regulatory subunit 6 isoform X2

UniProtKB/TrEMBL

B3KT66