PSMB9 proteasome 20S subunit beta 9 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PSMB9provided by HGNC
Official Full Name: proteasome 20S subunit beta 9provided by HGNC
Primary source: HGNC:HGNC:9546
See related: Ensembl:ENSG00000240065 MIM:177045; AllianceGenome:HGNC:9546
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: LMP2; PRAAS3; PSMB6i; RING12; beta1i
Summary: The proteasome is a multicatalytic proteinase complex with a highly ordered ring-shaped 20S core structure. The core structure 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. 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 member of the proteasome B-type family, also known as the T1B family, that is a 20S core beta subunit. This gene is located in the class II region of the MHC (major histocompatibility complex). Expression of this gene is induced by gamma interferon and this gene product replaces catalytic subunit 1 (proteasome beta 6 subunit) in the immunoproteasome. Proteolytic processing is required to generate a mature subunit. [provided by RefSeq, Mar 2010]
Expression: Broad expression in spleen (RPKM 72.3), lymph node (RPKM 60.9) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6p21.32

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (32854192..32859851)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (32675567..32681226)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (32821969..32827628)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Deciphering the tumor-suppressive role of PSMB9 in melanoma through multi-omics and single-cell transcriptome analyses.
Title: Deciphering the tumor-suppressive role of PSMB9 in melanoma through multi-omics and single-cell transcriptome analyses.
Immunohistochemical Identification and Assessment of the Location of Immunoproteasome Subunits LMP2 and LMP7 in Acquired Cholesteatoma.
Title: Immunohistochemical Identification and Assessment of the Location of Immunoproteasome Subunits LMP2 and LMP7 in Acquired Cholesteatoma.
Immunoproteasome-specific subunit PSMB9 induction is required to regulate cellular proteostasis upon mitochondrial dysfunction.
Title: Immunoproteasome-specific subunit PSMB9 induction is required to regulate cellular proteostasis upon mitochondrial dysfunction.
Variants in PSMB9 and FGR differentially affect Parkinson's disease risk in GBA and LRRK2 mutation carriers.
Title: Variants in PSMB9 and FGR differentially affect Parkinson's disease risk in GBA and LRRK2 mutation carriers.
Increased expression of the immunoproteasome subunits PSMB8 and PSMB9 by cancer cells correlate with better outcomes for triple-negative breast cancers.
Title: Increased expression of the immunoproteasome subunits PSMB8 and PSMB9 by cancer cells correlate with better outcomes for triple-negative breast cancers.
Identification of PSMB9 and CXCL13 as Immune-related Diagnostic Markers for Rheumatoid Arthritis by Machine Learning.
Title: Identification of PSMB9 and CXCL13 as Immune-related Diagnostic Markers for Rheumatoid Arthritis by Machine Learning.
Transcriptome-wide association study identifies PSMB9 as a susceptibility gene for coal workers' pneumoconiosis.
Title: Transcriptome-wide association study identifies PSMB9 as a susceptibility gene for coal workers' pneumoconiosis.
Heterozygous missense variant of the proteasome subunit beta-type 9 causes neonatal-onset autoinflammation and immunodeficiency.
Title: Heterozygous missense variant of the proteasome subunit β-type 9 causes neonatal-onset autoinflammation and immunodeficiency.
Successful treatment of a novel type I interferonopathy due to a de novo PSMB9 gene mutation with a Janus kinase inhibitor.
Title: Successful treatment of a novel type I interferonopathy due to a de novo PSMB9 gene mutation with a Janus kinase inhibitor.
The dominant model of LMP2 CfoI might be a risk factor for IDDM in Asian population. Whereas, the allelic and dominant models of LMP7 G37360T might be protective factors for IDDM in Caucasian population
Title: The genetic association between LMP2 and LMP7 polymorphisms and susceptibility of insulin dependent diabetes mellitus: A meta-analysis.

Submit: New GeneRIF Correction See all GeneRIFs (54)

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

Associated conditions

Description	Tests
Proteasome-associated autoinflammatory syndrome 3 MedGen: C4747850 OMIM: 617591 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
A genome-wide association study identifies 2 susceptibility Loci for Crohn's disease in a Japanese population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies susceptibility loci for IgA nephropathy. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic variants associated with lumbar disc degeneration in northern Europeans: a meta-analysis of 4600 subjects. 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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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	HIV-1 Tat represses transcription of the LMP2 gene by competing with STAT1 (signal transducer and activator of transcription 1) for binding to IRF-1 (interferon-regulatory factor-1) at the LMP2 promoter	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
retropepsin	gag-pol	Positional proteomics analysis identifies the cleavage of human proteasome (prosome, macropain) subunit, beta type, 9 (PSMB9) at amino acid residues 25-26 by the HIV-1 protease	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

LMP2 (e-PCR)
- UniSTS:44373

GDB:543001 (e-PCR)
- UniSTS:157583

PMC115886P1 (e-PCR)
- UniSTS:270304

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables endopeptidase activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables threonine-type endopeptidase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in immune system process	IEA Inferred from Electronic Annotation more info
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of cysteine-type endopeptidase activity	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in cytosol	TAS Traceable Author Statement more info
located_in extracellular exosome	HDA more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
part_of proteasome complex	TAS Traceable Author Statement more info	PubMed
part_of proteasome core complex	ISS Inferred from Sequence or Structural Similarity more info
part_of proteasome core complex, beta-subunit complex	IBA Inferred from Biological aspect of Ancestor more info
part_of proteasome core complex, beta-subunit complex	ISS Inferred from Sequence or Structural Similarity more info
part_of spermatoproteasome complex	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: proteasome subunit beta type-9

Names: large multifunctional peptidase 2; low molecular mass protein 2; macropain chain 7; multicatalytic endopeptidase complex chain 7; proteasome (prosome, macropain) subunit, beta type, 9 (large multifunctional peptidase 2); proteasome catalytic subunit 1i; proteasome chain 7; proteasome subunit beta 6i; proteasome subunit beta 9; proteasome subunit beta-1i; proteasome subunit beta1i; proteasome-related gene 2; really interesting new gene 12 protein

NP_002791.1

EC 3.4.25.1

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_002800.5 → NP_002791.1 proteasome subunit beta type-9 precursor

See identical proteins and their annotated locations for NP_002791.1

Status: REVIEWED

Source sequence(s)

AI310206, BC065513, BF513693

Consensus CDS

CCDS4759.1

UniProtKB/Swiss-Prot

B0V0T1, P28065, Q16523, Q5JNW4

UniProtKB/TrEMBL

A0A1U9X8D7, A0A1U9X8E2, A0A1U9X8E3

Related

ENSP00000363993.2, ENST00000374859.3

Conserved Domains (1) summary

cd03762
Location:21 → 207

proteasome_beta_type_6; proteasome beta type-6 subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that ...

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

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

32854192..32859851

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GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

NT_167244.2 Reference GRCh38.p14 ALT_REF_LOCI_1

Range

4159057..4164713

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GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

Range

4266391..4272052

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GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

Range

4097762..4103421

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GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_4

Genomic

NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

Range

4273545..4279205

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GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

Range

4153261..4158917

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GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_6

Genomic

NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

Range

4048480..4054140

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GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_7

Genomic

NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

Range

4253444..4259100

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GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060930.1 Alternate T2T-CHM13v2.0

Range

32675567..32681226

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GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_148954.2: Suppressed sequence

Description

NM_148954.2: This RefSeq was permanently suppressed because it represents a poorly supported variant with non-consensus splice sites.