PSMA4 proteasome 20S subunit alpha 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PSMA4provided by HGNC
Official Full Name: proteasome 20S subunit alpha 4provided by HGNC
Primary source: HGNC:HGNC:9533
See related: Ensembl:ENSG00000041357 MIM:176846; AllianceGenome:HGNC:9533
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: HC9; PSC9; HsT17706
Summary: This gene encodes a core alpha subunit of the 20S proteosome, which is a highly ordered ring-shaped structure composed of four rings of 28 non-identical subunits. Proteasomes cleave peptides in an ATP- and ubiquitin-dependent manner. [provided by RefSeq, Aug 2016]
Expression: Ubiquitous expression in appendix (RPKM 63.8), lymph node (RPKM 63.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 15q25.1

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (78540405..78552417)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (76403080..76415091)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (78832747..78844759)

Chromosome 15 - NC_000015.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Potentially functional genetic variants of VAV2 and PSMA4 in the immune-activation pathway and non-small cell lung cancer survival.
Title: Potentially functional genetic variants of VAV2 and PSMA4 in the immune-activation pathway and non-small cell lung cancer survival.
All four variants were significantly associated (P < 1.4 x 10(-6)) with blood DNA methylation of IREB2, CHRNA3 and PSMA4, of which two, including IREB2 and PSMA4, were also differentially methylated in Chronic obstructive pulmonary disease cases and controls
Title: Understanding the role of the chromosome 15q25.1 in COPD through epigenetics and transcriptomics.
Five of these SNPs acted as cis-eQTLs, being associated with the transcription of IREB2 (rs2568494, rs16969968, rs11634351, rs6495309), PSMA4 (rs6495309) and ERCC1 (rs735482), out of 10,821 genes analyzed in lung. For these three genes, we obtained experimental evidence of differential allelic expression in lung tissue, pointing to the existence of in-cis genomic variants that regulate their transcription.
Title: Genetic susceptibility variants for lung cancer: replication study and assessment as expression quantitative trait loci.
rs12901682 is associated with lung cancer risk in a Chinese Han population.
Title: Association of PSMA4 polymorphisms with lung cancer susceptibility and response to cisplatin-based chemotherapy in a Chinese Han population.
study concludes polymorphisms of TGM5, PPAP2B and PSMA4 are not major contributors tonon-small cell lung cancer susceptibility in never-smoking hinese population, this primarily can be attributed to the significantly distinct genetic background of Asian populations from western populations
Title: Association between TGM5, PPAP2B and PSMA4 polymorphisms and NSCLC in never-smoking Chinese population.
Observational study of gene-disease association. (HuGE Navigator)
Title: Fine mapping of chromosome 15q25.1 lung cancer susceptibility in African-Americans.
Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
Title: Genome-wide association scan of tag SNPs identifies a susceptibility locus for lung cancer at 15q25.1.
Parkin interacts with the proteasome subunit alpha4
Title: Parkin interacts with the proteasome subunit alpha4.
Unexpected interaction between alpha4 and alpha7 subunits may provide a molecular basis for the formation of previously reported 13S and 16S assembly intermediates.
Title: The alpha4 and alpha7 subunits and assembly of the 20S proteasome.

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A susceptibility locus for lung cancer maps to nicotinic acetylcholine receptor subunit genes on 15q25. EBI GWAS Catalog EBI GWAS CatalogPubMed
Biological insights from 108 schizophrenia-associated genetic loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Familial aggregation of common sequence variants on 15q24-25.1 in lung cancer. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association analysis implicates the involvement of eight loci with response to tocilizumab for the treatment of rheumatoid arthritis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association scan of tag SNPs identifies a susceptibility locus for lung cancer at 15q25.1. EBI GWAS Catalog EBI GWAS CatalogPubMed
IREB2 and GALC are Associated with Pulmonary Artery Enlargement in Chronic Obstructive Pulmonary Disease. 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 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

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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

WI-9202 (e-PCR)
- UniSTS:30996

G62016 (e-PCR)
- UniSTS:139094

D15S636E (e-PCR)
- UniSTS:58748

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 P-body	ISS Inferred from Sequence or Structural Similarity more info
is_active_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
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 intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	HDA more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	IDA Inferred from Direct Assay more info	PubMed
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 core complex	IDA Inferred from Direct Assay more info	PubMed
part_of proteasome core complex	ISS Inferred from Sequence or Structural Similarity more info
part_of proteasome core complex, alpha-subunit complex	IBA Inferred from Biological aspect of Ancestor more info
part_of proteasome core complex, alpha-subunit complex	IDA Inferred from Direct Assay more info	PubMed
part_of proteasome core complex, alpha-subunit complex	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: proteasome subunit alpha type-4

Names: alpha-3; macropain subunit C9; multicatalytic endopeptidase complex subunit C9; proteasome (prosome, macropain) subunit, alpha type, 4; proteasome component C9; proteasome subunit HC9; proteasome subunit L; proteasome subunit alpha 4; proteasome subunit alpha-3; proteasome subunit alpha3

NP_001096137.1

EC 3.4.25.1

NP_001096138.1

EC 3.4.25.1

NP_001317602.1

EC 3.4.25.1

NP_001317604.1

EC 3.4.25.1

NP_001317605.1

EC 3.4.25.1

NP_002780.1

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_001102667.2 → NP_001096137.1 proteasome subunit alpha type-4 isoform 1

See identical proteins and their annotated locations for NP_001096137.1

Status: REVIEWED

Source sequence(s)

BG208993, BG528289, BG616186, BU930105, CD365826

Consensus CDS

CCDS10303.1

UniProtKB/Swiss-Prot

D3DW86, P25789, Q53XP2, Q567Q5, Q8TBD1

UniProtKB/TrEMBL

H0YL69

Related

ENSP00000453887.1, ENST00000559082.5

Conserved Domains (1) summary

cd03752
Location:3 → 216

proteasome_alpha_type_4; 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 stack on top of one another forming ...
NM_001102668.3 → NP_001096138.1 proteasome subunit alpha type-4 isoform 2

See identical proteins and their annotated locations for NP_001096138.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an exon in the 5' coding region and uses a downstream start codon, compared to variant 1. It encodes isoform 2, which has a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AC027228, BC093069, BG208993, BG528289, CN337296

Consensus CDS

CCDS45319.1

UniProtKB/Swiss-Prot

P25789

Related

ENSP00000402118.2, ENST00000413382.6

Conserved Domains (1) summary

cl00467
Location:1 → 145

Ntn_hydrolase; The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a ...
NM_001330673.2 → NP_001317602.1 proteasome subunit alpha type-4 isoform 3

Status: REVIEWED

Source sequence(s)

AC027228, BF589105, BG208993, BU188756

Consensus CDS

CCDS86478.1

UniProtKB/TrEMBL

H0YLC2, H0YMA1

Related

ENSP00000453145.1, ENST00000558281.5

Conserved Domains (1) summary

cl00467
Location:3 → 169

Ntn_hydrolase; The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a ...
NM_001330675.2 → NP_001317604.1 proteasome subunit alpha type-4 isoform 4

Status: REVIEWED

Source sequence(s)

AC027228

Consensus CDS

CCDS86479.1

UniProtKB/TrEMBL

H0YL69, H0YN18

Related

ENSP00000453829.1, ENST00000560217.5

Conserved Domains (1) summary

cl00467
Location:3 → 185

Ntn_hydrolase; The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a ...
NM_001330676.2 → NP_001317605.1 proteasome subunit alpha type-4 isoform 1

Status: REVIEWED

Source sequence(s)

AC027228, BG208993, BG772003, D00763

Consensus CDS

CCDS10303.1

UniProtKB/Swiss-Prot

D3DW86, P25789, Q53XP2, Q567Q5, Q8TBD1

UniProtKB/TrEMBL

H0YL69

Related

ENSP00000453802.1, ENST00000559365.5

Conserved Domains (1) summary

cd03752
Location:3 → 216

proteasome_alpha_type_4; 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 stack on top of one another forming ...
NM_002789.6 → NP_002780.1 proteasome subunit alpha type-4 isoform 1

See identical proteins and their annotated locations for NP_002780.1

Status: REVIEWED

Source sequence(s)

AC027228, BC022445, BC030529, BG208993, BG528289, CD365826

Consensus CDS

CCDS10303.1

UniProtKB/Swiss-Prot

D3DW86, P25789, Q53XP2, Q567Q5, Q8TBD1

UniProtKB/TrEMBL

H0YL69

Related

ENSP00000044462.7, ENST00000044462.12

Conserved Domains (1) summary

cd03752
Location:3 → 216

proteasome_alpha_type_4; 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 stack on top of one another forming ...