The protein encoded by this gene belongs to the paraneoplastic antigen MA (PNMA) family, which shares homology with retroviral Gag proteins. The PNMA antigens are highly expressed in the brain and also in a range of tumors associated with serious neurological phenotypes. PMID:16407312 reports the presence of a functional -1 ribosomal frameshift signal (consisting of a heptanucl... See more...

Aliases for PNMA3 Gene

Aliases for PNMA3 Gene

  • PNMA Family Member 3 2 3 5
  • MA3 2 3 4
  • Paraneoplastic Cancer-Testis-Brain Antigen 2 3
  • Paraneoplastic Ma Antigen 3 2 3
  • Paraneoplastic Antigen Ma3 3 4
  • MA5 2 3
  • Paraneoplastic Antigen MA3 2
  • MGC132756 2
  • MGC132758 2
  • PNMA3 5

External Ids for PNMA3 Gene

Previous GeneCards Identifiers for PNMA3 Gene

  • GC0XP146564
  • GC0XP148882
  • GC0XP149972
  • GC0XP150843
  • GC0XP151895
  • GC0XP151975
  • GC0XP152224
  • GC0XP141026

Summaries for PNMA3 Gene

Entrez Gene Summary for PNMA3 Gene

  • The protein encoded by this gene belongs to the paraneoplastic antigen MA (PNMA) family, which shares homology with retroviral Gag proteins. The PNMA antigens are highly expressed in the brain and also in a range of tumors associated with serious neurological phenotypes. PMID:16407312 reports the presence of a functional -1 ribosomal frameshift signal (consisting of a heptanucleotide shift motif followed 3' by a pseudoknot structure) in this gene, however, the frame-shifted product has not been characterized. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2013]

GeneCards Summary for PNMA3 Gene

PNMA3 (PNMA Family Member 3) is a Protein Coding gene. Diseases associated with PNMA3 include Cd3zeta Deficiency and Tracheitis. Gene Ontology (GO) annotations related to this gene include nucleic acid binding. An important paralog of this gene is PNMA5.

Additional gene information for PNMA3 Gene

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PNMA3 Gene

Genomics for PNMA3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PNMA3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ153055 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE CraniofacialAtlas 618.7 +0.0 42 2.5 NRF1 MGA USF1 VEZF1 EZH2 L3MBTL2 PNMA3 lnc-PNMA5-2 PNMA6A
GH0XJ153032 Promoter/Enhancer 1.5 EPDnew ENCODE CraniofacialAtlas 609.2 -23.7 -23708 1.3 CTCF POLR2A TARDBP ZHX2 ZNF143 ZIC2 REST RAD21 ZNF501 HDAC1 PNMA3 PNMA6A ENSG00000234200 ENSG00000229979 lnc-PNMA5-5 lnc-PNMA5-2 PNMA5
GH0XJ153057 Enhancer 0.5 Ensembl 600.7 +1.5 1492 0.2 ATF4 CEBPG IKZF1 L3MBTL2 ZBTB40 NONHSAG055536.2 PNMA3 lnc-PNMA5-2 PNMA6A
GH0XJ153179 Promoter 1.1 EPDnew Ensembl 6.6 +123.2 123191 0.8 ZNF740 NRF1 POLR2A ZBTB11 GABPA TFDP1 CREM SMAD5 VEZF1 ETV1 MAGEA1 NONHSAG055539.2 PNMA6A PNMA3 lnc-MAGEA1-2 ENSG00000235219 RF00017-8798 ENSG00000278803
GH0XJ153003 Enhancer 0.3 ENCODE 15.7 -52.1 -52115 1.2 FOXA1 ENSG00000234200 PNMA3 PNMA5 lnc-PNMA5-1 piR-60985-145 lnc-PNMA5-2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PNMA3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PNMA3

Top Transcription factor binding sites by QIAGEN in the PNMA3 gene promoter:
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • HOXA5
  • SREBP-1a
  • SREBP-1b
  • SREBP-1c

Genomic Locations for PNMA3 Gene

Genomic Locations for PNMA3 Gene
chrX:153,056,409-153,060,467
(GRCh38/hg38)
Size:
4,059 bases
Orientation:
Plus strand
chrX:152,224,766-152,228,827
(GRCh37/hg19)
Size:
4,062 bases
Orientation:
Plus strand

Genomic View for PNMA3 Gene

Genes around PNMA3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PNMA3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PNMA3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PNMA3 Gene

Proteins for PNMA3 Gene

  • Protein details for PNMA3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UL41-PNMA3_HUMAN
    Recommended name:
    Paraneoplastic antigen Ma3
    Protein Accession:
    Q9UL41
    Secondary Accessions:
    • D3DWT7
    • Q9H0A4

    Protein attributes for PNMA3 Gene

    Size:
    463 amino acids
    Molecular mass:
    52376 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • Antibodies against PNMA3 are present in sera from patients suffering of paraneoplastic neurological disorders.

    Alternative splice isoforms for PNMA3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PNMA3 Gene

Post-translational modifications for PNMA3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PNMA3 Gene

No data available for DME Specific Peptides for PNMA3 Gene

Domains & Families for PNMA3 Gene

Gene Families for PNMA3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for PNMA3 Gene

InterPro:
Blocks:
  • C2HC-type zinc-finger signature
ProtoNet:

Suggested Antigen Peptide Sequences for PNMA3 Gene

GenScript: Design optimal peptide antigens:
  • Paraneoplastic antigen Ma3 (PNMA3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9UL41

UniProtKB/Swiss-Prot:

PNMA3_HUMAN :
  • Belongs to the PNMA family.
Family:
  • Belongs to the PNMA family.
genes like me logo Genes that share domains with PNMA3: view

Function for PNMA3 Gene

Gene Ontology (GO) - Molecular Function for PNMA3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0008270 zinc ion binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PNMA3: view
genes like me logo Genes that share phenotypes with PNMA3: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PNMA3

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PNMA3 Gene

Localization for PNMA3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PNMA3 Gene

Nucleus, nucleolus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PNMA3 gene
Compartment Confidence
nucleus 4
cytosol 3
plasma membrane 2
extracellular 2
cytoskeleton 2
mitochondrion 2
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for PNMA3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005730 nucleolus IEA --
genes like me logo Genes that share ontologies with PNMA3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PNMA3 Gene

Pathways & Interactions for PNMA3 Gene

PathCards logo

SuperPathways for PNMA3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PNMA3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0043065 positive regulation of apoptotic process ISS --
genes like me logo Genes that share ontologies with PNMA3: view

No data available for Pathways by source and SIGNOR curated interactions for PNMA3 Gene

Drugs & Compounds for PNMA3 Gene

No Compound Related Data Available

Transcripts for PNMA3 Gene

mRNA/cDNA for PNMA3 Gene

2 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PNMA3

Alternative Splicing Database (ASD) splice patterns (SP) for PNMA3 Gene

No ASD Table

Relevant External Links for PNMA3 Gene

GeneLoc Exon Structure for
PNMA3

Expression for PNMA3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PNMA3 Gene

mRNA differential expression in normal tissues according to GTEx for PNMA3 Gene

This gene is overexpressed in Brain - Cortex (x7.7), Brain - Frontal Cortex (BA9) (x6.6), Brain - Anterior cingulate cortex (BA24) (x5.3), and Brain - Hypothalamus (x4.5).

Protein differential expression in normal tissues from HIPED for PNMA3 Gene

This gene is overexpressed in Retina (28.5), Fetal testis (27.2), and Heart (8.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PNMA3 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PNMA3

SOURCE GeneReport for Unigene cluster for PNMA3 Gene:

Hs.449627

mRNA Expression by UniProt/SwissProt for PNMA3 Gene:

Q9UL41-PNMA3_HUMAN
Tissue specificity: Expressed at high levels in the brain and testis. Expressed at lower levels in the heart, trachea and kidney.

Evidence on tissue expression from TISSUES for PNMA3 Gene

  • Nervous system(5)
  • Skin(2.7)
  • Blood(2.3)
  • Liver(2.1)
  • Heart(2.1)
  • Intestine(2)
  • Kidney(2)
genes like me logo Genes that share expression patterns with PNMA3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for PNMA3 Gene

Orthologs for PNMA3 Gene

This gene was present in the common ancestor of mammals.

Orthologs for PNMA3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PNMA3 30 31
  • 99.78 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Pnma3 30
  • 79.73 (n)
Mouse
(Mus musculus)
Mammalia Pnma3 30 17 31
  • 79.05 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia -- 31
  • 28 (a)
ManyToMany
Species where no ortholog for PNMA3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • Cow (Bos Taurus)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for PNMA3 Gene

ENSEMBL:
Gene Tree for PNMA3 (if available)
TreeFam:
Gene Tree for PNMA3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PNMA3: view image

Paralogs for PNMA3 Gene

(8) SIMAP similar genes for PNMA3 Gene using alignment to 1 proteins:

  • PNMA3_HUMAN
genes like me logo Genes that share paralogs with PNMA3: view

Variants for PNMA3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PNMA3 Gene

SNP ID Clinical significance and condition Chr 0X pos Variation AA Info Type
rs35603712 - p.Arg386Gln
rs36042591 - p.Gly382Ser

Additional dbSNP identifiers (rs#s) for PNMA3 Gene

Structural Variations from Database of Genomic Variants (DGV) for PNMA3 Gene

Variant ID Type Subtype PubMed ID
nsv472048 CNV novel sequence insertion 20440878

Variation tolerance for PNMA3 Gene

Residual Variation Intolerance Score: 57% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.56; 12.17% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PNMA3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PNMA3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PNMA3 Gene

Disorders for PNMA3 Gene

MalaCards: The human disease database

(2) MalaCards diseases for PNMA3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
cd3zeta deficiency
tracheitis
  • acute tracheitis
- elite association - COSMIC cancer census association via MalaCards
Search PNMA3 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with PNMA3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PNMA3 Gene

Publications for PNMA3 Gene

  1. Molecular and clinical diversity in paraneoplastic immunity to Ma proteins. (PMID: 11558790) Rosenfeld MR … Dalmau J (Annals of neurology 2001) 2 3 4
  2. A functional -1 ribosomal frameshift signal in the human paraneoplastic Ma3 gene. (PMID: 16407312) Wills NM … Atkins JF (The Journal of biological chemistry 2006) 3 23
  3. The human PNMA family: novel neuronal proteins implicated in paraneoplastic neurological disease. (PMID: 16214224) Schüller M … Voltz R (Journal of neuroimmunology 2005) 3 4
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  5. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3

Products for PNMA3 Gene

Sources for PNMA3 Gene