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Aliases for PYM1 Gene

Aliases for PYM1 Gene

  • PYM Homolog 1, Exon Junction Complex Associated Factor 2 3 5
  • Partner Of Y14 And Mago 2 3 4
  • Protein Wibg Homolog 3 4
  • WIBG 3 4
  • PYM 3 4
  • PYM Homolog 1 Exon Junction Complex-Associated Factor 4
  • Within Bgcn Homolog (Drosophila) 2
  • Within Bgcn Homolog 3

External Ids for PYM1 Gene

Previous HGNC Symbols for PYM1 Gene

  • WIBG

Summaries for PYM1 Gene

GeneCards Summary for PYM1 Gene

PYM1 (PYM Homolog 1, Exon Junction Complex Associated Factor) is a Protein Coding gene. Diseases associated with PYM1 include Tongue Disease. Among its related pathways are RNA transport and mRNA surveillance pathway.

UniProtKB/Swiss-Prot for PYM1 Gene

  • Key regulator of the exon junction complex (EJC), a multiprotein complex that associates immediately upstream of the exon-exon junction on mRNAs and serves as a positional landmark for the intron exon structure of genes and directs post-transcriptional processes in the cytoplasm such as mRNA export, nonsense-mediated mRNA decay (NMD) or translation. Acts as an EJC disassembly factor, allowing translation-dependent EJC removal and recycling by disrupting mature EJC from spliced mRNAs. Its association with the 40S ribosomal subunit probably prevents a translation-independent disassembly of the EJC from spliced mRNAs, by restricting its activity to mRNAs that have been translated. Interferes with NMD and enhances translation of spliced mRNAs, probably by antagonizing EJC functions. May bind RNA; the relevance of RNA-binding remains unclear in vivo, RNA-binding was detected by PubMed:14968132, while PubMed:19410547 did not detect RNA-binding activity independently of the EJC.

Additional gene information for PYM1 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PYM1 Gene

Genomics for PYM1 Gene

GeneHancer (GH) Regulatory Elements for PYM1 Gene

Promoters and enhancers for PYM1 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
GH12J055925 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 622.8 -0.7 -720 16.2 HDGF SP1 ZFX ZNF652 CC2D1A ELF3 CTCF ZNF148 NKRF POLR2A PYM1 DGKA BAZ2A RN7SL809P TMEM198B DNAJC14 CDK2 RNU6-343P ZC3H10 MMP19
GH12J056187 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 23.7 -256.6 -256584 4 ZNF652 SP1 CC2D1A ZFX CTCF ELF3 ZNF148 NKRF POLR2A MLLT1 ENSG00000258199 SMARCC2 GC12P056192 TRS-CGA4-1 NEMP1 BAZ2A ENSG00000257740 ANKRD52 PHC1P1 ZC3H10
GH12J056220 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 20.3 -290.2 -290238 5.7 HDGF ZNF652 SP1 CC2D1A ZFX CTCF ELF3 MNT NKRF POLR2A NABP2 RNF41 NEMP1 BAZ2A PAN2 DNAJC14 ZBTB39 TMEM198B PHC1P1 ANKRD52
GH12J055715 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 14.4 +214.1 214096 7.4 CC2D1A SP1 ELF3 ZFX CTCF CBFA2T2 ZNF148 NKRF RERE GTF2F1 RDH5 ITGA7 BLOC1S1 PIR49113 PIR46127 BAZ2A TMEM198B DNAJC14 RN7SL809P PAN2
GH12J056683 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 12.1 -754.2 -754153 7.8 CC2D1A ZFX SP1 ELF3 SIX5 ZNF148 NKRF POLR2A MLLT1 ZNF121 PTGES3 GC12M056688 BAZ2A NEMP1 ZC3H10 ENSG00000258317 RNU6-343P RN7SL809P DNAJC14 PRIM1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PYM1 on UCSC Golden Path with GeneCards custom track

Genomic Locations for PYM1 Gene

Genomic Locations for PYM1 Gene
chr12:55,901,413-55,932,618
(GRCh38/hg38)
Size:
31,206 bases
Orientation:
Minus strand
chr12:56,295,197-56,326,402
(GRCh37/hg19)
Size:
31,206 bases
Orientation:
Minus strand

Genomic View for PYM1 Gene

Genes around PYM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PYM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PYM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PYM1 Gene

Proteins for PYM1 Gene

  • Protein details for PYM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BRP8-PYM1_HUMAN
    Recommended name:
    Partner of Y14 and mago
    Protein Accession:
    Q9BRP8
    Secondary Accessions:
    • B6ZDM5
    • Q8IXJ8
    • Q8N8E7

    Protein attributes for PYM1 Gene

    Size:
    204 amino acids
    Molecular mass:
    22656 Da
    Quaternary structure:
    • Interacts (via N-terminus) with MAGOH and RBM8A; the interaction is direct. Associates (eIF2A-like region) with the 40S ribosomal subunit and the 48S preinitiation complex.

    Alternative splice isoforms for PYM1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PYM1 Gene

Post-translational modifications for PYM1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PYM1 Gene

No data available for DME Specific Peptides for PYM1 Gene

Domains & Families for PYM1 Gene

Gene Families for PYM1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for PYM1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PYM1 Gene

GenScript: Design optimal peptide antigens:
  • WIBG protein (Q96DC3_HUMAN)
  • Protein wibg homolog (WIBG_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9BRP8

UniProtKB/Swiss-Prot:

PYM1_HUMAN :
  • The eIF2A-like region shares sequence similarity with eIF2A and mediates the interaction with the 40S ribosomal subunit and the 48S preinitiation complex.
  • Belongs to the pym family.
Domain:
  • The eIF2A-like region shares sequence similarity with eIF2A and mediates the interaction with the 40S ribosomal subunit and the 48S preinitiation complex.
Family:
  • Belongs to the pym family.
genes like me logo Genes that share domains with PYM1: view

Function for PYM1 Gene

Molecular function for PYM1 Gene

UniProtKB/Swiss-Prot Function:
Key regulator of the exon junction complex (EJC), a multiprotein complex that associates immediately upstream of the exon-exon junction on mRNAs and serves as a positional landmark for the intron exon structure of genes and directs post-transcriptional processes in the cytoplasm such as mRNA export, nonsense-mediated mRNA decay (NMD) or translation. Acts as an EJC disassembly factor, allowing translation-dependent EJC removal and recycling by disrupting mature EJC from spliced mRNAs. Its association with the 40S ribosomal subunit probably prevents a translation-independent disassembly of the EJC from spliced mRNAs, by restricting its activity to mRNAs that have been translated. Interferes with NMD and enhances translation of spliced mRNAs, probably by antagonizing EJC functions. May bind RNA; the relevance of RNA-binding remains unclear in vivo, RNA-binding was detected by PubMed:14968132, while PubMed:19410547 did not detect RNA-binding activity independently of the EJC.

Phenotypes From GWAS Catalog for PYM1 Gene

Gene Ontology (GO) - Molecular Function for PYM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IBA 21873635
GO:0005515 protein binding IPI 16209946
GO:0043022 ribosome binding IDA 18026120
genes like me logo Genes that share ontologies with PYM1: view
genes like me logo Genes that share phenotypes with PYM1: view

Animal Model Products

CRISPR Products

miRNA for PYM1 Gene

miRTarBase miRNAs that target PYM1

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PYM1

Clone Products

  • Applied Biological Materials (abm): Clones for PYM1 - Now 50% OFF >
  • * PYM1 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * PYM1 tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PYM1 Gene

Localization for PYM1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PYM1 Gene

Cytoplasm. Nucleus, nucleolus. Nucleus, nucleoplasm. Note=Shuttles between the nucleus and the cytoplasm (PubMed:14968132). Nuclear export is mediated by XPO1/CRM1 (PubMed:14968132). {ECO:0000269 PubMed:14968132}.

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 PYM1 gene
Compartment Confidence
nucleus 5
cytosol 5
extracellular 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleoli (3)
  • Nucleus (3)
  • Cell Junctions (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PYM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm IEA --
GO:0005730 nucleolus IEA,IDA --
GO:0005737 cytoplasm IBA 21873635
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with PYM1: view

Pathways & Interactions for PYM1 Gene

PathCards logo

SuperPathways for PYM1 Gene

genes like me logo Genes that share pathways with PYM1: view

Pathways by source for PYM1 Gene

2 KEGG pathways for PYM1 Gene

Gene Ontology (GO) - Biological Process for PYM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IDA 19410547
GO:0006417 regulation of translation IEA --
GO:0045727 positive regulation of translation IDA 18026120
GO:1903259 exon-exon junction complex disassembly IDA,IBA 19410547
genes like me logo Genes that share ontologies with PYM1: view

No data available for SIGNOR curated interactions for PYM1 Gene

Drugs & Compounds for PYM1 Gene

(2) Drugs for PYM1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(3) Additional Compounds for PYM1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with PYM1: view

Transcripts for PYM1 Gene

mRNA/cDNA for PYM1 Gene

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PYM1

Clone Products

  • Applied Biological Materials (abm): Clones for PYM1 - Now 50% OFF >
  • * PYM1 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * PYM1 tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

Alternative Splicing Database (ASD) splice patterns (SP) for PYM1 Gene

No ASD Table

Relevant External Links for PYM1 Gene

GeneLoc Exon Structure for
PYM1
ECgene alternative splicing isoforms for
PYM1

Expression for PYM1 Gene

NURSA nuclear receptor signaling pathways regulating expression of PYM1 Gene:

PYM1

Evidence on tissue expression from TISSUES for PYM1 Gene

  • Liver(4.2)
  • Pancreas(4.2)
No Expression Related Data Available

No data available for mRNA expression in normal human tissues , mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PYM1 Gene

Orthologs for PYM1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PYM1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia WIBG 35 34
  • 99.67 (n)
OneToOne
dog
(Canis familiaris)
Mammalia WIBG 35 34
  • 92.15 (n)
OneToOne
cow
(Bos Taurus)
Mammalia WIBG 34 35
  • 91.27 (n)
mouse
(Mus musculus)
Mammalia Wibg 34 35
  • 86.67 (n)
Pym1 17
rat
(Rattus norvegicus)
Mammalia Wibg 34
  • 83.68 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia WIBG 35
  • 74 (a)
OneToOne
chicken
(Gallus gallus)
Aves WIBG 34 35
  • 67.72 (n)
lizard
(Anolis carolinensis)
Reptilia WIBG 35
  • 63 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia wibg 34
  • 65.74 (n)
Str.846 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.13484 34
zebrafish
(Danio rerio)
Actinopterygii wibg 34 35
  • 66.87 (n)
zgc65891 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.6860 34
fruit fly
(Drosophila melanogaster)
Insecta wibg 35
  • 33 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea T20G5.9 35
  • 31 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 33 (a)
OneToOne
Species where no ortholog for PYM1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)
  • wheat (Triticum aestivum)

Evolution for PYM1 Gene

ENSEMBL:
Gene Tree for PYM1 (if available)
TreeFam:
Gene Tree for PYM1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PYM1: view image

Paralogs for PYM1 Gene

No data available for Paralogs for PYM1 Gene

Variants for PYM1 Gene

Sequence variations from dbSNP and Humsavar for PYM1 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000000622 -- 55,926,607(-) A/C intron_variant
rs1000160488 -- 55,925,061(-) C/T intron_variant
rs1000165254 -- 55,902,108(-) C/T coding_sequence_variant, missense_variant
rs1000181334 -- 55,920,841(-) T/C intron_variant
rs1000260623 -- 55,924,795(-) A/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PYM1 Gene

Variant ID Type Subtype PubMed ID
esv1266306 CNV insertion 17803354
nsv1051961 CNV gain 25217958
nsv832424 CNV loss 17160897

Variation tolerance for PYM1 Gene

Residual Variation Intolerance Score: 53.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.71; 32.50% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PYM1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PYM1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PYM1 Gene

Disorders for PYM1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PYM1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
tongue disease
  • abnormality of the tongue
- elite association - COSMIC cancer census association via MalaCards
Search PYM1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PYM1

genes like me logo Genes that share disorders with PYM1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PYM1 Gene

Publications for PYM1 Gene

  1. Disassembly of exon junction complexes by PYM. (PMID: 19410547) Gehring NH … Hentze MW (Cell 2009) 3 4 23 58
  2. PYM binds the cytoplasmic exon-junction complex and ribosomes to enhance translation of spliced mRNAs. (PMID: 18026120) Diem MD … Dreyfuss G (Nature structural & molecular biology 2007) 3 4 23 58
  3. REF1/Aly and the additional exon junction complex proteins are dispensable for nuclear mRNA export. (PMID: 12438415) Gatfield D … Izaurralde E (The Journal of cell biology 2002) 2 3 4 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. Molecular insights into the interaction of PYM with the Mago-Y14 core of the exon junction complex. (PMID: 14968132) Bono F … Conti E (EMBO reports 2004) 4 23 58

Products for PYM1 Gene

Sources for PYM1 Gene

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