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    Pym1 PYM homolog 1, exon junction complex associated factor [ Mus musculus (house mouse) ]

    Gene ID: 78428, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Pym1provided by MGI
    Official Full Name
    PYM homolog 1, exon junction complex associated factorprovided by MGI
    Primary source
    MGI:MGI:1925678
    See related
    Ensembl:ENSMUSG00000064030 AllianceGenome:MGI:1925678
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Pym; Wibg; A030010B05Rik
    Summary
    Predicted to enable RNA binding activity and ribosome binding activity. Predicted to be involved in exon-exon junction complex disassembly; nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; and positive regulation of translation. Predicted to be located in cell junction; cytosol; and nuclear lumen. Predicted to be part of exon-exon junction complex. Predicted to be active in cytoplasm. Orthologous to human PYM1 (PYM homolog 1, exon junction complex associated factor). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 18.3), thymus adult (RPKM 15.1) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Pym1 in Genome Data Viewer
    Location:
    10 D3; 10 77.14 cM
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (128579989..128602437)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (128747879..128766568)

    Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene ribosomal protein L12 pseudogene Neighboring gene RAB5B, member RAS oncogene family Neighboring gene STARR-positive B cell enhancer ABC_E50 Neighboring gene STARR-positive B cell enhancer ABC_E2974 Neighboring gene premelanosome protein Neighboring gene cyclin dependent kinase 2 Neighboring gene diacylglycerol kinase, alpha Neighboring gene STARR-positive B cell enhancer ABC_E5201 Neighboring gene STARR-seq mESC enhancer starr_28299 Neighboring gene STARR-positive B cell enhancer ABC_E10661 Neighboring gene STARR-seq mESC enhancer starr_28300 Neighboring gene predicted gene, 31504 Neighboring gene ribosomal protein SA, pseudogene 2 Neighboring gene matrix metallopeptidase 19 Neighboring gene transmembrane protein 198b

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. REF1/Aly and the additional exon junction complex proteins are dispensable for nuclear mRNA export. Gatfield D, et al. J Cell Biol, 2002 Nov 25. PMID 12438415, Free PMC Article
    2. Vti1b promotes TRPV1 sensitization during inflammatory pain. Sondermann JR, et al. Pain, 2019 Feb. PMID 30335684
    3. Gene expression in the developing mouse retina by EST sequencing and microarray analysis. Mu X, et al. Nucleic Acids Res, 2001 Dec 15. PMID 11812828, Free PMC Article
    4. Assembly, verification, and initial annotation of the NIA mouse 7.4K cDNA clone set. VanBuren V, et al. Genome Res, 2002 Dec. PMID 12466305, Free PMC Article
    5. Tagging genes with cassette-exchange sites. Cobellis G, et al. Nucleic Acids Res, 2005 Mar 1. PMID 15741177, Free PMC Article

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ribosome binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ribosome binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in exon-exon junction complex disassembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in exon-exon junction complex disassembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in exon-exon junction complex disassembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of translation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of translation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in cell junction IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cell junction ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of exon-exon junction complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of exon-exon junction complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of exon-exon junction complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleolus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    partner of Y14 and mago
    Names
    protein wibg homolog
    within bgcn homolog

    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)

    1. NM_001170869.2 → NP_001164340.1  partner of Y14 and mago isoform 2

      See identical proteins and their annotated locations for NP_001164340.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains an alternate 5' exon and thus differs in the 5' UTR and 5' coding region, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC131081, BI989958
      Consensus CDS
      CCDS48730.1
      UniProtKB/Swiss-Prot
      Q8CHP5
      Related
      ENSMUSP00000067623.9, ENSMUST00000065210.10
      Conserved Domains (1) summary
      pfam09282
      Location:11 → 37
      Mago-bind; Mago binding

    2. NM_001253704.1 → NP_001240633.1  partner of Y14 and mago isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and 5' coding region, and includes an alternate exon that causes a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (3) is significantly shorter and is entirely distinct from isoform 1, but it contains the same N-terminus as found in isoform 2.
      Source sequence(s)
      AC131081, BI989958
      Consensus CDS
      CCDS88115.1
      UniProtKB/TrEMBL
      A0A1W2P7L0
      Related
      ENSMUSP00000151691.2, ENSMUST00000218218.2

    3. NM_001253705.1 → NP_001240634.1  partner of Y14 and mago isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate splice site that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (4) has a distinct and shorter C-terminus, compared to isoform 1.
      Source sequence(s)
      AC131081
      Conserved Domains (1) summary
      pfam09282
      Location:14 → 38
      Mago-bind; Mago binding

    4. NM_030100.4 → NP_084376.2  partner of Y14 and mago isoform 1

      See identical proteins and their annotated locations for NP_084376.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC131081, AK020702
      Consensus CDS
      CCDS48729.1
      UniProtKB/Swiss-Prot
      Q80YD2, Q8CHP5
      Related
      ENSMUSP00000129789.3, ENSMUST00000163377.10
      Conserved Domains (1) summary
      pfam09282
      Location:14 → 38
      Mago-bind; Mago binding

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000076.7 Reference GRCm39 C57BL/6J

      Range
      128579989..128602437
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036156105.1 → XP_036011998.1  partner of Y14 and mago isoform X3

    2. XM_036156106.1 → XP_036011999.1  partner of Y14 and mago isoform X4

    3. XM_030245391.1 → XP_030101251.1  partner of Y14 and mago isoform X1

      Conserved Domains (1) summary
      pfam09282
      Location:54 → 78
      Mago-bind; Mago binding

    4. XM_036156107.1 → XP_036012000.1  partner of Y14 and mago isoform X5

    5. XM_030245394.1 → XP_030101254.1  partner of Y14 and mago isoform X6

      Conserved Domains (1) summary
      pfam09282
      Location:11 → 37
      Mago-bind; Mago binding

    6. XM_030245393.1 → XP_030101253.1  partner of Y14 and mago isoform X3

    7. XM_030245392.2 → XP_030101252.1  partner of Y14 and mago isoform X3

    8. XM_006514320.3 → XP_006514383.1  partner of Y14 and mago isoform X2

      Conserved Domains (1) summary
      pfam09282
      Location:25 → 49
      Mago-bind; Mago binding

    RNA

    1. XR_003948819.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8CHP5.2 GenPept UniProtKB/Swiss-Prot:Q8CHP5

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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