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

Gene ID: 78428, updated on 27-Nov-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, Nov 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

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