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    PYM1 PYM homolog 1, exon junction complex associated factor [ Homo sapiens (human) ]

    Gene ID: 84305, updated on 10-Dec-2024

    Summary

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    Official Symbol
    PYM1provided by HGNC
    Official Full Name
    PYM homolog 1, exon junction complex associated factorprovided by HGNC
    Primary source
    HGNC:HGNC:30258
    See related
    Ensembl:ENSG00000170473 MIM:619753; AllianceGenome:HGNC:30258
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PYM; WIBG
    Summary
    Enables ribosome binding activity. Involved in exon-exon junction complex disassembly; nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; and positive regulation of translation. Located in cell junction; cytosol; and nuclear lumen. Part of exon-exon junction complex. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in esophagus (RPKM 16.0), colon (RPKM 12.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PYM1 in Genome Data Viewer
    Location:
    12q13.2
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (55901413..55927894, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (55868158..55894956, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (56295197..56321678, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene U1 spliceosomal RNA Neighboring gene glutathione S-transferase pi 1 pseudogene 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:56302402-56302550 Neighboring gene uncharacterized LOC124902941 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4539 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:56320788-56321368 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:56321369-56321949 Neighboring gene diacylglycerol kinase alpha Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:56333724-56334224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:56334225-56334725 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:56350689-56351190 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:56354315-56354815 Neighboring gene premelanosome protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6464 Neighboring gene cyclin dependent kinase 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: 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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    Related articles in PubMed

    1. Kaposi's sarcoma-associated herpesvirus ORF57 protein interacts with PYM to enhance translation of viral intronless mRNAs. Boyne JR, et al. EMBO J, 2010 Jun 2. PMID 20436455, Free PMC Article
    2. A combined proteomics/genomics approach links hepatitis C virus infection with nonsense-mediated mRNA decay. Ramage HR, et al. Mol Cell, 2015 Jan 22. PMID 25616068, Free PMC Article
    3. PYM binds the cytoplasmic exon-junction complex and ribosomes to enhance translation of spliced mRNAs. Diem MD, et al. Nat Struct Mol Biol, 2007 Dec. PMID 18026120
    4. NMD factors UPF2 and UPF3 bridge UPF1 to the exon junction complex and stimulate its RNA helicase activity. Chamieh H, et al. Nat Struct Mol Biol, 2008 Jan. PMID 18066079
    5. The hierarchy of exon-junction complex assembly by the spliceosome explains key features of mammalian nonsense-mediated mRNA decay. Gehring NH, et al. PLoS Biol, 2009 May 26. PMID 19478851, Free PMC Article

    See all (81) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC13064

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ribosome binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of translation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cell junction IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    part_of exon-exon junction complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of exon-exon junction complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    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_001143853.1 → NP_001137325.1  partner of Y14 and mago isoform 2

      See identical proteins and their annotated locations for NP_001137325.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) is 1 aa shorter and has a distinct N-terminus compared to isoform 1.
      Source sequence(s)
      BC006135, BC014976, DB466388
      Consensus CDS
      CCDS44916.1
      UniProtKB/Swiss-Prot
      Q9BRP8
      Related
      ENSP00000381271.4, ENST00000398213.4
      Conserved Domains (1) summary
      pfam09282
      Location:11 → 37
      Mago-bind; Mago binding

    2. NM_032345.3 → NP_115721.1  partner of Y14 and mago isoform 1

      See identical proteins and their annotated locations for NP_115721.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC023055, AC025162
      Consensus CDS
      CCDS41795.1
      UniProtKB/Swiss-Prot
      B6ZDM5, Q8IXJ8, Q8N8E7, Q9BRP8
      Related
      ENSP00000386156.2, ENST00000408946.7
      Conserved Domains (1) summary
      pfam09282
      Location:14 → 38
      Mago-bind; Mago binding

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      55901413..55927894 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      55868158..55894956 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BRP8.1 GenPept UniProtKB/Swiss-Prot:Q9BRP8

    Gene LinkOut

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

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