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

Gene ID: 84305, updated on 7-Apr-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, Apr 2022]
Expression
Ubiquitous expression in esophagus (RPKM 16.0), colon (RPKM 12.9) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
12q13.2
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (55901413..55927894, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (55868158..55894956, complement)
105.20220307 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 (74) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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)

Genotypes

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_2023_10

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

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