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    Ptcd3 pentatricopeptide repeat domain 3 [ Mus musculus (house mouse) ]

    Gene ID: 69956, updated on 25-Apr-2024

    Summary

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    Official Symbol
    Ptcd3provided by MGI
    Official Full Name
    pentatricopeptide repeat domain 3provided by MGI
    Primary source
    MGI:MGI:1917206
    See related
    Ensembl:ENSMUSG00000063884 AllianceGenome:MGI:1917206
    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
    MRP-S39; 2610034F17Rik; 2810422B04Rik
    Summary
    Predicted to enable rRNA binding activity and ribosomal small subunit binding activity. Predicted to be involved in mitochondrial translation. Predicted to act upstream of or within regulation of translation. Located in mitochondrion. Is expressed in several structures, including alimentary system; brain; cardiovascular system; genitourinary system; and immune system. Human ortholog(s) of this gene implicated in combined oxidative phosphorylation deficiency 51. Orthologous to human PTCD3 (pentatricopeptide repeat domain 3). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 15.2), liver E14 (RPKM 12.3) and 24 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    6 C1; 6 32.21 cM
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (71857622..71886080, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (71880638..71908773, complement)

    Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_16268 Neighboring gene mitochondrial ribosomal protein L35 Neighboring gene inner membrane protein, mitochondrial Neighboring gene ribosomal protein L7A pseudogene Neighboring gene small nucleolar RNA, C/D box 94 Neighboring gene STARR-positive B cell enhancer ABC_E9096 Neighboring gene polymerase (RNA) I polypeptide A Neighboring gene STARR-positive B cell enhancer ABC_E6439 Neighboring gene STARR-seq mESC enhancer starr_16273 Neighboring gene eukaryotic translation initiation factor 3, subunit H pseudogene Neighboring gene STARR-seq mESC enhancer starr_16274 Neighboring gene STARR-seq mESC enhancer starr_16275 Neighboring gene CapStarr-seq enhancer MGSCv37_chr6:71912891-71913074 Neighboring gene predicted gene, 26628

    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. Ribosome. The structure of the human mitochondrial ribosome. Amunts A, et al. Science, 2015 Apr 3. PMID 25838379, Free PMC Article
    2. Structure and Function of the Mitochondrial Ribosome. Greber BJ, et al. Annu Rev Biochem, 2016 Jun 2. PMID 27023846
    3. Decreased expression levels of Ifi genes is associated to the increased resistance to spontaneous arthritis disease in mice deficiency of IL-1RA. Liu X, et al. BMC Immunol, 2016 Aug 2. PMID 27480124, Free PMC Article
    4. Ex vivo Quantitative Proteomic Analysis of Serotonin Transporter Interactome: Network Impact of the SERT Ala56 Coding Variant. Quinlan MA, et al. Front Mol Neurosci, 2020. PMID 32581705, Free PMC Article
    5. Matrix-screening reveals a vast potential for direct protein-protein interactions among RNA binding proteins. Lang B, et al. Nucleic Acids Res, 2021 Jul 9. PMID 34133714, Free PMC Article

    See all (29) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Targeted (2) 

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables rRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables rRNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ribosomal small subunit binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ribosomal small subunit binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in mitochondrial translation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mitochondrial translation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in mitochondrial translation NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of translation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in mitochondrial inner membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of mitochondrial small ribosomal subunit NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in mitochondrion HDA PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of ribonucleoprotein complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in ribosome IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    small ribosomal subunit protein mS39
    Names
    28S ribosomal protein S39, mitochondrial
    pentatricopeptide repeat domain-containing protein 3, mitochondrial
    pentatricopeptide repeat-containing protein 3, mitochondrial

    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_001362068.1 → NP_001348997.1  small ribosomal subunit protein mS39 isoform 2 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AC122200
      UniProtKB/TrEMBL
      Q3UK51
      Conserved Domains (3) summary
      sd00004
      Location:257 → 284
      PPR; PPR repeat [structural motif]
      pfam13041
      Location:289 → 343
      PPR_2; PPR repeat family
      cl25449
      Location:253 → 299
      PPR_2; PPR repeat family

    2. NM_001362069.1 → NP_001348998.1  small ribosomal subunit protein mS39 isoform 3 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks two alternate in-frame exons compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AC122200
      UniProtKB/TrEMBL
      Q3UK51
      Conserved Domains (3) summary
      sd00004
      Location:257 → 284
      PPR; PPR repeat [structural motif]
      pfam13041
      Location:289 → 343
      PPR_2; PPR repeat family
      cl25449
      Location:253 → 299
      PPR_2; PPR repeat family

    3. NM_027275.3 → NP_081551.2  small ribosomal subunit protein mS39 isoform 1 precursor

      See identical proteins and their annotated locations for NP_081551.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AK013131, AK146005, BB844000, BF020753
      Consensus CDS
      CCDS20235.1
      UniProtKB/Swiss-Prot
      Q14C51, Q3UKH5, Q5XG65, Q6P9N5, Q9CZ12
      UniProtKB/TrEMBL
      Q3UK51
      Related
      ENSMUSP00000080743.3, ENSMUST00000082094.5
      Conserved Domains (2) summary
      sd00004
      Location:257 → 284
      PPR; PPR repeat [structural motif]
      pfam13041
      Location:289 → 343
      PPR_2; PPR repeat family

    RNA

    1. NR_155284.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate splice junction compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC122200

    2. NR_155285.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) contains an alternate exon and uses an alternate splice junction compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC122200
      Related
      ENSMUST00000206879.2

    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_000072.7 Reference GRCm39 C57BL/6J

      Range
      71857622..71886080 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006506574.3 → XP_006506637.1  small ribosomal subunit protein mS39 isoform X1

      Conserved Domains (3) summary
      sd00004
      Location:116 → 143
      PPR; PPR repeat [structural motif]
      pfam13812
      Location:177 → 240
      PPR_3; Pentatricopeptide repeat domain
      pfam13041
      Location:148 → 202
      PPR_2; PPR repeat family

    2. XM_011241461.3 → XP_011239763.1  small ribosomal subunit protein mS39 isoform X2

    RNA

    1. XR_001785166.3 RNA Sequence

    2. XR_001785167.3 RNA Sequence

    3. XR_001785164.3 RNA Sequence

    4. XR_868886.4 RNA Sequence

    5. XR_868888.4 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q14C51.2 GenPept UniProtKB/Swiss-Prot:Q14C51

    Gene LinkOut

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

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