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    Ptcd3 Pentatricopeptide repeat domain 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 500199, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Ptcd3provided by RGD
    Official Full Name
    Pentatricopeptide repeat domain 3provided by RGD
    Primary source
    RGD:1565582
    See related
    EnsemblRapid:ENSRNOG00000009484 AllianceGenome:RGD:1565582
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable rRNA binding activity and ribosomal small subunit binding activity. Predicted to be involved in mitochondrial translation. Predicted to be located in cytosol; nucleoplasm; and plasma membrane. Predicted to be part of ribonucleoprotein complex. Predicted to be active in mitochondrion. 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, Dec 2024]
    Expression
    Biased expression in Kidney (RPKM 365.8), Heart (RPKM 265.2) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Ptcd3 in Genome Data Viewer
    Location:
    4q32
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (105480699..105508007, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (103922440..103957445, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (99795646..99822960, complement)

    Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene mitochondrial ribosomal protein L35 Neighboring gene inner membrane mitochondrial protein Neighboring gene small nucleolar RNA, C/D box 94 Neighboring gene RNA polymerase I subunit A Neighboring gene transmembrane protein 94, pseudogene 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Pentatricopeptide repeat domain protein 3 associates with the mitochondrial small ribosomal subunit and regulates translation. Davies SM, et al. FEBS Lett, 2009 Jun 18. PMID 19427859
    2. p38α MAPK proximity assay reveals a regulatory mechanism of alternative splicing in cardiomyocytes. Dumont AA, et al. Biochim Biophys Acta Mol Cell Res, 2019 Dec. PMID 31505169
    3. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Baltz AG, et al. Mol Cell, 2012 Jun 8. PMID 22681889
    4. A mitochondrial protein compendium elucidates complex I disease biology. Pagliarini DJ, et al. Cell, 2008 Jul 11. PMID 18614015, Free PMC Article
    5. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Castello A, et al. Cell, 2012 Jun 8. PMID 22658674

    See all (7) 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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    Markers

    Homology

    Clone Names

    • MGC112724

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    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 regulation of translation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in mitochondrial matrix IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrial matrix ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    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
    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_001134718.4 → NP_001128190.2  small ribosomal subunit protein mS39

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000004
      UniProtKB/TrEMBL
      A0A0G2JU15
      Related
      ENSRNOP00000068923.2, ENSRNOT00000078991.3
      Conserved Domains (3) summary
      PLN03077
      Location:241 → 304
      PLN03077; Protein ECB2; Provisional
      sd00004
      Location:256 → 283
      PPR; PPR repeat [structural motif]
      pfam13812
      Location:317 → 380
      PPR_3; Pentatricopeptide repeat domain

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086022.1 Reference GRCr8

      Range
      105480699..105508007 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039108141.2 → XP_038964069.1  small ribosomal subunit protein mS39 isoform X1

      UniProtKB/TrEMBL
      A0A8I6ANU2, A0A8I6G4Q3
      Related
      ENSRNOP00000097950.1, ENSRNOT00000118960.2
      Conserved Domains (3) summary
      sd00004
      Location:281 → 308
      PPR; PPR repeat [structural motif]
      pfam13812
      Location:342 → 405
      PPR_3; Pentatricopeptide repeat domain
      pfam13041
      Location:277 → 323
      PPR_2; PPR repeat family

    2. XM_039108144.2 → XP_038964072.1  small ribosomal subunit protein mS39 isoform X2

      UniProtKB/TrEMBL
      A0A0G2JU15
      Conserved Domains (3) summary
      sd00004
      Location:156 → 183
      PPR; PPR repeat [structural motif]
      pfam13812
      Location:217 → 280
      PPR_3; Pentatricopeptide repeat domain
      pfam13041
      Location:152 → 198
      PPR_2; PPR repeat family

    3. XM_063286518.1 → XP_063142588.1  small ribosomal subunit protein mS39 isoform X3

      UniProtKB/TrEMBL
      D3ZGM1
      Related
      ENSRNOP00000012622.7, ENSRNOT00000012622.9

    4. XM_039108145.2 → XP_038964073.1  small ribosomal subunit protein mS39 isoform X4

      Conserved Domains (3) summary
      sd00004
      Location:281 → 308
      PPR; PPR repeat [structural motif]
      pfam13812
      Location:342 → 405
      PPR_3; Pentatricopeptide repeat domain
      pfam13041
      Location:277 → 323
      PPR_2; PPR repeat family

    RNA

    1. XR_010065693.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001037796.1: Suppressed sequence

      Description
      NM_001037796.1: This RefSeq was removed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein Strain
    Heading Accession and Version

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