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

    Gene ID: 69956, updated on 23-Jun-2021

    Summary

    Official Symbol
    Ptcd3provided by MGI
    Official Full Name
    pentatricopeptide repeat domain 3provided by MGI
    Primary source
    MGI:MGI:1917206
    See related
    Ensembl:ENSMUSG00000063884
    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; AA589622; AU045708; 2610034F17Rik; 2810422B04Rik
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 15.2), liver E14 (RPKM 12.3) and 24 other tissues See more
    Orthologs
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    Genomic context

    See Ptcd3 in Genome Data Viewer
    Location:
    6; 6 C1
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    109 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)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 6 NC_000072.5 (71830632..71858756, complement)

    Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes 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 polymerase (RNA) I polypeptide A Neighboring gene eukaryotic translation initiation factor 3, subunit H pseudogene Neighboring gene predicted gene, 26628

    Genomic regions, transcripts, and products

    Expression

    • 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

    Variation

    Alleles

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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    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
    PubMed 
    enables rRNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables ribosomal small subunit binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    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
    PubMed 
    involved_in mitochondrial translation ISO
    Inferred from Sequence Orthology
    more info
     
    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 mitochondrion HDA PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    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
     
    located_in ribosome IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001362068.1NP_001348997.1  pentatricopeptide repeat domain-containing protein 3, mitochondrial 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
      Conserved Domains (3) summary
      sd00004
      Location:257284
      PPR; PPR repeat [structural motif]
      pfam13041
      Location:289343
      PPR_2; PPR repeat family
      cl25449
      Location:253299
      PPR_2; PPR repeat family
    2. NM_001362069.1NP_001348998.1  pentatricopeptide repeat domain-containing protein 3, mitochondrial 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
      Conserved Domains (3) summary
      sd00004
      Location:257284
      PPR; PPR repeat [structural motif]
      pfam13041
      Location:289343
      PPR_2; PPR repeat family
      cl25449
      Location:253299
      PPR_2; PPR repeat family
    3. NM_027275.3NP_081551.2  pentatricopeptide repeat domain-containing protein 3, mitochondrial 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
      Related
      ENSMUSP00000080743.3, ENSMUST00000082094.5
      Conserved Domains (2) summary
      sd00004
      Location:257284
      PPR; PPR repeat [structural motif]
      pfam13041
      Location:289343
      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: Mus musculus Annotation Release 109 details...Open this link in a new tab

    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_006506574.3XP_006506637.1  pentatricopeptide repeat domain-containing protein 3, mitochondrial isoform X1

      Conserved Domains (3) summary
      sd00004
      Location:116143
      PPR; PPR repeat [structural motif]
      pfam13812
      Location:177240
      PPR_3; Pentatricopeptide repeat domain
      pfam13041
      Location:148202
      PPR_2; PPR repeat family
    2. XM_011241461.3XP_011239763.1  pentatricopeptide repeat domain-containing protein 3, mitochondrial 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

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