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

Gene ID: 500199, updated on 4-Apr-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
Ensembl: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 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, Apr 2022]
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
  
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, ENSRNOT00000078991.2
    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
    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

  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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