U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Ptcd1 pentatricopeptide repeat domain 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 304278, updated on 6-Jun-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Ptcd1provided by RGD
    Official Full Name
    pentatricopeptide repeat domain 1provided by RGD
    Primary source
    RGD:1311473
    See related
    Ensembl:ENSRNOG00000000987 AllianceGenome:RGD:1311473
    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 tRNA binding activity. Predicted to be involved in mitochondrial translation and tRNA 3'-end processing. Located in mitochondrial matrix. Orthologous to human ATP5MF-PTCD1 (ATP5MF-PTCD1 readthrough) and PTCD1 (pentatricopeptide repeat domain 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Kidney (RPKM 94.8), Heart (RPKM 93.5) and 9 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Ptcd1 in Genome Data Viewer
    Location:
    12p11
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 12 NC_086030.1 (14559419..14577198)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 12 NC_051347.1 (9445656..9463434)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 12 NC_005111.4 (11215795..11233633)

    Chromosome 12 - NC_086030.1Genomic Context describing neighboring genes Neighboring gene histidine triad nucleotide binding protein 1 like 2 Neighboring gene ATP synthase membrane subunit f Neighboring gene cleavage and polyadenylation specific factor 4 Neighboring gene BUD31 homolog Neighboring gene PDGFA associated protein 1 Neighboring gene actin related protein 2/3 complex, subunit 1B

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. PTCD1 Is Required for 16S rRNA Maturation Complex Stability and Mitochondrial Ribosome Assembly. Perks KL, et al. Cell Rep, 2018 Apr 3. PMID 29617655
    2. Pentatricopeptide repeat domain protein 1 lowers the levels of mitochondrial leucine tRNAs in cells. Rackham O, et al. Nucleic Acids Res, 2009 Sep. PMID 19651879, Free PMC Article
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables tRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables tRNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in mitochondrial translation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in tRNA 3'-end processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in tRNA 3'-end processing ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in mitochondrial matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrial matrix IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

    Go to the top of the page Help
    Preferred Names
    pentatricopeptide repeat-containing protein 1, mitochondrial

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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_001401119.1 → NP_001388048.1  pentatricopeptide repeat-containing protein 1, mitochondrial

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000012
      UniProtKB/Swiss-Prot
      A2VD13
      UniProtKB/TrEMBL
      A6K1F1, D4AA10
      Related
      ENSRNOP00000068093.1, ENSRNOT00000076896.3

    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_086030.1 Reference GRCr8

      Range
      14559419..14577198
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006248873.3 → XP_006248935.1  pentatricopeptide repeat-containing protein 1, mitochondrial isoform X2

      UniProtKB/TrEMBL
      A6K1F1, D4AA10
      Conserved Domains (2) summary
      sd00004
      Location:465 → 491
      PPR; PPR repeat [structural motif]
      pfam13041
      Location:495 → 538
      PPR_2; PPR repeat family

    2. XM_039089344.1 → XP_038945272.1  pentatricopeptide repeat-containing protein 1, mitochondrial isoform X4

      Conserved Domains (3) summary
      PLN03218
      Location:120 → 377
      PLN03218; maturation of RBCL 1; Provisional
      sd00004
      Location:165 → 191
      PPR; PPR repeat [structural motif]
      pfam13041
      Location:165 → 208
      PPR_2; PPR repeat family

    3. XM_039089342.2 → XP_038945270.1  pentatricopeptide repeat-containing protein 1, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      A2VD13
      UniProtKB/TrEMBL
      A6K1F1, D4AA10
      Related
      ENSRNOP00000057644.2
      Conserved Domains (3) summary
      PLN03218
      Location:120 → 322
      PLN03218; maturation of RBCL 1; Provisional
      sd00004
      Location:165 → 191
      PPR; PPR repeat [structural motif]
      pfam13041
      Location:165 → 208
      PPR_2; PPR repeat family

    4. XM_039089343.2 → XP_038945271.1  pentatricopeptide repeat-containing protein 1, mitochondrial isoform X3

      Conserved Domains (3) summary
      PLN03218
      Location:10 → 190
      PLN03218; maturation of RBCL 1; Provisional
      sd00004
      Location:14 → 40
      PPR; PPR repeat [structural motif]
      pfam13041
      Location:14 → 57
      PPR_2; PPR repeat family

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001109665.1: Suppressed sequence

      Description
      NM_001109665.1: This RefSeq was removed because currently there is insufficient support for the transcript.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A2VD13.1 GenPept UniProtKB/Swiss-Prot:A2VD13

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools