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

Gene ID: 304278, updated on 13-Apr-2024

Summary

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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
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Genomic context

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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

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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. 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

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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

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

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000012
    UniProtKB/Swiss-Prot
    A2VD13
    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

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