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    ptcd1 pentatricopeptide repeat domain 1 [ Danio rerio (zebrafish) ]

    Gene ID: 570247, updated on 9-Dec-2024

    Summary

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    Official Symbol
    ptcd1provided by ZNC
    Official Full Name
    pentatricopeptide repeat domain 1provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-6146
    See related
    Ensembl:ENSDARG00000076176 AllianceGenome:ZFIN:ZDB-GENE-030131-6146
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    wu:fi36d06
    Summary
    Predicted to enable tRNA binding activity. Predicted to be involved in tRNA 3'-end processing. Predicted to be active in mitochondrial matrix. Orthologous to human PTCD1 (pentatricopeptide repeat domain 1). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See ptcd1 in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 1 NC_007112.7 (8555328..8566567, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 1 NC_007112.6 (7871257..7882555, complement)

    Chromosome 1 - NC_007112.7Genomic Context describing neighboring genes Neighboring gene mitochondrial elongation factor 2 Neighboring gene Smith-Magenis syndrome chromosome region, candidate 8b Neighboring gene zgc:112980 Neighboring gene si:ch211-160d14.9 Neighboring gene uncharacterized LOC110439701

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. The zebrafish gene map defines ancestral vertebrate chromosomes. Woods IG, et al. Genome Res, 2005 Sep. PMID 16109975, Free PMC Article
    2. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
    3. 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 ZFIN

    Function Evidence Code Pubs
    enables tRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in tRNA 3'-end processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in mitochondrial matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    pentatricopeptide repeat-containing protein 1; pentatricopeptide repeat-containing protein 1, mitochondrial

    NCBI Reference Sequences (RefSeq)

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    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007112.7 Reference GRCz11 Primary Assembly

      Range
      8555328..8566567 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_021475942.2 → XP_021331617.1  pentatricopeptide repeat-containing protein 1, mitochondrial isoform X2

      UniProtKB/TrEMBL
      A0A8M9PJI3
      Conserved Domains (4) summary
      sd00004
      Location:174 → 203
      PPR; PPR repeat [structural motif]
      pfam13041
      Location:177 → 220
      PPR_2; PPR repeat family
      cl23646
      Location:149 → 303
      PPR_3; Pentatricopeptide repeat domain
      cl25449
      Location:454 → 564
      PPR_2; PPR repeat family

    2. XM_693706.9 → XP_698798.2  pentatricopeptide repeat-containing protein 1, mitochondrial isoform X1

      UniProtKB/TrEMBL
      A0A8N7UVC5, E7F3M0
      Related
      ENSDARP00000104026.2, ENSDART00000114613.4
      Conserved Domains (3) summary
      TIGR00756
      Location:177 → 209
      PPR; pentatricopeptide repeat domain (PPR motif)
      sd00004
      Location:174 → 203
      PPR; PPR repeat [structural motif]
      pfam13041
      Location:172 → 220
      PPR_2; PPR repeat family

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018394460.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      19819..30340 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_021471105.2 → XP_021326780.1  pentatricopeptide repeat-containing protein 1, mitochondrial isoform X1

      UniProtKB/TrEMBL
      A0A2R8RTA8, A0A8M9Q0A0
      Conserved Domains (4) summary
      sd00004
      Location:174 → 203
      PPR; PPR repeat [structural motif]
      pfam13041
      Location:177 → 220
      PPR_2; PPR repeat family
      cl23646
      Location:166 → 337
      PPR_3; Pentatricopeptide repeat domain
      cl25449
      Location:482 → 598
      PPR_2; PPR repeat family
    Nucleotide Protein Strain
    Heading Accession and Version

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