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

Gene ID: 570247, updated on 2-Nov-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, Nov 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 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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