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    PTCD1 pentatricopeptide repeat domain 1 [ Homo sapiens (human) ]

    Gene ID: 26024, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PTCD1provided by HGNC
    Official Full Name
    pentatricopeptide repeat domain 1provided by HGNC
    Primary source
    HGNC:HGNC:22198
    See related
    Ensembl:ENSG00000106246 MIM:614774; AllianceGenome:HGNC:22198
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    This gene encodes a mitochondrial protein that binds leucine tRNAs and other mitochondrial RNAs and plays a role in the regulation of translation. Increased expression of this gene results in decreased mitochondrial leucine tRNA levels. Naturally occurring read-through transcription exists between upstream ATP5J2 (ATP synthase, H+ transporting, mitochondrial Fo complex, subunit F2) and this gene. [provided by RefSeq, Aug 2015]
    Expression
    Ubiquitous expression in testis (RPKM 5.8), bone marrow (RPKM 4.7) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See PTCD1 in Genome Data Viewer
    Location:
    7q22.1
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (99416739..99438798, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (100655640..100677699, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (99014362..99036421, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901707 Neighboring gene small nucleolar RNA U13 Neighboring gene BUD31 homolog Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18409 Neighboring gene ATP5MF-PTCD1 readthrough Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99020619-99021120 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:99027477-99028073 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:99032915-99033062 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99034189-99034714 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26315 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18410 Neighboring gene SAP domain containing ribonucleoprotein pseudogene Neighboring gene cleavage and polyadenylation specific factor 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99049670-99050230 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99053345-99054147 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99058948-99059448 Neighboring gene ATP synthase membrane subunit f Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:99062959-99063576 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:99063577-99064192

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. The role of mammalian PPR domain proteins in the regulation of mitochondrial gene expression. Rackham O, et al. Biochim Biophys Acta, 2012 Sep-Oct. PMID 22051507
    2. Mitochondrial leucine tRNA level and PTCD1 are regulated in response to leucine starvation. Schild C, et al. Amino Acids, 2014 Jul. PMID 24710704
    3. PTCD1 Is Required for Mitochondrial Oxidative-Phosphorylation: Possible Genetic Association with Alzheimer's Disease. Fleck D, et al. J Neurosci, 2019 Jun 12. PMID 30948477, Free PMC Article
    4. 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
    5. Human pentatricopeptide proteins: only a few and what do they do? Lightowlers RN, et al. RNA Biol, 2013. PMID 23635806, Free PMC Article

    See all (49) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. reduced PTCD1 activity disrupts neuronal energy homeostasis and dampens spontaneous neural transmission in Alzheimer's Disease
      Title: PTCD1 Is Required for Mitochondrial Oxidative-Phosphorylation: Possible Genetic Association with Alzheimer's Disease.
    2. Leucine starvation decreased PTCD1 on the protein level.
      Title: Mitochondrial leucine tRNA level and PTCD1 are regulated in response to leucine starvation.
    3. ELAC2 and PTCD1 affect the 3' end processing of tRNAs.
      Title: RNA processing in human mitochondria.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Readthrough ATP5MF-PTCD1

    Readthrough gene: ATP5MF-PTCD1, Included gene: ATP5MF

    Homology

    Clone Names

    • KIAA0632

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables tRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables tRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in mitochondrial matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrial matrix ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in mitochondrion HTP PubMed 
    located_in mitochondrion 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.

    Genomic

    1. NG_042827.1 RefSeqGene

      Range
      5042..27101
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_015545.4 → NP_056360.2  pentatricopeptide repeat-containing protein 1, mitochondrial

      See identical proteins and their annotated locations for NP_056360.2

      Status: REVIEWED

      Source sequence(s)
      AB014532, DA770648
      Consensus CDS
      CCDS34691.1
      UniProtKB/Swiss-Prot
      O75127, Q3ZB78, Q66K60, Q9UDV2
      UniProtKB/TrEMBL
      A4D273, Q3ZB84
      Related
      ENSP00000292478.5, ENST00000292478.9
      Conserved Domains (3) summary
      TIGR00756
      Location:176 → 208
      PPR; pentatricopeptide repeat domain (PPR motif)
      sd00004
      Location:176 → 202
      PPR; PPR repeat [structural motif]
      pfam13041
      Location:553 → 596
      PPR_2; PPR repeat family

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      99416739..99438798 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      100655640..100677699 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75127.2 GenPept UniProtKB/Swiss-Prot:O75127

    Gene LinkOut

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

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