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Aliases for PTCD1 Gene

Aliases for PTCD1 Gene

  • Pentatricopeptide Repeat Domain 1 2 3 5
  • KIAA0632 4

External Ids for PTCD1 Gene

Previous GeneCards Identifiers for PTCD1 Gene

  • GC07M098626
  • GC07M098659
  • GC07M098852
  • GC07M099014
  • GC07M093652

Summaries for PTCD1 Gene

Entrez Gene Summary for PTCD1 Gene

  • 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]

GeneCards Summary for PTCD1 Gene

PTCD1 (Pentatricopeptide Repeat Domain 1) is a Protein Coding gene. GO annotations related to this gene include poly(A) RNA binding and tRNA binding. An important paralog of this gene is ATP5J2-PTCD1.

UniProtKB/Swiss-Prot for PTCD1 Gene

  • Mitochondrial protein implicated in negative regulation of leucine tRNA levels, as well as negative regulation of mitochondria-encoded proteins and COX activity. Affects also the 3-processing of mitochondrial tRNAs.

Additional gene information for PTCD1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PTCD1 Gene

Genomics for PTCD1 Gene

Regulatory Elements for PTCD1 Gene

Enhancers for PTCD1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH07H099471 1.1 ENCODE 55 -6.4 -6441 3 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 ZSCAN25 PTCD1 PPP1R35 TRRAP TRIM4 MEPCE STAG3L5P LOC100419643 AP4M1 LOC101927550
GH07H099557 1.7 Ensembl ENCODE dbSUPER 35.3 -94.8 -94824 7.9 HNRNPUL1 HDGF PKNOX1 FOXA2 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZSCAN25 PTCD1 ZNF655 TRIM4 ZNF394 LOC101927550 ZNF3 LOC100419643 PPP1R35 TRRAP
GH07H099223 1.5 Ensembl ENCODE dbSUPER 39.9 +241.2 241219 1.9 PKNOX1 ATF1 ARNT YBX1 TCF12 GTF3C2 CBX5 ATF7 FOS TSHZ1 ZSCAN25 TRIM4 ZNF655 SMURF1 ZNF3 PTCD1 TRRAP LOC100419643 LOC101927550 ENSG00000242798
GH07H099616 1.4 ENCODE dbSUPER 41.7 -152.1 -152106 4.5 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 ZNF766 ZSCAN25 TRRAP ZNF3 AP4M1 TRIM4 ENSG00000242798 LOC100131859 LOC100419643 PPP1R35 PTCD1
GH07H099373 1.8 FANTOM5 ENCODE dbSUPER 29.3 +87.9 87855 9 HDGF PKNOX1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B ZNF143 ZNF207 ZSCAN25 TRRAP LOC101927550 ZNF655 ZNF394 TRIM4 ENSG00000242798 AP4M1 PTCD1 ZNF3
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PTCD1 on UCSC Golden Path with GeneCards custom track

Promoters for PTCD1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000215668 163 1201 HDGF PKNOX1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1

Genomic Locations for PTCD1 Gene

Genomic Locations for PTCD1 Gene
chr7:99,416,739-99,466,163
(GRCh38/hg38)
Size:
49,425 bases
Orientation:
Minus strand
chr7:99,014,362-99,063,787
(GRCh37/hg19)

Genomic View for PTCD1 Gene

Genes around PTCD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PTCD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PTCD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PTCD1 Gene

Proteins for PTCD1 Gene

  • Protein details for PTCD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75127-PTCD1_HUMAN
    Recommended name:
    Pentatricopeptide repeat-containing protein 1, mitochondrial
    Protein Accession:
    O75127
    Secondary Accessions:
    • Q3ZB78
    • Q66K60
    • Q9UDV2

    Protein attributes for PTCD1 Gene

    Size:
    700 amino acids
    Molecular mass:
    78856 Da
    Quaternary structure:
    • Associates with mitochondrial leucine tRNAs. Interacts with ELAC2.
    SequenceCaution:
    • Sequence=BAA31607.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

neXtProt entry for PTCD1 Gene

Post-translational modifications for PTCD1 Gene

  • Ubiquitination at isoforms=241, Lys659, and Lys676
  • Modification sites at PhosphoSitePlus

Other Protein References for PTCD1 Gene

No data available for DME Specific Peptides for PTCD1 Gene

Domains & Families for PTCD1 Gene

Gene Families for PTCD1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for PTCD1 Gene

Graphical View of Domain Structure for InterPro Entry

O75127

UniProtKB/Swiss-Prot:

PTCD1_HUMAN :
  • Belongs to the PTCD1 family.
Family:
  • Belongs to the PTCD1 family.
genes like me logo Genes that share domains with PTCD1: view

Function for PTCD1 Gene

Molecular function for PTCD1 Gene

UniProtKB/Swiss-Prot Function:
Mitochondrial protein implicated in negative regulation of leucine tRNA levels, as well as negative regulation of mitochondria-encoded proteins and COX activity. Affects also the 3-processing of mitochondrial tRNAs.

Phenotypes From GWAS Catalog for PTCD1 Gene

Gene Ontology (GO) - Molecular Function for PTCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000049 tRNA binding IDA 19651879
GO:0003723 RNA binding IDA 22658674
genes like me logo Genes that share ontologies with PTCD1: view
genes like me logo Genes that share phenotypes with PTCD1: view

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PTCD1 Gene

Localization for PTCD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PTCD1 Gene

Mitochondrion. Mitochondrion matrix.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PTCD1 gene
Compartment Confidence
mitochondrion 5
peroxisome 1
nucleus 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PTCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA,IDA 19651879
GO:0005759 mitochondrial matrix ISS --
genes like me logo Genes that share ontologies with PTCD1: view

Pathways & Interactions for PTCD1 Gene

SuperPathways for PTCD1 Gene

No Data Available

Interacting Proteins for PTCD1 Gene

Gene Ontology (GO) - Biological Process for PTCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008033 tRNA processing IEA --
GO:0042780 tRNA 3-end processing IDA 21857155
genes like me logo Genes that share ontologies with PTCD1: view

No data available for Pathways by source and SIGNOR curated interactions for PTCD1 Gene

Drugs & Compounds for PTCD1 Gene

No Compound Related Data Available

Transcripts for PTCD1 Gene

Unigene Clusters for PTCD1 Gene

Pentatricopeptide repeat domain 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PTCD1 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9
SP1: - -
SP2: -
SP3:

Relevant External Links for PTCD1 Gene

GeneLoc Exon Structure for
PTCD1
ECgene alternative splicing isoforms for
PTCD1

Expression for PTCD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PTCD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PTCD1 Gene

This gene is overexpressed in Lung (39.2), Adrenal (11.3), and Bone (8.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PTCD1 Gene



Protein tissue co-expression partners for PTCD1 Gene

NURSA nuclear receptor signaling pathways regulating expression of PTCD1 Gene:

PTCD1

SOURCE GeneReport for Unigene cluster for PTCD1 Gene:

Hs.632313

mRNA Expression by UniProt/SwissProt for PTCD1 Gene:

O75127-PTCD1_HUMAN
Tissue specificity: Abundant in testes, skeletal muscle and heart.

Evidence on tissue expression from TISSUES for PTCD1 Gene

  • Nervous system(4.1)
genes like me logo Genes that share expression patterns with PTCD1: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for PTCD1 Gene

Orthologs for PTCD1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PTCD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia -- 34
  • 99 (a)
OneToMany
cow
(Bos Taurus)
Mammalia -- 34
  • 78 (a)
OneToMany
dog
(Canis familiaris)
Mammalia -- 34
  • 76 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Ptcd1 34
  • 73 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 57 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 46 (a)
OneToMany
chicken
(Gallus gallus)
Aves -- 34
  • 55 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 53 (a)
OneToMany
zebrafish
(Danio rerio)
Actinopterygii ptcd1 34
  • 45 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta CG4611 34
  • 26 (a)
OneToMany
Species where no ortholog for PTCD1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PTCD1 Gene

ENSEMBL:
Gene Tree for PTCD1 (if available)
TreeFam:
Gene Tree for PTCD1 (if available)

Paralogs for PTCD1 Gene

Paralogs for PTCD1 Gene

(1) SIMAP similar genes for PTCD1 Gene using alignment to 7 proteins:

genes like me logo Genes that share paralogs with PTCD1: view

Variants for PTCD1 Gene

Sequence variations from dbSNP and Humsavar for PTCD1 Gene

SNP ID Clin Chr 07 pos Sequence Context AA Info Type
rs201365604 Uncertain significance 99,434,948(+) TCTCC(A/G)GGAGG reference, missense
rs886043246 Uncertain significance 99,420,092(+) CCACT(A/G)CTTGT downstream-variant-500B, reference, stop-gained
rs1000026358 -- 99,416,421(+) TTGTT(G/T)TTTGT intron-variant, downstream-variant-500B
rs1000236639 -- 99,440,374(+) GAGAC(-/AG)GGGCC intron-variant, upstream-variant-2KB
rs1000426419 -- 99,428,196(+) AGAGC(A/G)AGACC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PTCD1 Gene

Variant ID Type Subtype PubMed ID
nsv951382 CNV deletion 24416366
nsv831069 CNV loss 17160897
nsv5864 CNV insertion 18451855
esv3542149 CNV deletion 23714750
esv2734882 CNV deletion 23290073

Variation tolerance for PTCD1 Gene

Residual Variation Intolerance Score: 90.5% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PTCD1 Gene

Human Gene Mutation Database (HGMD)
PTCD1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PTCD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PTCD1 Gene

Disorders for PTCD1 Gene

Relevant External Links for PTCD1

Genetic Association Database (GAD)
PTCD1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PTCD1

No disorders were found for PTCD1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PTCD1 Gene

Publications for PTCD1 Gene

  1. Pentatricopeptide repeat domain protein 1 lowers the levels of mitochondrial leucine tRNAs in cells. (PMID: 19651879) Rackham O … Filipovska A (Nucleic acids research 2009) 3 4 22 60
  2. RNA processing in human mitochondria. (PMID: 21857155) Sanchez MI … Filipovska A (Cell cycle (Georgetown, Tex.) 2011) 3 4 60
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 60
  4. The DNA sequence of human chromosome 7. (PMID: 12853948) Hillier LW … Wilson RK (Nature 2003) 3 4 60
  5. Prediction of the coding sequences of unidentified human genes. X. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PMID: 9734811) Ishikawa K … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1998) 3 4 60

Products for PTCD1 Gene

Sources for PTCD1 Gene

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