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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.

No data available for 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
GH07F099557 1.4 Ensembl ENCODE 11.2 -94.8 -94824 7.9 HDGF PKNOX1 ARNT CREB3L1 WRNIP1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 PDAP1 ZSCAN25 ATP5J2 RN7SL416P BUD31 LOC100131859 ENSG00000244219 ZNF789 ATP5J2-PTCD1 PTCD1
GH07F099207 1.6 FANTOM5 Ensembl ENCODE 3.1 +256.1 256146 5.9 HDGF PKNOX1 MLX ARID4B SIN3A DMAP1 YY1 ZNF121 FOS SP5 SMURF1 ARPC1B TRIM4 PDAP1 BUD31 ARPC1A FAM200A ZNF655 PTCD1 KPNA7
GH07F099371 1.3 FANTOM5 ENCODE 2.2 +93.4 93413 1.6 ATF1 MLX ZFP64 ARID4B DMAP1 ZNF48 SP5 NFYC MXD4 MIER2 ARPC1B ATP5J2 PILRB CPSF4 PTCD1 PIR48819
GH07F099692 1.6 FANTOM5 Ensembl ENCODE 1.4 -228.1 -228086 2.7 PKNOX1 MLX ARID4B DMAP1 YY1 SLC30A9 CBX5 KLF13 ZNF263 SP5 NYAP1 PDAP1 MBLAC1 ZKSCAN5 CYP3A5 SAP25 ZSCAN25 ENSG00000244219 CYP3A43 CYP3A4
GH07F099464 1.2 ENCODE 0.8 +0.4 359 2.0 HDGF PKNOX1 ARNT CREB3L1 MLX WRNIP1 ARID4B SIN3A DMAP1 ZNF2 ZSCAN25 ZNF655 LOC100131859 TRRAP LOC101927550 LOC100419643 SMURF1 AP4M1 ENSG00000242798 STAG3L5P
- 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
ENSR00001562248 163 1600 HDGF PKNOX1 ARNT CREB3L1 MLX WRNIP1 ARID4B SIN3A DMAP1 ZNF2
ENSR00001894465 1263 201

Genomic Location for PTCD1 Gene

Chromosome:
7
Start:
99,416,739 bp from pter
End:
99,466,163 bp from pter
Size:
49,425 bases
Orientation:
Minus strand

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 Lys 241, Lys 659, and Lys 676
  • 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

Protein Domains for PTCD1 Gene

Graphical View of Domain Structure for InterPro Entry

O75127

UniProtKB/Swiss-Prot:

PTCD1_HUMAN :
  • Belongs to the PTCD1 family.
  • Contains 9 PPR (pentatricopeptide) repeats.
Family:
  • Belongs to the PTCD1 family.
Similarity:
  • Contains 9 PPR (pentatricopeptide) repeats.
genes like me logo Genes that share domains with PTCD1: view

No data available for Gene Families for PTCD1 Gene

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.

Gene Ontology (GO) - Molecular Function for PTCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000049 tRNA binding IDA 19651879
GO:0044822 poly(A) 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

Animal Model Products

Inhibitory RNA Products

Clone Products

Flow Cytometry 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

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

Transcripts for PTCD1 Gene

Unigene Clusters for PTCD1 Gene

Pentatricopeptide repeat domain 1:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry 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 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.
genes like me logo Genes that share expression patterns with PTCD1: view

Primer Products

No data available for mRNA differential expression in normal tissues 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 -- 35
  • 99 (a)
OneToMany
cow
(Bos Taurus)
Mammalia -- 35
  • 78 (a)
OneToMany
dog
(Canis familiaris)
Mammalia -- 35
  • 76 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Ptcd1 35
  • 73 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 57 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 46 (a)
OneToMany
chicken
(Gallus gallus)
Aves -- 35
  • 55 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 53 (a)
OneToMany
zebrafish
(Danio rerio)
Actinopterygii ptcd1 35
  • 45 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta CG4611 35
  • 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
rs1004387 -- 99,418,701(-) TGGAA(C/T)CTGGG intron-variant, utr-variant-3-prime
rs1004388 -- 99,418,700(-) GGAAT(A/C)TGGGC intron-variant, utr-variant-3-prime
rs10215854 -- 99,439,297(+) CCTCT(A/G)GATCC intron-variant, upstream-variant-2KB
rs10235168 -- 99,422,332(+) CCCAT(C/T)CGGGC intron-variant

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

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

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 Res. 2009) 3 4 22 64
  2. RNA processing in human mitochondria. (PMID: 21857155) Sanchez M.I. … Filipovska A. (Cell Cycle 2011) 3 4 64
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  4. The DNA sequence of human chromosome 7. (PMID: 12853948) Hillier L.W. … Wilson R.K. (Nature 2003) 3 4 64
  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 Res. 1998) 3 4 64

Products for PTCD1 Gene

Sources for PTCD1 Gene

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