Human Gene PTCD3 (ENST00000254630.12_5) from GENCODE V47lift37
  Description: pentatricopeptide repeat domain 3 (from RefSeq NM_017952.6)
Gencode Transcript: ENST00000254630.12_5
Gencode Gene: ENSG00000132300.19_7
Transcript (Including UTRs)
   Position: hg19 chr2:86,333,358-86,369,280 Size: 35,923 Total Exon Count: 24 Strand: +
Coding Region
   Position: hg19 chr2:86,333,371-86,364,682 Size: 31,312 Coding Exon Count: 24 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:86,333,358-86,369,280)mRNA (may differ from genome)Protein (689 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PTCD3_HUMAN
DESCRIPTION: RecName: Full=Pentatricopeptide repeat-containing protein 3, mitochondrial; AltName: Full=Transformation-related gene 15 protein; Short=TRG-15; Flags: Precursor;
FUNCTION: Mitochondrial RNA-binding protein that has a role in mitochondrial translation.
SUBUNIT: Associated with the 12S mitochondrial rRNA (12S mt-rRNA). Associated with the small subunit of the mitochondrial ribosome.
SUBCELLULAR LOCATION: Mitochondrion.
TISSUE SPECIFICITY: Abundant in testes, skeletal muscle and heart tissue.
SIMILARITY: Belongs to the PTCD3 family.
SIMILARITY: Contains 10 PPR (pentatricopeptide) repeats.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 18.29 RPKM in Testis
Total median expression: 474.46 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
3' UTR -1399.204598-0.304 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR002885 - Pentatricopeptide_repeat

Pfam Domains:
PF01535 - PPR repeat
PF13041 - PPR repeat family
PF13812 - Pentatricopeptide repeat domain
PF17177 - Pentacotripeptide-repeat region of PRORP

SCOP Domains:
48452 - TPR-like

ModBase Predicted Comparative 3D Structure on Q96EY7
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0019843 rRNA binding
GO:0043024 ribosomal small subunit binding

Biological Process:
GO:0006417 regulation of translation
GO:0032543 mitochondrial translation
GO:0070125 mitochondrial translational elongation
GO:0070126 mitochondrial translational termination

Cellular Component:
GO:0005654 nucleoplasm
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005829 cytosol
GO:0005840 ribosome
GO:0005886 plasma membrane


-  Descriptions from all associated GenBank mRNAs
  LF384123 - JP 2014500723-A/191626: Polycomb-Associated Non-Coding RNAs.
AK293962 - Homo sapiens cDNA FLJ57349 complete cds.
BC011832 - Homo sapiens Pentatricopeptide repeat domain 3, mRNA (cDNA clone MGC:19979 IMAGE:3939273), complete cds.
AB528740 - Synthetic construct DNA, clone: pF1KB9960, Homo sapiens PTCD3 gene for Pentatricopeptide repeat domain 3, without stop codon, in Flexi system.
JD520292 - Sequence 501316 from Patent EP1572962.
LF362965 - JP 2014500723-A/170468: Polycomb-Associated Non-Coding RNAs.
JD206575 - Sequence 187599 from Patent EP1572962.
JD288272 - Sequence 269296 from Patent EP1572962.
LF362958 - JP 2014500723-A/170461: Polycomb-Associated Non-Coding RNAs.
KJ902749 - Synthetic construct Homo sapiens clone ccsbBroadEn_12143 PTCD3 gene, encodes complete protein.
CU680072 - Synthetic construct Homo sapiens gateway clone IMAGE:100019839 5' read PTCD3 mRNA.
AK315676 - Homo sapiens cDNA, FLJ96770.
LF362955 - JP 2014500723-A/170458: Polycomb-Associated Non-Coding RNAs.
JD539713 - Sequence 520737 from Patent EP1572962.
JD113867 - Sequence 94891 from Patent EP1572962.
JD559876 - Sequence 540900 from Patent EP1572962.
AK000765 - Homo sapiens cDNA FLJ20758 fis, clone HEP01508.
JD059444 - Sequence 40468 from Patent EP1572962.
BC001758 - Homo sapiens Pentatricopeptide repeat domain 3, mRNA (cDNA clone IMAGE:3353343), partial cds.
AL832520 - Homo sapiens mRNA; cDNA DKFZp666K071 (from clone DKFZp666K071).
JD060414 - Sequence 41438 from Patent EP1572962.
AY277598 - Homo sapiens transformation-related protein 15 (TRG15) mRNA, complete cds.
LF362950 - JP 2014500723-A/170453: Polycomb-Associated Non-Coding RNAs.
LF362948 - JP 2014500723-A/170451: Polycomb-Associated Non-Coding RNAs.
LF362945 - JP 2014500723-A/170448: Polycomb-Associated Non-Coding RNAs.
LF362944 - JP 2014500723-A/170447: Polycomb-Associated Non-Coding RNAs.
LF362939 - JP 2014500723-A/170442: Polycomb-Associated Non-Coding RNAs.
JD094376 - Sequence 75400 from Patent EP1572962.
JD067406 - Sequence 48430 from Patent EP1572962.
JD302124 - Sequence 283148 from Patent EP1572962.
JD365196 - Sequence 346220 from Patent EP1572962.
JD287640 - Sequence 268664 from Patent EP1572962.
JD392124 - Sequence 373148 from Patent EP1572962.
JD282404 - Sequence 263428 from Patent EP1572962.
JD549707 - Sequence 530731 from Patent EP1572962.
JD469527 - Sequence 450551 from Patent EP1572962.
JD275344 - Sequence 256368 from Patent EP1572962.
JD231792 - Sequence 212816 from Patent EP1572962.
JD269705 - Sequence 250729 from Patent EP1572962.
JD156661 - Sequence 137685 from Patent EP1572962.
JD518120 - Sequence 499144 from Patent EP1572962.
JD106120 - Sequence 87144 from Patent EP1572962.
MA619700 - JP 2018138019-A/191626: Polycomb-Associated Non-Coding RNAs.
MA598542 - JP 2018138019-A/170468: Polycomb-Associated Non-Coding RNAs.
MA598535 - JP 2018138019-A/170461: Polycomb-Associated Non-Coding RNAs.
MA598532 - JP 2018138019-A/170458: Polycomb-Associated Non-Coding RNAs.
MA598527 - JP 2018138019-A/170453: Polycomb-Associated Non-Coding RNAs.
MA598525 - JP 2018138019-A/170451: Polycomb-Associated Non-Coding RNAs.
MA598522 - JP 2018138019-A/170448: Polycomb-Associated Non-Coding RNAs.
MA598521 - JP 2018138019-A/170447: Polycomb-Associated Non-Coding RNAs.
MA598516 - JP 2018138019-A/170442: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q96EY7 (Reactome details) participates in the following event(s):

R-HSA-5368279 MTIF3 binds 28S ribosomal subunit
R-HSA-5419273 Hydrolysis of GTP and dissociation of 28S and 39S subunits
R-HSA-5389849 28S subunit:MTIF3 binds MTIF2:GTP, mRNA, and formylMet-tRNA
R-HSA-5389839 39S subunit binds 28S subunit:mRNA:fMet-tRNA
R-HSA-5389848 TUFM:GTP:aminoacyl-tRNA binds 55S ribosome:mRNA:fMet-tRNA
R-HSA-5389857 Peptide transfer from P-site to A-site (peptide bond formation)
R-HSA-5389842 TUFM hydrolyzes GTP and TUFM:GDP dissociates from 55S ribosome
R-HSA-5419261 55S ribosome with peptidyl-tRNA in A site binds GFM1:GTP
R-HSA-5419281 MRRF binds 55S ribosome:mRNA:tRNA
R-HSA-5419279 Translocation of peptidyl-tRNA from A-site to P-site (and translocation of 55S ribosome by 3 bases along mRNA)
R-HSA-5419264 MTRF1L (MTRF1a) or ICT1 binds stop codon in 55S ribosome:mRNA:peptidyl-tRNA
R-HSA-5419277 GFM2:GTP binds 55S ribosome:mRNA:tRNA:MRRF releasing mRNA and tRNA
R-HSA-5368286 Mitochondrial translation initiation
R-HSA-5419276 Mitochondrial translation termination
R-HSA-5368287 Mitochondrial translation
R-HSA-5389840 Mitochondrial translation elongation
R-HSA-72766 Translation
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: A6NHD2, D6W5M1, ENST00000254630.1, ENST00000254630.10, ENST00000254630.11, ENST00000254630.2, ENST00000254630.3, ENST00000254630.4, ENST00000254630.5, ENST00000254630.6, ENST00000254630.7, ENST00000254630.8, ENST00000254630.9, MRPS39, NM_017952, PTCD3_HUMAN, Q597H0, Q658Y9, Q96EY7, Q9BUZ8, Q9NWL0, TRG15, uc317fot.1, uc317fot.2
UCSC ID: ENST00000254630.12_5
RefSeq Accession: NM_017952.6
Protein: Q96EY7 (aka PTCD3_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.