Human Gene PTCD2 (uc003kcb.3)
  Description: Homo sapiens pentatricopeptide repeat domain 2 (PTCD2), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr5:71,616,200-71,655,180 Size: 38,981 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg19 chr5:71,616,210-71,654,254 Size: 38,045 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:71,616,200-71,655,180)mRNA (may differ from genome)Protein (388 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PTCD2_HUMAN
DESCRIPTION: RecName: Full=Pentatricopeptide repeat-containing protein 2, mitochondrial;
FUNCTION: Involved in mitochondrial RNA maturation and mitochondrial respiratory chain function (By similarity).
SUBCELLULAR LOCATION: Mitochondrion.
SIMILARITY: Belongs to the PTCD2 family.
SIMILARITY: Contains 1 PPR (pentatricopeptide) repeat.
CAUTION: It is uncertain whether Met-1 or Met-6 is the initiator.
SEQUENCE CAUTION: Sequence=AAH18720.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAB14162.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=EAW95706.1; Type=Erroneous gene model prediction;

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PTCD2
CDC HuGE Published Literature: PTCD2

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 4.48 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 99.40 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 -246.84926-0.267 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
IPR019266 - Ribosomal_S27_mit

Pfam Domains:
PF01535 - PPR repeat
PF10037 - Mitochondrial 28S ribosomal protein S27
PF13812 - Pentatricopeptide repeat domain

ModBase Predicted Comparative 3D Structure on Q8WV60
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 orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding

Biological Process:
GO:0001822 kidney development
GO:0001889 liver development
GO:0006397 mRNA processing
GO:0007005 mitochondrion organization
GO:0007507 heart development
GO:0010468 regulation of gene expression
GO:0048747 muscle fiber development
GO:0050684 regulation of mRNA processing
GO:0055010 ventricular cardiac muscle tissue morphogenesis

Cellular Component:
GO:0005739 mitochondrion


-  Descriptions from all associated GenBank mRNAs
  AK303776 - Homo sapiens cDNA FLJ55874 complete cds, highly similar to Homo sapiens pentatricopeptide repeat domain 2 (PTCD2), mRNA.
AK056761 - Homo sapiens cDNA FLJ32199 fis, clone PLACE6002710, highly similar to Homo sapiens pentatricopeptide repeat domain 2 (PTCD2), mRNA.
AK298750 - Homo sapiens cDNA FLJ51278 complete cds, highly similar to Homo sapiens pentatricopeptide repeat domain 2 (PTCD2), mRNA.
BC018720 - Homo sapiens pentatricopeptide repeat domain 2, mRNA (cDNA clone MGC:31807 IMAGE:4552964), complete cds.
AK303639 - Homo sapiens cDNA FLJ50338 complete cds, highly similar to Homo sapiens pentatricopeptide repeat domain 2 (PTCD2), mRNA.
AK022660 - Homo sapiens cDNA FLJ12598 fis, clone NT2RM4001384.
JD059227 - Sequence 40251 from Patent EP1572962.
JD056879 - Sequence 37903 from Patent EP1572962.
CU676288 - Synthetic construct Homo sapiens gateway clone IMAGE:100017614 5' read PTCD2 mRNA.
KJ903229 - Synthetic construct Homo sapiens clone ccsbBroadEn_12623 PTCD2 gene, encodes complete protein.
CR457290 - Homo sapiens full open reading frame cDNA clone RZPDo834H049D for gene FLJ12598, hypothetical protein FLJ12598; complete cds, incl. stopcodon.
JD248700 - Sequence 229724 from Patent EP1572962.
JD226776 - Sequence 207800 from Patent EP1572962.
JD553375 - Sequence 534399 from Patent EP1572962.
JD430624 - Sequence 411648 from Patent EP1572962.
JD515809 - Sequence 496833 from Patent EP1572962.
JD520195 - Sequence 501219 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_024754, NP_079030, PTCD2_HUMAN, Q6IA65, Q8WV60, Q9H9R0
UCSC ID: uc003kcb.3
RefSeq Accession: NM_024754
Protein: Q8WV60 (aka PTCD2_HUMAN)
CCDS: CCDS4014.2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_024754.3
exon count: 10CDS single in 3' UTR: no RNA size: 2103
ORF size: 1167CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2402.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 530# strange splices: 0
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.