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
Data last updated at UCSC: 2013-06-14
Sequence and Links to Tools and Databases
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
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
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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
Microarray Expression Data
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mRNA Secondary Structure of 3' and 5' UTRs
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
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.
Gene Ontology (GO) Annotations with Structured Vocabulary
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, Q9H9R0UCSC ID: uc003kcb.3RefSeq 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:
10 CDS single in 3' UTR:
no
RNA size:
2103
ORF size:
1167 CDS single in intron:
no
Alignment % ID:
100.00
txCdsPredict score:
2402.00 frame 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
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Methods, Credits, and Use Restrictions
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for details on how this gene model was made and data restrictions if any.