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PTCD1 Gene

protein-coding   GIFtS: 50
GCID: GC07M099014

Pentatricopeptide Repeat Domain 1

  Search for PTCD1
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Pentatricopeptide Repeat Domain 11 2
KIAA06323 5
Pentatricopeptide Repeat-Containing Protein 1, Mitochondrial2

External Ids:    HGNC: 221981   Entrez Gene: 260242   Ensembl: ENSG000001062467   OMIM: 6147745   UniProtKB: O751273   

Export aliases for PTCD1 gene to outside databases

Previous GC identifers: GC07M098626 GC07M098659 GC07M098852 GC07M093652


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for PTCD1 Gene:
PTCD1 (pentatricopeptide repeat domain 1) is a protein-coding gene. GO annotations related to this gene include tRNA binding. An important paralog of this gene is ATP5J2-PTCD1.

UniProtKB/Swiss-Prot: PTCD1_HUMAN, O75127
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




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000007.14  NC_018918.2  NT_007933.16  
Regulatory elements:
   Regulatory transcription factor binding sites in the PTCD1 gene promoter:
         STAT1   Pax-6   Pax-2   STAT1beta   Pax-2a   STAT1alpha   RORalpha1   FAC1   FOXJ2   Pax-4a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): PTCD1 promoter sequence
   Search Chromatin IP Primers for PTCD1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PTCD1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 7q22.1   Ensembl cytogenetic band:  7q22.1   HGNC cytogenetic band: 7q22.1

PTCD1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PTCD1 gene location

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07M099014:  view genomic region     (about GC identifiers)

Start:
99,014,362 bp from pter      End:
99,063,787 bp from pter
Size:
49,426 bases      Orientation:
minus strand

1 alternative location:
Chr7-,CRA_TCAG 98,374,136-98,396,236     

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: PTCD1_HUMAN, O75127 (See protein sequence)
Recommended Name: Pentatricopeptide repeat-containing protein 1, mitochondrial  
Size: 700 amino acids; 78856 Da
Subunit: Associates with mitochondrial leucine tRNAs. Interacts with ELAC2
Sequence caution: Sequence=BAA31607.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Secondary accessions: Q3ZB78 Q66K60 Q9UDV2

Explore the universe of human proteins at neXtProt for PTCD1: NX_O75127

Explore proteomics data for PTCD1 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys241, Lys659, Lys676
  • Modification sites at PhosphoSitePlus

  • See PTCD1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_056360.2  
    ENSEMBL proteins: 
     ENSP00000292478   ENSP00000390530   ENSP00000408059   ENSP00000401600   ENSP00000450995  

    PTCD1 Human Recombinant Protein Products:

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    Cloud-Clone Corp. CLIAs for PTCD1


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR002885 Pentatricopeptide_repeat

    Graphical View of Domain Structure for InterPro Entry O75127

    ProtoNet protein and cluster: O75127

    UniProtKB/Swiss-Prot: PTCD1_HUMAN, O75127
    Similarity: Belongs to the PTCD1 family
    Similarity: Contains 9 PPR (pentatricopeptide) repeats


    PTCD1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PTCD1_HUMAN, O75127
    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): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000049tRNA binding IDA19651879
    GO:0044822poly(A) RNA binding IDA--
         
    PTCD1 for ontologies           About GeneDecksing


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for PTCD1
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    miRNA
    Products:
        
    miRTarBase miRNAs that target PTCD1:
    hsa-mir-1914-3p (MIRT035774), hsa-mir-505-3p (MIRT041066), hsa-let-7b-5p (MIRT032324)

    Block miRNA regulation of human, mouse, rat PTCD1 using miScript Target Protectors
    8 qRT-PCR Assays for microRNAs that regulate PTCD1:
    hsa-miR-4303 hsa-miR-206 hsa-miR-492 hsa-miR-1 hsa-miR-197 hsa-miR-370 hsa-miR-613 hsa-miR-3652
    SwitchGear 3'UTR luciferase reporter plasmidPTCD1 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat PTCD1

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PTCD1


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    PTCD1_HUMAN, O75127: Mitochondrion. Mitochondrion matrix (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    mitochondrion5
    cytosol1
    nucleus1
    peroxisome1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005739mitochondrion IDA19651879
    GO:0005759mitochondrial matrix ISS--

    PTCD1 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for PTCD1
    Interactions:

        Search GeneGlobe Interaction Network for PTCD1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for PTCD1 (O751272, 3 ENSP000002924784) via UniProtKB, MINT, STRING, and/or I2D (see all 264)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ICT1Q141972, 3, ENSP000003015854MINT-8079030 I2D: score=1 STRING: ENSP00000301585
    MOV10Q9HCE12, ENSP000003500284MINT-8079030 STRING: ENSP00000350028
    MTERFQ995512, ENSP000002486434MINT-8079030 STRING: ENSP00000248643
    KARSQ150462, ENSP000003254484MINT-8079030 STRING: ENSP00000325448
    MTERFD1Q96E292, ENSP000002870254MINT-8079030 STRING: ENSP00000287025
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0042780tRNA 3'-end processing IDA--

    PTCD1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for PTCD1



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for PTCD1 gene: 
    NM_015545.3  

    Unigene Cluster for PTCD1:

    Pentatricopeptide repeat domain 1
    Hs.632313  [show with all ESTs]
    Unigene Representative Sequence: NM_001198879
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000292478(uc003uqh.3 uc011kiw.2) ENST00000485746 ENST00000430982
    ENST00000430029 ENST00000419981 ENST00000555673
    miRNA
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    8 qRT-PCR Assays for microRNAs that regulate PTCD1:
    hsa-miR-4303 hsa-miR-206 hsa-miR-492 hsa-miR-1 hsa-miR-197 hsa-miR-370 hsa-miR-613 hsa-miR-3652
    SwitchGear 3'UTR luciferase reporter plasmidPTCD1 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat PTCD1
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    Primer
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    OriGene qPCR primer pairs and template standards for PTCD1
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      QuantiTect SYBR Green Assays in human, mouse, rat PTCD1
      QuantiFast Probe-based Assays in human, mouse, rat PTCD1

    Additional mRNA sequence: 

    AB014532.1 AB073644.1 AK001615.1 AK291004.1 AK307981.1 BC003688.1 BC024042.1 BC080580.1 
    BC103495.1 BC103502.1 BC103661.1 

    12 DOTS entries:

    DT.102837314  DT.119015  DT.100808868  DT.100760958  DT.121072369  DT.92443205  DT.100812325  DT.70100295 
    DT.91703358  DT.102837312  DT.102837322  DT.121072433 

    Selected AceView cDNA sequences (see all 116):

    BU729750 BM273091 BQ188261 BM760511 CR598273 CB306863 BI856888 BU185585 
    AW080380 BU623604 AA773750 BQ434710 CK820007 NM_015545 AW615427 AB014532 
    BU855942 BQ934198 BM760549 BX953527 BQ051534 BU500188 BM783321 BC024042 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for PTCD1    About this scheme

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


    ECgene alternative splicing isoforms for PTCD1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    PTCD1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AAGGTAGAAC
    PTCD1 Expression
    About this image


    PTCD1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Liver (Hepatobiliary System)
             Liver Bud
    PTCD1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PTCD1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.632313

    UniProtKB/Swiss-Prot: PTCD1_HUMAN, O75127
    Tissue specificity: Abundant in testes, skeletal muscle and heart

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PTCD1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for PTCD1 gene from Selected species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves --
    Uncharacterized protein
    55(a)
    1 → many
    14(4378843-4392311) ENSGALG00000004711
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    53(a)
    1 → many
    GL343725.1(237232-254715)
    zebrafish
    (Danio rerio)
    Actinopterygii ptcd16
    pentatricopeptide repeat domain 1
    45(a)
    1 → many
    1(7631407-7642651) ENSDARG00000076176
    fruit fly
    (Drosophila melanogaster)
    Insecta CG46116
    --
    26(a)
    1 → many
    3L(5129476-5131779)
            Species with no ortholog for PTCD1

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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PTCD1 gene
    ATP5J2-PTCD12  
    1 SIMAP similar gene for PTCD1 using alignment to 7 protein entries:     PTCD1_HUMAN (see all proteins):
    ATP5J2-PTCD1

    PTCD1 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    2 SNPs for PTCD1    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 7 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs347145131,2,4
    ----see VAR_0529362 mis40--------
    rs356337281,2,4
    ----see VAR_0529372 mis40--------

    HapMap Linkage Disequilibrium report for PTCD1 (99014362 - 99063787 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for PTCD1:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2734882CNV Deletion23290073
    nsv5864CNV Insertion18451855
    dgv7397n71CNV Loss21882294
    dgv7396n71CNV Loss21882294
    nsv831069CNV Loss17160897

    Human Gene Mutation Database (HGMD): PTCD1
    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing PTCD1
    DNA2.0 Custom Variant and Variant Library Synthesis for PTCD1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 614774    OMIM disorders: --


    PTCD1 for disorders           About GeneDecksing

    Genetic Association Database (GAD): PTCD1

    Export disorders for PTCD1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for PTCD1 gene, integrated from 10 sources (see all 15):
    (articles sorted by number of sources associating them with PTCD1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Pentatricopeptide repeat domain protein 1 lowers the levels of mitochondrial leucine tRNAs in cells. (PubMed id 19651879)1, 2, 9 Rackham O....Filipovska A. (Nucleic Acids Res. 2009)
    2. RNA processing in human mitochondria. (PubMed id 21857155)1, 2 Sanchez M.I.... Filipovska A. (Cell Cycle 2011)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    4. The DNA sequence of human chromosome 7. (PubMed id 12853948)1, 2 Hillier L.W.... Wilson R.K. (Nature 2003)
    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. (PubMed id 9734811)1, 2 Ishikawa K.... Ohara O. (DNA Res. 1998)
    6. DBIRD complex integrates alternative mRNA splicing with RNA polymerase II transcript elongation. (PubMed id 22446626)1 Close P.... Svejstrup J.Q. (Nature 2012)
    7. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (Cell 2012)
    8. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)
    9. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (amp 2011)
    10. A functional peptidyl-tRNA hydrolase, ICT1, has been recruited into the human mitochondrial ribosome. (PubMed id 20186120)1 Richter R....Chrzanowska-Lightowlers Z.M. (EMBO J. 2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 26024 HGNC: 22198 AceView: PTCD1 Ensembl:ENSG00000106246 euGenes: HUgn26024
    ECgene: PTCD1 H-InvDB: PTCD1

    (According to HUGE)
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    HUGE: KIAA0632

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for PTCD1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for PTCD1 gene:
    Search GeneIP for patents involving PTCD1

    GeneCards and IP:
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    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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