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PTCHD4 Gene

protein-coding   GIFtS: 34
GCID: GC06M047845

Patched Domain Containing 4

(Previous name: chromosome 6 open reading frame 138)
(Previous symbol: C6orf138)
  Search for PTCHD4
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
Patched Domain Containing 41 2
C6orf1381 2 3
Chromosome 6 Open Reading Frame 1381
dJ402H5.22
Patched Domain-Containing Protein 42
Patched Domain-Containing Protein C6orf1382

External Ids:    HGNC: 213451   Entrez Gene: 4422132   Ensembl: ENSG000002446947   UniProtKB: Q6ZW053   

Export aliases for PTCHD4 gene to outside databases


(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 PTCHD4 Gene:
PTCHD4 (patched domain containing 4) is a protein-coding gene. GO annotations related to this gene include hedgehog receptor activity. An important paralog of this gene is PTCHD3.


(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_000006.12  NT_007592.16  NC_018917.2  
Regulatory elements:
   Search for regulatory transcription factor binding sites for PTCHD4
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for PTCHD4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PTCHD4


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

Entrez Gene cytogenetic band: 6p12.3   Ensembl cytogenetic band:  6p12.3   HGNC cytogenetic band: 6p12.3

PTCHD4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PTCHD4 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M047845:  view genomic region     (about GC identifiers)

Start:
47,845,764 bp from pter      End:
48,036,425 bp from pter
Size:
190,662 bases      Orientation:
minus strand

(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, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: PTHD4_HUMAN, Q6ZW05 (See protein sequence)
Recommended Name: Patched domain-containing protein 4  
Size: 846 amino acids; 96371 Da
Sequence caution: Sequence=BAC85703.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=BAC85703.1; Type=Frameshift; Positions=Several; Sequence=CAI20456.1; Type=Erroneous gene model
prediction; Sequence=EAX04325.1; Type=Erroneous gene model prediction;
Secondary accessions: B4DRK3 Q5T884

Explore the universe of human proteins at neXtProt for PTCHD4: NX_Q6ZW05

Explore proteomics data for PTCHD4 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn762
  • Modification sites at PhosphoSitePlus

  • See PTCHD4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001013754.3  NP_997382.2  

    ENSEMBL proteins: 
     ENSP00000341914   ENSP00000381722   ENSP00000439864  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    2 InterPro protein domains:
     IPR003392 Patched
     IPR000731 SSD

    Graphical View of Domain Structure for InterPro Entry Q6ZW05

    ProtoNet protein and cluster: Q6ZW05

    UniProtKB/Swiss-Prot: PTHD4_HUMAN, Q6ZW05
    Similarity: Belongs to the patched family
    Similarity: Contains 1 SSD (sterol-sensing) domain


    PTCHD4 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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         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
    GO:0008158hedgehog receptor activity IEA--
         
    PTCHD4 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for PTCHD4:
     Decreased POU5F1-GFP protein e 

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    (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
    PTHD4_HUMAN, Q6ZW05: Membrane; Multi-pass membrane protein (Potential)

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575cellular_component ND--
    GO:0016020membrane ----
    GO:0016021integral component of membrane IEA--

    PTCHD4 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 PTCHD4
    Interactions:

        Search GeneGlobe Interaction Network for PTCHD4

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008150biological_process ND--

    PTCHD4 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
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      Browse compounds at ApexBio 

    Browse Tocris compounds for PTCHD4 (PTHD4)



    (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,
    Conferences by KenesGroup, 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 PTCHD4 gene (2 alternative transcripts): 
    NM_001013732.3  NM_207499.2  

    Unigene Cluster for PTCHD4:

    Patched domain containing 4
    Hs.659409  [show with all ESTs]
    Unigene Representative Sequence: NM_207499
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000339488(uc011dwm.2 uc011dwn.2) ENST00000398738(uc003ozf.2)
    ENST00000543600
    miRNA
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    Additional mRNA sequence: 

    AK123835.1 AK299301.1 AK300335.1 BC136779.1 BC137359.1 BC137364.1 

    3 DOTS entries:

    DT.101958698  DT.121376511  DT.97765362 

    GeneLoc Exon Structure


    (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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    PTCHD4 expression in normal human tissues (normalized intensities)      PTCHD4 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ATTCTATATA
    PTCHD4 Expression
    About this image


    PTCHD4 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Neural Tube (Nervous System)    fully expand to see all 2 entries
             Metencephalon
     
     Brain (Nervous System)
             Medulla Oblongata
    PTCHD4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PTCHD4 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.659409
        Custom PCR Arrays for PTCHD4
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    In Situ
    Assay Products:
     

     
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    (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 PTCHD4 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ptchd41 , 5 RIKEN cDNA 3110082D06 gene5
    patched domain containing 41
    92.57(n)1
    96.2(a)1
      17 (19.65 cM)5
    6276261  NM_028474.11  NP_082750.11 
     423159475 
    chicken
    (Gallus gallus)
    Aves C3H6ORF1381 chromosome 3 open reading frame, human C6orf138 81.95(n)
    88.06(a)
      422064  NM_001195562.1  NP_001182491.1 
    lizard
    (Anolis carolinensis)
    Reptilia PTCHD46
    patched domain containing 4
    83(a)
    1 ↔ 1
    1(137944643-138052768)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia ptchd41 patched domain containing 4 74.57(n)
    79.3(a)
      100497488  XM_002935989.2  XP_002936035.2 
    zebrafish
    (Danio rerio)
    Actinopterygii ptchd41 patched domain containing 4 71.27(n)
    73.99(a)
      564097  NM_001030185.1  NP_001025356.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Ptr6
    Patched-related
    17(a)
    1 → many
    2R(2069253-2083867)
    worm
    (Caenorhabditis elegans)
    Secernentea ptr-106
    ptr-26
    (see all 23)
    Protein PTR-2 (ptr-2) mRNA, complete cds
    (see all 23)
    21(a)
    21(a)
    (see all 23)
    many ↔ many
    many ↔ many
    (see all 23)
    I(5662143-5667144) WBGene00004224
    I(3789306-3792797) WBGene00004217


    ENSEMBL Gene Tree for PTCHD4 (if available)
    TreeFam Gene Tree for PTCHD4 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PTCHD4 gene
    PTCHD32  PTCHD12  
    2 SIMAP similar genes for PTCHD4 using alignment to 3 protein entries:     PTHD4_HUMAN (see all proteins):
    C6orf138    PTCHD1

    PTCHD4 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for PTCHD4
    PGOHUM00000243182


    (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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    Selected SNPs for PTCHD4 (see all 4049)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1431143831,2
    --47845559(+) GAAGTC/TCTTTG 1 -- ds50010--------
    rs18878981,2
    C,H--47845646(+) AAAGTG/ACCATG 1 -- ds500112Minor allele frequency- A:0.00NA WA CSA EA 375
    rs1466687191,2
    C--47845776(+) TTGATG/TCATCC 1 -- ut310--------
    rs1907491831,2
    --47845808(+) ATTACA/CTCCAG 1 -- ut310--------
    rs18878991,2
    C,F,O,A,H--47845813(+) ATCCAT/GAAACT 1 -- ut3127Minor allele frequency- G:0.35MN NS EA NA WA CSA 2674
    rs759821691,2
    C,F--47845839(+) ACAAGG/TTTGCA 1 -- ut311Minor allele frequency- T:0.03WA 118
    rs1508843091,2
    C--47845850(+) ATAAC-/TTTTTT 1 -- ut310--------
    rs1391652311,2
    C--47845889(+) AGAAGA/CAGGCA 1 -- ut310--------
    rs1820375701,2
    --47845897(+) GCACCC/TTGAAG 1 -- ut310--------
    rs571200461,2
    C--47846009(+) CTGGAA/GAAGAA 1 -- ut314Minor allele frequency- G:0.07WA NA EA 360

    HapMap Linkage Disequilibrium report for PTCHD4 (47845764 - 48036425 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for PTCHD4: --
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing PTCHD4
    DNA2.0 Custom Variant and Variant Library Synthesis for PTCHD4

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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      --

    (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 PTCHD4 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with PTCHD4)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    2. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1 Bailey S.D....Anand S. (Diabetes Care 2010)
    3. Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip. (PubMed id 19913121)1 Talmud P.J.... . (Am. J. Hum. Genet. 2009)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)
    5. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)2 Mungall A.J.... Beck S. (Nature 2003)
    6. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    7. The sequence of the human genome. (PubMed id 11181995)1 Venter J.C.... Zhu X. (Science 2001)

    (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: 442213 HGNC: 21345 Ensembl:ENSG00000244694 euGenes: HUgn442213 ECgene: PTCHD4
    H-InvDB: PTCHD4

    (According to HUGE)
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      --

    (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 PTCHD4 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 PTCHD4 gene:
    Search GeneIP for patents involving PTCHD4

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (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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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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