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TDGF1P3 Gene

pseudogene   GIFtS: 29
GCID: GC0XP109765

Teratocarcinoma-Derived Growth Factor 1 Pseudogene 3

(Previous names: teratocarcinoma-derived growth factor 3, pseudogene)
(Previous symbol: TDGF3)
  See TDGF1P3-related diseases
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
Teratocarcinoma-Derived Growth Factor 1 Pseudogene 31 2 3     CRIPTO2
TDGF31 2 3     CRIPTO-32
CRIPTO32 3     TDGF12
TDGF22 3     Cripto-3 Growth Factor3
Teratocarcinoma-Derived Growth Factor 3, Pseudogene1     Epidermal Growth Factor-Like Cripto Protein CR33
CR-32     

External Ids:    HGNC: 117031   Entrez Gene: 69982   Ensembl: ENSG000002253667   UniProtKB: P518643   

Export aliases for TDGF1P3 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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Entrez Gene summary for TDGF1P3 Gene:
The TDGF3 locus has characteristics of a retrotransposon, including lack of introns and a poly(A) sequence.
(provided by RefSeq, Jul 2008)

GeneCards Summary for TDGF1P3 Gene:
TDGF1P3 (teratocarcinoma-derived growth factor 1 pseudogene 3) is a pseudogene. Diseases associated with TDGF1P3 include teratocarcinoma, and endometrial carcinoma. GO annotations related to this gene include growth factor activity.

UniProtKB/Swiss-Prot: TDGF3_HUMAN, P51864
Function: Could play a role in the determination of the epiblastic cells that subsequently give rise to the
mesoderm. Activates the Nodal-dependent signaling pathway




(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 at NCBI GenBank:
NC_000023.10  NC_018934.2  NT_011651.18  
Regulatory elements:
   Search for regulatory transcription factor binding sites for TDGF1P3
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTDGF1P3 promoter sequence
   Search Chromatin IP Primers for TDGF1P3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TDGF1P3


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

Entrez Gene cytogenetic band: Xq22.3   Ensembl cytogenetic band:  Xq23   HGNC cytogenetic band: Xq23

TDGF1P3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TDGF1P3 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XP109765:  view genomic region     (about GC identifiers)

Start:
109,763,540 bp from pter      End:
109,766,249 bp from pter
Size:
2,710 bases      Orientation:
plus 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: TDGF3_HUMAN, P51864 (See protein sequence)
Recommended Name: Putative teratocarcinoma-derived growth factor 3  
Size: 188 amino acids; 21181 Da
Caution: Could be the product of a pseudogene. The TDGF3 locus has characteristics of a retrotransposon, including
lack of introns and a poly(A) sequence

Explore the universe of human proteins at neXtProt for TDGF1P3: NX_P51864

Post-translational modifications: 

  • Glycosylation2 at Asn79

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    antibodies-online proteins for TDGF1P3 (23 products) 

     
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    antibodies-online antibodies for TDGF1P3 (102 products) 

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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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    3 InterPro protein domains:
     IPR019011 Cryptic/Cripto_CFC-dom
     IPR013032 EGF-like_CS
     IPR017047 Cripto_growth_factor

    Graphical View of Domain Structure for InterPro Entry P51864

    ProtoNet protein and cluster: P51864

    UniProtKB/Swiss-Prot: TDGF3_HUMAN, P51864
    Similarity: Contains 1 EGF-like domain


    Find genes that share domains with TDGF1P3           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: TDGF3_HUMAN, P51864
    Function: Could play a role in the determination of the epiblastic cells that subsequently give rise to the
    mesoderm. Activates the Nodal-dependent signaling pathway

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008083growth factor activity NAS1882841
         
    Find genes that share ontologies with TDGF1P3           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for TDGF1P3

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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
    TDGF3_HUMAN, P51864: Cell membrane

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane IEA--
    GO:0009279cell outer membrane IDA18835250

    Find genes that share ontologies with TDGF1P3           About GenesLikeMe


    (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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    Selected Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for TDGF1P3 (see all 56)
        Nuclear Receptor Activation by Vitamin-A
    Paxillin Interactions
    Telomerase Components in Cell Signaling
    Mitochondrial Apoptosis
    Molecular Mechanisms of Cancer


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    Interactions:

        Search GeneGlobe Interaction Network for TDGF1P3

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007165signal transduction IDA18835250

    Find genes that share ontologies with TDGF1P3           About GenesLikeMe



    (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 TDGF1P3 (TDGF3)

    2 Novoseek inferred chemical compound relationships for TDGF1P3 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    retinoic acid 15.4 6 8635871 (2), 9285688 (2)
    agar 14.2 4 8635871 (2), 8302592 (1)



    Find genes that share compounds with TDGF1P3           About GenesLikeMe



    (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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    Unigene Cluster for TDGF1P3:

    Teratocarcinoma-derived growth factor 1 pseudogene 3
    Hs.592361  [show with all ESTs]
    Unigene Representative Sequence: NR_002718
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000602699 ENST00000493351(uc004eos.1)
    miRNA
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    Additional mRNA sequence: 

    M96956.1 NR_002718.2 

    5 DOTS entries:

    DT.100725583  DT.213859  DT.102830280  DT.120853654  DT.120853660 

    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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    TDGF1P3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTCTTCAGAA
    TDGF1P3 Expression
    About this image


    TDGF1P3 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Inner Cell Mass (Early Embryonic Tissues)    fully expand to see all 2 entries
             Human embryonic stem cells (family)
    TDGF1P3 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

    SOURCE GeneReport for Unigene cluster: Hs.592361

    UniProtKB/Swiss-Prot: TDGF3_HUMAN, P51864
    Tissue specificity: Expressed weakly in lung, colon and breast. Expressed also strongly in primary cancer tissues;
    lung and colon cancers

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TDGF1P3

    (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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    ENSEMBL Gene Tree for TDGF1P3 (if available)
    TreeFam Gene Tree for TDGF1P3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for TDGF1P3 gene
    1 SIMAP similar gene for TDGF1P3 using alignment to 1 protein entry:     TDGF3_HUMAN:
    TDGF1

    Find genes that share paralogs with TDGF1P3           About GenesLikeMe



    (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 TDGF1P3 (see all 69)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs59429521,2
    C,F,A,H--109761594(+) ATGAGT/AAAACA 1 -- us2k16Minor allele frequency- A:0.17WA NA CSA 12
    rs600148241,2
    C--109761683(+) TCTCCA/CGTTCA 1 -- us2k10--------
    rs1814179901,2
    --109761768(+) ATGGCA/GGGCAC 1 -- us2k10--------
    rs1852702151,2
    --109761782(+) CACCAC/GAGAGA 1 -- us2k10--------
    rs59429531,2
    C,F,A,H--109761850(+) AAATCA/CCAGTC 1 -- us2k124Minor allele frequency- C:0.41NS EA NA WA CSA 2307
    rs1884095421,2
    --109761900(+) ACATGC/TGAACA 1 -- us2k10--------
    rs1818670891,2
    --109762181(+) CTTGTG/TTGCGT 1 -- us2k10--------
    rs1468173931,2
    --109762326(+) GCTAAA/GTGCTA 1 -- us2k10--------
    rs1870854761,2
    --109762544(+) ATCAGC/TATAAA 1 -- us2k10--------
    rs1489703401,2
    --109762551(+) TAAATG/TAATCA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for TDGF1P3 (109763540 - 109766249 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for TDGF1P3: --
    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing TDGF1P3
    DNA2.0 Custom Variant and Variant Library Synthesis for TDGF1P3

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    5 diseases for TDGF1P3:    
    About MalaCards
    teratocarcinoma    endometrial carcinoma    bladder carcinoma    germ cell tumors
    colon cancer


    Find genes that share disorders with TDGF1P3           About GenesLikeMe

    Selected Novoseek inferred disease relationships for TDGF1P3 gene (see all 16)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    teratocarcinoma 64.5 3 9285688 (1), 8661720 (1), 10393436 (1)
    colorectal carcinoma 52.2 5 1938601 (3), 8669884 (1), 1715580 (1)
    colon carcinoma 50.1 4 8302592 (1), 9466051 (1)
    carcinoma embryonal 46.1 9 9285688 (4), 8635871 (3)
    colorectal tumors 45.3 1 8302592 (1)
    bladder carcinoma 41.1 1 8976875 (1)
    colon cancer 41.1 9 8302592 (2), 10024674 (1), 1715580 (1)
    carcinoma 36.9 4 8976875 (1), 9641241 (1), 7814196 (1), 1938601 (1)
    endometrial carcinoma 33.6 2 9641241 (2)
    adenoma 26.5 1 8976875 (1)


    Export disorders for TDGF1P3 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 TDGF1P3 gene, integrated from 10 sources (see all 35):
    (articles sorted by number of sources associating them with TDGF1P3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Isolation and characterization of the CRIPTO autosomal gene and its X-linked related sequence. (PubMed id 1882841)1, 2, 3 Dono R....Persico M.G. (Am. J. Hum. Genet. 1991)
    2. CRIPTO3, a presumed pseudogene, is expressed in cancer. (PubMed id 18835250)1, 2, 9 Sun C.... Carulli J.P. (Biochem. Biophys. Res. Commun. 2008)
    3. The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (Nature 2005)
    4. Germ cell nuclear factor is a repressor of CRIPTO-1 and CRIPTO-3. (PubMed id 16954206)1 Hentschke M....HA1bner C.A. (J. Biol. Chem. 2006)
    5. Transfection with a CRIPTO anti-sense plasmid suppresses endogenous CRIPTO expression and inhibits transformation in a human embryonal carcinoma cell line. (PubMed id 8635871)9 Baldassarre G....Ciardiello F. (Int. J. Cancer 1996)
    6. Expression of teratocarcinoma-derived growth factor-1 (TDGF-1) in testis germ cell tumors and its effects on growth and differentiation of embryonal carcinoma cell line NTERA2/D1. (PubMed id 9285688)9 Baldassarre G....Viglietto G. (Oncogene 1997)
    7. TDGF1 is a novel predictive marker for metachronous metastasis of colorectal cancer. (PubMed id 20126975)9 Miyoshi N....Mori M. (Int. J. Oncol. 2010)
    8. Cripto, a member of the epidermal growth factor family, is over-expressed in human pancreatic cancer and chronic pancreatitis. (PubMed id 8314343)9 Friess H....Korc M. (Int. J. Cancer 1994)
    9. Inhibition of CRIPTO expression and tumorigenicity in human colon cancer cells by antisense RNA and oligodeoxynucleotides. (PubMed id 8302592)9 Ciardiello F....Persico M.G. (Oncogene 1994)
    10. (PubMed id 17490101)9 

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    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: 6998 HGNC: 11703 Ensembl:ENSG00000225366 euGenes: HUgn6998 ECgene: TDGF1P3
    H-InvDB: TDGF1P3

    (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 TDGF1P3 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 TDGF1P3 gene:
    Search GeneIP for patents involving TDGF1P3

    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, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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 genOway)
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