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TDH Gene

pseudogene   GIFtS: 39
GCID: GC08P011198

L-Threonine Dehydrogenase (Pseudogene)

(Previous name: L-threonine dehydrogenase)
  See 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
L-Threonine Dehydrogenase (Pseudogene)1 2
L-Threonine Dehydrogenase1
Member 1 (Pseudogene)1
Short Chain Dehydrogenase/Reductase Family 14E1
SDR14E1P2

External Ids:    HGNC: 155471   Entrez Gene: 1577392   Ensembl: ENSG000001543167   OMIM: 6151745   UniProtKB: Q8IZJ63   

Export aliases for TDH gene to outside databases

Previous GC identifers: GC00U990976 GC08P011076 GC08P011242 GC08P011234 GC08P010127


(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 TDH Gene:
This gene appears to be an evolving pseudogene of L-threonine 3-dehydrogenase (TDH). In both prokaryotes and
eukaryotes, TDH catalyzes the first of two steps in one of two L-threonine degradation pathways. However, in
human, the single gene with sequence similarity to TDH is not capable of encoding a functional TDH protein; the
predicted protein lacks most of the C-terminus and parts of the NAD+ binding motif when compared to other
species' TDH proteins. This suggests that the human gene is therefore a pseudogene. Transcripts of this gene are
found in all tissues and alternatively spliced transcripts have been described. It is not known if these
transcripts are translated, or if the possible protein product provides any functional role. (provided by RefSeq,
Jul 2008)

GeneCards Summary for TDH Gene:
TDH (L-threonine dehydrogenase (pseudogene)) is a pseudogene. Diseases associated with TDH include acalculous cholecystitis, and keratolytic winter erythema. GO annotations related to this gene include coenzyme binding.




(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_000008.11  NC_018919.2  NT_077531.5  
Regulatory elements:
   Regulatory transcription factor binding sites in the TDH gene promoter:
         GR   C/EBPbeta   AML1a   p53   Ik-3   GATA-1   E47   Hand1   GR-alpha   Pax-4a   
         Other transcription factors

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

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


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

Entrez Gene cytogenetic band: 8p23.1   Ensembl cytogenetic band:  8p23.1   HGNC cytogenetic band: 8p23.1

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

GeneLoc information about chromosome 8         GeneLoc Exon Structure

GeneLoc location for GC08P011198:  view genomic region     (about GC identifiers)

Start:
11,197,146 bp from pter      End:
11,225,961 bp from pter
Size:
28,816 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for TDH

(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: TDH_HUMAN, Q8IZJ6 (See protein sequence)
Recommended Name: Inactive L-threonine 3-dehydrogenase, mitochondrial precursor  
Size: 230 amino acids; 25407 Da
Caution: According to PubMed:12361482, the human TDH gene is an expressed pseudogene encoding non-functional
truncated proteins that are unable to make appropriate contacts with the substrates, L-threonine and NAD(+).
Although all exons expected to encode a functional L-threonine 3-dehydrogenase of 369 residues are present in the
human genome, all transcripts described encode truncated proteins that result from mutations within the gene
causing the loss of acceptor splice site preceding exon 4 and exon 6
Secondary accessions: Q8IZJ5 Q96LV6
Alternative splicing: 3 isoforms:  Q8IZJ6-1   Q8IZJ6-2   Q8IZJ6-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for TDH: NX_Q8IZJ6

Explore proteomics data for TDH at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

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


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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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    HGNC Gene Families:
    SDRE: Short chain dehydrogenase/reductase superfamily / Extended SDR fold

    2 InterPro protein domains:
     IPR001509 Epimerase_deHydtase
     IPR016040 NAD(P)-bd_dom

    Graphical View of Domain Structure for InterPro Entry Q8IZJ6

    ProtoNet protein and cluster: Q8IZJ6

    UniProtKB/Swiss-Prot: TDH_HUMAN, Q8IZJ6
    Similarity: Belongs to the NAD(P)-dependent epimerase/dehydratase family


    TDH 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:0003824catalytic activity IEA--
    GO:0050662coenzyme binding IEA--
         
    TDH for ontologies           About GeneDecksing


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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
    TDH_HUMAN, Q8IZJ6: Mitochondrion (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol2
    mitochondrion2
    nucleus2
    golgi apparatus1
    peroxisome1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005739mitochondrion IEA--

    TDH 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 TDH
    Interactions:

        Search GeneGlobe Interaction Network for TDH

    1 Interacting protein for TDH (Q8IZJ63) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ADD1P356113I2D: score=4 
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0044237cellular metabolic process IEA--

    TDH 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 TDH

    2 HMDB Compounds for TDH    About this table
    CompoundSynonyms CAS #PubMed Ids
    2-Hydroxybutyric acid(RS)-2-Hydroxybutyrate (see all 29)600-15-711731084
    NAD3-Carbamoyl-1-D-ribofuranosylpyridinium hydroxide 5'-ester with adenosine 5'-pyrophosphate (see all 28)53-84-9--

    4 Novoseek inferred chemical compound relationships for TDH gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    2-amino-3-ketobutyrate 92.6 1 8439306 (1)
    threonine 36 9 12867457 (4), 12361482 (2), 10476630 (1), 8439306 (1)
    nadh 23.8 1 12361482 (1)
    oligonucleotide 20 2 8126441 (1), 10379807 (1)



    TDH for compounds           About GeneDecksing



    (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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    Unigene Cluster for TDH:

    L-threonine dehydrogenase
    Hs.583896  [show with all ESTs]
    Unigene Representative Sequence: AK057762
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000525246(uc003wtt.1 uc003wtq.1) ENST00000534302(uc003wts.1)
    ENST00000531764 ENST00000525664 ENST00000326605
    miRNA
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    Additional mRNA sequence: 

    AJ301562.1 AJ301563.1 AK057762.1 AY101186.1 AY101187.1 BC074983.2 BC080558.1 NR_001578.1 
    NR_026814.1 

    7 DOTS entries:

    DT.97841330  DT.70104426  DT.95103741  DT.91750010  DT.100019866  DT.95265121  DT.99948767 

    Selected AceView cDNA sequences (see all 43):

    BQ055552 BQ059744 NR_001578 BQ063907 BQ063270 AI474649 BQ056232 AY101186 
    AJ301563 BQ642283 BQ062075 AJ301562 NM_054017 BQ057711 BQ056212 BC074983 
    BQ642778 BX091784 AW193679 BE514180 BM051842 BI226083 AK057762 BF953738 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for TDH    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b · 12c ^ 13
    SP1:        -     -                                         -     -                       -         
    SP2:                                            -           -     -                                 
    SP3:                                            -                 -                                 
    SP4:                                                                                                


    ECgene alternative splicing isoforms for TDH

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


    TDH expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 6) fully expand
     
     Epithelial Cells
             Fetal Matrix Cells Hair Follicle
     
     Hypoblast (Extraembryonic Tissues)
             Visceral Endoderm Cells Visceral Endoderm
     
     Hair (Integumentary System)
             Fetal Matrix Cells Hair Follicle
     
     Inner Cell Mass (Early Embryonic Tissues)
             Blimp1- mVenus and stella-ECFP genetically modified stem cells
     
     Yolk Sac (Extraembryonic Tissues)
             Visceral Endoderm Cells Visceral Endoderm
    TDH Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    TDH Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.583896

    UniProtKB/Swiss-Prot: TDH_HUMAN, Q8IZJ6
    Tissue specificity: Expressed in all tissues examined. Detected in most cell types examined, but not observed in
    endothelial cells, glioma cell lines and some leukemia cell lines

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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 human and mouse.

    Orthologs for TDH gene from 1 species (see representative species )    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Tdh5 L-threonine dehydrogenase   --   14 (33.31 cM) 63492347 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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      --

    (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 TDH (see all 664)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 8 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1489599481,2
    --11195177(+) AAGTAA/GACTCG 1 -- us2k10--------
    rs1437503331,2
    --11195248(+) ATTTGA/CCATAT 1 -- us2k10--------
    rs117863131,2
    C,F,H--11195250(+) ttgccA/Gtatct 1 -- us2k16Minor allele frequency- G:0.01NS EA NA 424
    rs1908237071,2
    --11195409(+) ACTGCC/GACCAC 1 -- us2k10--------
    rs1477261331,2
    --11195504(+) AGCAGC/TTTCAG 1 -- us2k10--------
    rs1818482661,2
    --11195601(+) AGGAGC/TAATGA 1 -- us2k10--------
    rs1426202711,2
    --11195605(+) GCAATA/GATTTG 1 -- us2k10--------
    rs9566631,2
    H--11195632(-) AAATTC/TTGAGT 1 -- us2k16Minor allele frequency- T:0.00EA NS 600
    rs9566621,2
    C,F,O,A--11195641(-) CAGGAC/TGCTAA 1 -- us2k19Minor allele frequency- T:0.07NA EA 695
    rs1859989311,2
    --11195690(+) TCTTTA/GGTAAA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for TDH (11197146 - 11225961 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 8 variations for TDH:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2658364CNV Deletion23128226
    esv2661653CNV Deletion23128226
    esv273248CNV Insertion20981092
    esv269551CNV Insertion20981092
    dgv7703n71CNV Loss21882294
    esv34097CNV Loss18971310
    nsv831233CNV Gain17160897
    nsv890354CNV Gain21882294

    Site Specific Mutation Identification with PCR Assays
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    (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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    OMIM gene information: 615174    OMIM disorders: --

    10 diseases for TDH:    
    About MalaCards
    acalculous cholecystitis    keratolytic winter erythema    gastroenteritis    cholecystitis
    congenital diaphragmatic hernia    diarrhea    cholera    endotheliitis
    breast cancer    leukemia

    1 disease from the University of Copenhagen DISEASES database for TDH:
    Acalculous cholecystitis

    TDH for disorders           About GeneDecksing

    2 Novoseek inferred disease relationships for TDH gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    gastroenteritis 59.8 1 8126441 (1)
    poisoning 25.2 3 15182493 (2), 8593076 (1)


    Export disorders for TDH 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 TDH gene, integrated from 10 sources (see all 42):
    (articles sorted by number of sources associating them with TDH)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The human L-threonine 3-dehydrogenase gene is an expressed pseudogene. (PubMed id 12361482)1, 2, 3, 9 Edgar A.J. (BMC Genet. 2002)
    2. The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative. (PubMed id 19027726)1, 3 Persson B.... Oppermann U. (Chem. Biol. Interact. 2009)
    3. Physical and transcriptional map of the critical region for keratolytic winter erythema (KWE) on chromosome 8p22-p23 between D8S550 and D8S1759. (PubMed id 11896452)1, 3 Appel S.... Rosenthal A. (Eur. J. Hum. Genet. 2002)
    4. DNA sequence and analysis of human chromosome 8. (PubMed id 16421571)2 Nusbaum C....Lander E.S. (Nature 2006)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)
    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. Inhibition and regulation of rat liver L-threonine dehydrogenase by different fatty acids and their derivatives. (PubMed id 11731084)6 Guerranti R....Marinello E. (Biochim. Biophys. Acta 2001)
    8. Interaction between L-threonine dehydrogenase and aminoacetone synthetase and mechanism of aminoacetone production. (PubMed id 3536927)1 Tressel T....Davis L. (J. Biol. Chem. 1986)
    9. The thermostable direct hemolysin gene (tdh) of Vibrio hollisae is dissimilar in prevalence to and phylogenetically distant from the tdh genes of other vibrios: implications in the horizontal transfer of the tdh gene. (PubMed id 8871530)9 Nishibuchi M....Ezaki T. (Microbiol. Immunol. 1996)
    10. Detection of a functional insertion sequence responsible for deletion of the thermostable direct hemolysin gene (tdh) in Vibrio parahaemolyticus. (PubMed id 18598741)9 Kamruzzaman M....Nishibuchi M. (Gene 2008)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 157739 HGNC: 15547 AceView: C8orf12 Ensembl:ENSG00000154316 euGenes: HUgn157739
    ECgene: TDH H-InvDB: TDH

    (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 TDH 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 TDH gene:
    Search GeneIP for patents involving TDH

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



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