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TMEM40 Gene

protein-coding   GIFtS: 41
GCID: GC03M012751

Transmembrane Protein 40

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(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
Transmembrane Protein 401 2

External Ids:    HGNC: 256201   Entrez Gene: 552872   Ensembl: ENSG000000887267   UniProtKB: Q8WWA13   

Export aliases for TMEM40 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 TMEM40 Gene:
TMEM40 (transmembrane protein 40) is a protein-coding gene.


(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_000003.11  NT_022517.19  NC_018914.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the TMEM40 gene promoter:
         Max1   AP-1   GCNF   ATF-2   NCX/Ncx   AP-4   CRE-BP1   GCNF-1   GCNF-2   c-Myc   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTMEM40 promoter sequence
   Search Chromatin IP Primers for TMEM40

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TMEM40


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

Entrez Gene cytogenetic band: 3p25.2   Ensembl cytogenetic band:  3p25.2   HGNC cytogenetic band: 3p25.2

TMEM40 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TMEM40 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03M012751:  view genomic region     (about GC identifiers)

Start:
12,775,024 bp from pter      End:
12,810,956 bp from pter
Size:
35,933 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, 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: TMM40_HUMAN, Q8WWA1 (See protein sequence)
Recommended Name: Transmembrane protein 40  
Size: 233 amino acids; 25495 Da
Secondary accessions: Q8NAL4 Q9NUZ4
Alternative splicing: 2 isoforms:  Q8WWA1-1   Q8WWA1-2   

Explore the universe of human proteins at neXtProt for TMEM40: NX_Q8WWA1

Explore proteomics data for TMEM40 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See TMEM40 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (4 alternative transcripts): 
    NP_001271335.1  NP_001271336.1  NP_001271337.1  NP_060776.2  

    ENSEMBL proteins: 
     ENSP00000322837   ENSP00000396895   ENSP00000405740   ENSP00000392140   ENSP00000264728  
     ENSP00000407396  

    TMEM40 Human Recombinant Protein Products:

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    antibodies-online kits for TMEM40 (4 products) 


    (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:
     IPR026181 TMEM40

    Graphical View of Domain Structure for InterPro Entry Q8WWA1

    ProtoNet protein and cluster: Q8WWA1


    Find genes that share domains with TMEM40           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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    Phenotypes:
         1 GenomeRNAi human phenotype for TMEM40:
     High actin ratio cells 

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for TMEM40

    miRNA
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    7 qRT-PCR Assays for microRNAs that regulate TMEM40:
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    SwitchGear 3'UTR luciferase reporter plasmidTMEM40 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat TMEM40

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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat TMEM40

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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
    TMM40_HUMAN, Q8WWA1: Membrane; Multi-pass membrane protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    peroxisome1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral component of membrane IEA--

    Find genes that share ontologies with TMEM40           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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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for TMEM40
    Interactions:

        Search GeneGlobe Interaction Network for TMEM40

    (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 TMEM40 (TMM40)



    (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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    REFSEQ mRNAs for TMEM40 gene (4 alternative transcripts): 
    NM_001284406.1  NM_001284407.1  NM_001284408.1  NM_018306.3  

    Unigene Cluster for TMEM40:

    Transmembrane protein 40
    Hs.475502  [show with all ESTs]
    Unigene Representative Sequence: NM_018306
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000314124(uc003bxg.1 uc003bxh.1 uc011auv.1) ENST00000435575
    ENST00000435218 ENST00000476331 ENST00000428020 ENST00000480698 ENST00000264728
    ENST00000485124 ENST00000431022
    miRNA
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    7 qRT-PCR Assays for microRNAs that regulate TMEM40:
    hsa-miR-661 hsa-miR-370 hsa-miR-3202 hsa-miR-1252 hsa-miR-323-5p hsa-miR-24 hsa-miR-548q
    SwitchGear 3'UTR luciferase reporter plasmidTMEM40 3' UTR sequence
    Inhib. RNA
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    Primer
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    OriGene qPCR primer pairs and template standards for TMEM40
    OriGene qSTAR qPCR primer pairs in human, mouse for TMEM40
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      QuantiTect SYBR Green Assays in human, mouse, rat TMEM40
      QuantiFast Probe-based Assays in human, mouse, rat TMEM40

    Additional mRNA sequence: 

    AK001898.1 AK092470.1 AK301984.1 BC020658.1 

    4 DOTS entries:

    DT.100021732  DT.208752  DT.91747776  DT.65286951 

    Selected AceView cDNA sequences (see all 65):

    BU680331 BF056052 AW135913 BC020658 CR621342 AI188578 BX458401 CR596715 
    BG319500 NM_018306 CR621156 AI651792 BX091636 CR619000 BM017019 CR609175 
    AK092470 AX747561 AI452552 BG677586 AI093911 AL554419 BX396431 BG675914 

    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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    TMEM40 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGGGCTCACA
    TMEM40 Expression
    About this image


    TMEM40 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 5) fully expand
     
     Hair (Integumentary System)
             Bulge Stem Cells Bulge
     
     Liver (Hepatobiliary System)
             Liver Lobule
     
     Blood (Cardiovascular System)
             Definitive Hematopoietic Stem Cells Definitive Yolk Sac
     
     Brain (Nervous System)
             Adult Oligodendrocyte Precursor Cells Lateral Ventricle
     
     Yolk Sac (Extraembryonic Tissues)
             Definitive Hematopoietic Stem Cells Definitive Yolk Sac
    TMEM40 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    TMEM40 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.475502
        Custom PCR Arrays for TMEM40
    Primer
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    OriGene qPCR primer pairs and template standards for TMEM40
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TMEM40

    (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 chordates.

    Orthologs for TMEM40 gene from Selected species (see all 7)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Tmem401 , 5 transmembrane protein 401, 5 80.42(n)1
    78.92(a)1
      6 (53.68 cM)5
    943461  NM_144805.21  NP_659054.21 
     1157291315 
    lizard
    (Anolis carolinensis)
    Reptilia TMEM406
    transmembrane protein 40
    43(a)
    1 ↔ 1
    2(160028094-160043517)


    ENSEMBL Gene Tree for TMEM40 (if available)
    TreeFam Gene Tree for TMEM40 (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 TMEM40 (see all 719)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs676982811,2
    C,F--12774921(+) AGAAAG/TAAAAT 1 -- ds50015Minor allele frequency- T:0.30WA CSA NA EA 362
    rs1157272921,2
    F--12774934(+) AATCAC/TAGCCA 1 -- ds50011Minor allele frequency- T:0.03WA 118
    rs76260481,2
    C,F,A,H--12775265(+) ttgctG/Aacagt 1 -- ds5001 ese312Minor allele frequency- A:0.12NS EA NA WA 1382
    rs1132316781,2
    C,F--12775268(+) CTGACG/AGTAGG 1 -- ds50011Minor allele frequency- A:0.50CSA 2
    rs3714168111,2
    C--12775399(+) TTTGT-/TTTTTTT 1 -- ut310--------
    rs46848731,2
    C,F,A,H--12775428(+) AGAAAG/CGATCT 1 -- ut3112Minor allele frequency- C:0.48NA WA CSA EA 260
    rs1384967071,2
    --12775565(+) TGTACC/TGCCAC 1 -- ut310--------
    rs1918550011,2
    --12775596(+) TTGTAA/GAGATG 1 -- ut310--------
    rs1829962971,2
    --12775634(+) TCTTGA/CACTCT 1 -- ut310--------
    rs1867214571,2
    C--12775693(+) AGTTGC/TGAGCC 1 -- ut310--------

    HapMap Linkage Disequilibrium report for TMEM40 (12775024 - 12810956 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10 variations for TMEM40:    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv850e199CNV Deletion23128226
    dgv810e201CNV Deletion23290073
    nsv821993CNV Loss20364138
    nsv460434CNV Loss19166990
    nsv470394CNV Gain18288195
    esv2751977CNV Gain17911159
    dgv597n27CNV Gain19166990
    nsv821994CNV Gain20364138
    nsv818127CNV Gain17921354
    nsv7351OTHER Inversion18451855

    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing TMEM40
    DNA2.0 Custom Variant and Variant Library Synthesis for TMEM40

    (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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      --

    (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 TMEM40 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with TMEM40)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. 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)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    3. Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. (PubMed id 12665801)1, 2 Gevaert K.... Vandekerckhove J. (Nat. Biotechnol. 2003)
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    5. Phosphorylation analysis of primary human T lymphocytes using sequential IMAC and titanium oxide enrichment. (PubMed id 19367720)2 Carrascal M.... Abian J. (J. Proteome Res. 2008)
    6. Comparative gene expression profiling of in vitro differentiated megakaryocytes and erythroblasts identifies novel activatory and inhibitory platelet membrane proteins. (PubMed id 17192395)1 Macaulay I.C....Ouwehand W.H. (Blood 2007)

    (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: 55287 HGNC: 25620 AceView: FLJ11036 Ensembl:ENSG00000088726 euGenes: HUgn55287
    ECgene: TMEM40 H-InvDB: TMEM40

    (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)
    About This Section

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    NameDescription
    PharmGKB entry for TMEM40 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 TMEM40 gene:
    Search GeneIP for patents involving TMEM40

    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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     Custom PCR Arrays for TMEM40 Search Chromatin IP Primers for TMEM40
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     Search Tocris compounds for TMEM40 (TMM40)
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     Search www.enzolifesciences.com for proteins, assays, substrates, inhibitors & antibodies

     Novus Tissue Slides
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     Browse compounds at ApexBio
     Search Addgene for plasmids for TMEM40
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      Search antibodies-online for proteins for TMEM40
           
    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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