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TMEM42 Gene

protein-coding   GIFtS: 41

GC03P044879
transmembrane protein 42
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
Products    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section

Aliases & Descriptions
transmembrane protein 421 2
MGC299561 2

External Ids:    HGNC: 284441   Entrez Gene: 1316162   Ensembl: ENSG000001699647   UniProtKB: Q69YG03   

Export aliases for TMEM42 gene to outside databases


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

  --

(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 60), Regulatory elements and Epigenetics data according to Qiagen and/or SABiosciences)
About This Section

Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the TMEM42 gene promoter:
         CUTL1   Arnt   AhR   YY1   CHOP-10   C/EBPalpha   FOXO3a   FOXO3b   AREB6   SRF   
         Other transcription factors

   Search SABiosciences Chromatin IP Primers for TMEM42

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays for TMEM42 


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

Entrez Gene cytogenetic band: 3p21.31   Ensembl cytogenetic band:  3p21.31   HGNC cytogenetic band: 3p21.31

TMEM42 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TMEM42 gene location

GeneLoc gene densities for chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03P044879:  view genomic region     (about GC identifiers)

Start:
44,903,361 bp from pter
End:
44,907,162 bp from pter
Size:
3,802 bases
Orientation:
plus strand
RefSeq DNA sequence:
NC_000003.11  NT_022517.18  

(According to 1UniProtKB, neXtProt, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Millipore, Sigma-Aldrich, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, and/or ProSpec,
Biochemical Assays by Millipore, Sigma-Aldrich, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Dec 2010 and Entrez Gene, Antibodies by Millipore, Sigma-Aldrich, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, and/or Epitomics)
About This Section

UniProtKB/Swiss-Prot: TMM42_HUMAN, Q69YG0 (See protein sequence)
Recommended Name: Transmembrane protein 42  
Size: 159 amino acids; 16991 Da
Subcellular location: Membrane; Multi-pass membrane protein (Potential)
Secondary accessions: Q8WUQ6

Explore the universe of human proteins at neXtProt for TMEM42: NX_Q69YG0 

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins: NP_653239.1  

    ENSEMBL proteins: 
    ENSP00000306564 


    Human Recombinant Proteins 
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    2 Gene Ontology (GO) cellular component terms (GO ID links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016020 membrane IEA--
    GO:0016021 integral to membrane IEA--
    About this table

    TMEM42 for ontologies           About GeneDecksing



    Antibodies for TMEM42: 
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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    ProtoNet protein and cluster: Q69YG0


    (According to UniProtKB, IUBMB,and/or Genatlas, Animal models from MGI Dec 24 2010,
    shRNA from OriGene, Sigma-Aldrich, RNAi from Millipore, siRNAs from Sigma-Aldrich, OriGene, Qiagen, Super-pooled esiRNAs from Sigma-Aldrich, microRNA from Sigma-Aldrich, Qiagen, SABiosciences, Clones from Millipore, Sigma-Aldrich, OriGene, GenScript, Sino Biological, Cell Lines from GenScript, Ontologies according to Gene Ontology Consortium 01 Dec 2010 via Entrez Gene.)
    About This Section

    Inhib.
    RNA:
        
    Browse for Gene Knock-down Tools from Millipore
    Browse Nano Scale siRNA at Sigma-Aldrich
    Sigma-Aldrich esiRNA and siRNA for TMEM42
    Sigma-Aldrich shRNA for TMEM42
    OriGene 29mer shRNA kits in GFP-retroviral vector: TMEM42
    OriGene shRNA RFP: TMEM42
    OriGene basic RS shRNA: TMEM42
    OriGene siRNA: TMEM42
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing of TMEM42 
    miRNA:Browse microRNA Mimics at Sigma-Aldrich
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of TMEM42 
    Search SABiosciences for Assays for microRNAs that regulate TMEM42

    Gene
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    Clones:Browse Clones for the Expression of Recombinant Proteins Available from Millipore
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    OriGene GFP tagged cDNA clones in CMV expression vector: TMEM42
    OriGene Myc/DDK tagged cDNA clones in CMV expression vector: TMEM42
    OriGene untagged cDNA clones in CMV expression vector: TMEM42
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    Cell
    Lines:
      
    GenScript Custom overexpressing Cell Line Services for TMEM42 


    (Pathways according to Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB, Sets of similar genes according to GeneDecks, PCR Arrays from SABiosciences, Proteins Network according to SABiosciences, Sigma-Aldrich, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Dec 2010 via Entrez Gene).
    About This Section

        SABiosciences Custom Pathway-Focused PCR Arrays for TMEM42 

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for TMEM42

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
    About This Section
    Browse Small Molecules at Sigma-Aldrich
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for TMEM42


    (GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 228 Homo sapiens; Dec 8 2010) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    non coding RNAs according to RNAdb,
    ESTs according to GeneTide,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from Millipore,
    siRNAs from Sigma-Aldrich, OriGene, Qiagen, Super-pooled esiRNAs from Sigma-Aldrich,
    shRNA from Sigma-Aldrich, OriGene, microRNA from Sigma-Aldrich, Qiagen, SABiosciences,
    Tagged/untagged cDNA clones from OriGene, Sigma-Aldrich, GenScript, Primers from OriGene and/or SABiosciences)
    About This Section

    Inhib.
    RNA:
         
    Browse for Gene Knock-down Tools from Millipore
    Browse Nano Scale siRNA at Sigma-Aldrich
    Sigma-Aldrich esiRNA and siRNA for TMEM42
    Sigma-Aldrich shRNA for TMEM42
    OriGene 29mer shRNA kits in GFP-retroviral vector: TMEM42
    OriGene shRNA RFP: TMEM42
    OriGene basic RS shRNA: TMEM42
    OriGene siRNA: TMEM42
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing of TMEM42 
    miRNA: Browse microRNA Mimics at Sigma-Aldrich
    Browse microRNA target validation systems at Sigma-Aldrich 
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of TMEM42 
    Search SABiosciences for Assays for microRNAs that regulate TMEM42
    Clones: Browse FLAG tag genes at Sigma-Aldrich
    OriGene GFP tagged cDNA clones in CMV expression vector: TMEM42
    OriGene Myc/DDK tagged cDNA clones in CMV expression vector: TMEM42
    OriGene untagged cDNA clones in CMV expression vector: TMEM42
    Browse 3'-UTR reporter clones for miRNA target validation 
    Browse OriGene MicroRNA Expression Plasmids 
    GenScript cDNA clone with any tag delivered in your preferred vector: TMEM42 
    Primers: OriGene genome-wide validated SYBR primer pairs: TMEM42
    Browse OriGene validated miRNA SYBR primer pairs 
    SABiosciences RT2 qPCR Primer Assay for TMEM42: PPH20125A

    REFSEQ mRNAs for TMEM42 gene: 

    NM_144638.1  

    Additional cDNA sequence: 

    AL834253.1 BC019851.1 CR591568.1 

    7 DOTS entries:

    DT.112950  DT.40111109  DT.97835089  DT.75137307  DT.40268235  DT.97765374  DT.97834951 

    24/85 AceView cDNA sequences (see all 85):

    AA947704 CD672509 BQ954252 BU856841 AA479205 CD672510 AI143662 BI962665 
    AW341950 CR591568 BI789091 BI962542 AA831324 AL834253 AI027205 AA192851 
    AA588165 C00919 BI789184 BE887409 BM012533 BM680622 AI198422 AA192231 

    highest scoring ESTs for TMEM42:

    AA478664 AA001650 AA192231 AA192851 AA394034 AA479205 AA588165 AA745123 AA873426 AA947704 

    Unigene Cluster for TMEM42:

    Transmembrane protein 42
    Hs.646856  [show with all ESTs]
    Unigene Representative Sequence: AL834253


    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for TMEM42

    ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4a · 4b · 4c · 4d · 4e
    SP1:                    -                                             
    SP2:                                                                  
    SP3:                                                                  
    SP4:                          -                                       
    SP5:                    -     -                                       

    About this scheme

    ECgene alternative splicing isoforms for TMEM42
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000302392(uc003cnz.2) ENST00000477126

    (Experimental results according to 1GeneNote and GNF BioGPS,
    probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 228 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
    Primers from OriGene and/or SABiosciences )
    About This Section

    TMEM42 expression in normal and diseased human tissues

    1  / 2  / 3

    3 probe-sets matching TMEM42 gene

    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
    44562_at2, 3 U95-B 1 0.75 1.00 1.00 1.00 AA478664 1.00 1.00 1.00 1
    226361_at2, 3 U133-B 1 0.55 1.00 -- -- BF056095 0.80 1.00 0.91 1
    226361_at2 U133Plus2 1 0.55 1.00 -- -- -- -- -- -- --
    About this table

    TMEM42 for expression           About GeneDecksing

    Data from Genenote  (Publications) and GNF BioGPS
        About these images
    TMEM42 gene expression
    TMEM42 gene electronic northern expression
    TMEM42 gene sage expression
    About these images

    CGAP SAGE TAG: CTTATGTATT

    SOURCE GeneReport for Unigene cluster: Hs.646856
    Primers: OriGene genome-wide validated SYBR primer pairs: TMEM42
    Browse OriGene validated miRNA SYBR primer pairs 
    SABiosciences RT2 qPCR Primer Assay for TMEM42: PPH20125A
        SABiosciences Custom PCR Arrays for TMEM42 


    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Dec 24 2010, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
    About This Section

    Orthologs for TMEM42 gene from 5 species
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    TMEM421   -- transmembrane protein 42 88.68(n)
    86.16(a)
    609611  XM_846899.1  XP_851992.1 
    chimpanzee
    (Pan troglodytes)
    TMEM421   -- transmembrane protein 42 99.79(n)
    100(a)
    738788  XM_001145991.1  XP_001145991.1 
    cow
    (Bos taurus)
    TMEM421   -- transmembrane protein 42 88.05(n)
    86.16(a)
    613945  NM_001076298.1  NP_001069766.1 
    rat
    (Rattus norvegicus)
    Tmem421   -- transmembrane protein 42 84.87(n)
    84.87(a)
    363171  XM_343510.3  XP_343511.2 
    mouse
    (Mus musculus)
    Tmem421 , 5 9 (73.52 cM)5
    transmembrane protein 421, 5 84.65(n)1
    83.55(a)1
    660791  NM_025339.31  NP_079615.11 
     AA9395065  AI8491875  (see all 14)
    About this table        Species with no ortholog for TMEM42

    ENSEMBL Gene Tree for TMEM42 (if available)

    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section
      --

    (SNPs according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Resequencing Primers from Qiagen)
    About This Section

    10/51 NCBI SNPs in TMEM42 are shown (see all 51)
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidChr 3 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ----------
    rs104291,2
    C,O,A,44906746(+) ACTGTG/ATCCTA 1 -- ut31 ese310Minor allele frequency- A:0.18MN NS EA NA WA 868
    rs10468271,2
    --44906814(+) GAGCAG/AGCTCT 1 -- ut311Minor allele frequency- A:0.00MN 184
    rs22921801,2
    C,F,44903349(+) AGGCTG/CCCATC 1 -- ng515Minor allele frequency- C:0.05EA NS 1886
    rs22921811,2
    C,44903434(+) CCGGGC/GCCTCC 2 G syn1 ref1 ese30--------
    rs32151521,2
    --44903272(+) GCCCC-/CTCCGA 1 -- ng510--------
    rs37491961,2
    --44903780(-) AgcgcC/Ggcccg 1 -- int10--------
    rs37491971,2
    --44903768(-) ggcccG/Tgggcc 1 -- int10--------
    rs37491981,2
    --44903717(-) CCCACC/GCCCGC 1 -- int10--------
    rs43288431,2
    A44902577(+) ctcccA/Gggttc 1 -- ng510--------
    rs58487131,2
    --44901871(+) CCGTG-/Tttttt 1 -- ng510--------
    About this table

    HapMap Linkage Disequilibrium images for TMEM42 (up to first 250kb)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for TMEM42: --

    QIAGEN SeqTarget long-range PCR primers for resequencing TMEM42 

    (in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, LSDB, HGMD, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
      --

    (Possibly Related Articles in Doctor's Guide)
    About This Section
      --

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6UniProtKB/TrEMBL, and/or 7Novoseek)
    About This Section

    3 PubMed articles for TMEM42 gene integrated from 7 sources:
    (articles sorted by number of sources associating them with TMEM42)
    1. 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. (2002)
    2. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (2007)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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)
    About This Section
    Entrez Gene: 131616 HGNC: 28444 AceView: MGC29956 Ensembl:ENSG00000169964 euGenes: HUgn131616
    ECgene: TMEM42 H-InvDB: TMEM42

    (According to HUGE)
    About This Section
      --

    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
      --

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from XenneX, Inc.)
    About This Section
    Patent Information for TMEM42 gene:
    Search GeneIP for patents involving TMEM42

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



    (Antibodies, recombinant proteins, and assays by Millipore, Sigma-Aldrich, R&D Systems, Qiagen, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Epitomics, ProSpec, Uscn,
    Clones available from Millipore, Sigma-Aldrich, OriGene, GenScript, Sino Biological, PCR Arrays from SABiosciences, Drugs and/or compounds by Sigma-Aldrich, Tocris Bioscience, and/or Enzo Life Sciences)
    About This Section

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     QIAGEN Custom miScript Target Protector blocks miRNA-binding site of TMEM42
     SeqTarget long-range PCR primers for resequencing TMEM42
     QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays for TMEM42
     QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing of TMEM42
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     Browse ELISAs and CLIAs at Uscn
           

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