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TMC3 Gene

protein-coding   GIFtS: 45
GCID: GC15M081624

Transmembrane Channel-Like 3

  See TMC3-related disease
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
Transmembrane Channel-Like 31 2
Transmembrane Channel-Like Protein 32

External Ids:    HGNC: 229951   Entrez Gene: 3421252   Ensembl: ENSG000001888697   UniProtKB: Q7Z5M53   

Export aliases for TMC3 gene to outside databases

Previous GC identifers: GC15M079192 GC15M079339 GC15M079410 GC15M058383


(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 TMC3 Gene:
TMC3 (transmembrane channel-like 3) is a protein-coding gene. Diseases associated with TMC3 include epidermodysplasia verruciformis. An important paralog of this gene is TMC7.

UniProtKB/Swiss-Prot: TMC3_HUMAN, Q7Z5M5
Function: Probable ion channel (By similarity)




(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_000015.9  NC_018926.2  NT_010194.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the TMC3 gene promoter:
         COUP-TF1   COUP   HNF-4alpha2   LCR-F1   YY1   HNF-4alpha1   HNF-1A   Evi-1   COUP-TF   HNF-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for TMC3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TMC3


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

Entrez Gene cytogenetic band: 15q25.1   Ensembl cytogenetic band:  15q25.1   HGNC cytogenetic band: 15q24.3

TMC3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TMC3 gene location

GeneLoc information about chromosome 15         GeneLoc Exon Structure

GeneLoc location for GC15M081624:  view genomic region     (about GC identifiers)

Start:
81,623,558 bp from pter      End:
81,666,554 bp from pter
Size:
42,997 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: TMC3_HUMAN, Q7Z5M5 (See protein sequence)
Recommended Name: Transmembrane channel-like protein 3  
Size: 1100 amino acids; 125685 Da
Sequence caution: Sequence=AAP78778.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Due to an
insert of 27 undefined residues;
Secondary accessions: A2RTY2 B2RXJ3 Q7Z405
Alternative splicing: 2 isoforms:  Q7Z5M5-1   Q7Z5M5-2   

Explore the universe of human proteins at neXtProt for TMC3: NX_Q7Z5M5

Explore proteomics data for TMC3 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn264
  • Modification sites at PhosphoSitePlus

  • See TMC3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001074001.1  
    ENSEMBL proteins: 
     ENSP00000452681   ENSP00000352413  

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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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    1 InterPro protein domain:
     IPR012496 TMC

    Graphical View of Domain Structure for InterPro Entry Q7Z5M5

    ProtoNet protein and cluster: Q7Z5M5

    1 Blocks protein domain: IPB012496 TMC

    UniProtKB/Swiss-Prot: TMC3_HUMAN, Q7Z5M5
    Similarity: Belongs to the TMC family


    Find genes that share domains with TMC3           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: TMC3_HUMAN, Q7Z5M5
    Function: Probable ion channel (By similarity)

    Phenotypes:
         1 MGI phenotypic allele for Tmc3 (no phenotypes)


    Find genes that share phenotypes with TMC3           About GenesLikeMe

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for TMC3

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    hsa-mir-192-5p (MIRT026133)

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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
    TMC3_HUMAN, Q7Z5M5: Membrane; Multi-pass membrane protein (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol3
    plasma membrane3
    golgi apparatus1

    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 TMC3           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 TMC3
    Interactions:

        Search GeneGlobe Interaction Network for TMC3

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006811ion transport IEA--

    Find genes that share ontologies with TMC3           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
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      Browse compounds at ApexBio 

    Browse Tocris compounds for TMC3



    (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 TMC3 gene: 
    NM_001080532.1  

    Unigene Cluster for TMC3:

    Transmembrane channel-like 3
    Hs.253489  [show with all ESTs]
    Unigene Representative Sequence: AY263163
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000558726(uc010blr.1) ENST00000359440(uc021ssj.1 uc021ssk.1)
    ENST00000559982(uc002bgp.3)
    miRNA
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      QuantiFast Probe-based Assays in human, mouse, rat TMC3

    Additional mRNA sequence: 

    AY236490.1 AY263163.1 BC132679.1 BC143410.1 BC157874.1 

    2 DOTS entries:

    DT.100697389  DT.91858296 

    9 AceView cDNA sequences:

    AA490253 AY236490 NM_181841 AY263163 BQ878522 AI088153 AI092720 AI272324 
    BX640632 

    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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    TMC3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GTTTCCCAGG
    TMC3 Expression
    About this image

    TMC3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    TMC3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.253489
        Custom PCR Arrays for TMC3
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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 TMC3 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Tmc31 , 5 transmembrane channel-like gene family 31, 5 82.52(n)1
    81.55(a)1
      7 (47.43 cM)5
    2334241  NM_177695.41  NP_808363.31 
     835849275 
    chicken
    (Gallus gallus)
    Aves TMC31 transmembrane channel-like 3 70.1(n)
    68.62(a)
      415470  NM_001005820.1  NP_001005820.1 
    lizard
    (Anolis carolinensis)
    Reptilia TMC36
    transmembrane channel-like 3
    48(a)
    1 ↔ 1
    GL343894.1(17743-53762)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia tmc31 transmembrane channel-like 3 65.65(n)
    66.27(a)
      100494092  XM_002932268.2  XP_002932314.2 
    zebrafish
    (Danio rerio)
    Actinopterygii TMC36
    transmembrane channel-like 3
    54(a)
    1 ↔ 1
    7(12442784-12490653) ENSDARG00000052723
    fruit fly
    (Drosophila melanogaster)
    Insecta CG32806
    --
    19(a)
    1 → many
    3L(9596701-9607009)
    worm
    (Caenorhabditis elegans)
    Secernentea tmc-26
    tmc-16
    Protein TMC-1 (tmc-1) mRNA, complete cds
    28(a)
    27(a)
    many ↔ many
    many ↔ many
    X(9303724-9310483) WBGene00015177
    X(1163153-1177160) WBGene00020490


    ENSEMBL Gene Tree for TMC3 (if available)
    TreeFam Gene Tree for TMC3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for TMC3 gene
    TMC72  TMC22  TMC82  TMC52  TMC42  TMC12  TMC62  
    2 SIMAP similar genes for TMC3 using alignment to 2 protein entries:     TMC3_HUMAN (see all proteins):
    TMC1    TMC2

    Find genes that share paralogs with TMC3           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 TMC3 (see all 1023)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 15 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1873717361,2
    --81624271(+) CAACGC/TAAGAC 1 -- ds50010--------
    rs44175181,2,,4
    C,F,A,H--81624768(+) GACATT/CTGAAC 2 /N /D mis138Minor allele frequency- C:0.18NS EA NA WA CSA EU 3915
    rs1919235611,2
    C--81624822(+) GGCCTC/TCCTCC 2 K E mis10--------
    rs2013019371,2
    C--81624869(-) CACCCA/CCAGCC 2 H P mis10--------
    rs1508436731,2
    C,F--81624929(+) CTGCCG/TACACG 2 * S stg11Minor allele frequency- T:0.03EU 555
    rs1837169241,2
    C--81624934(+) GACACA/GGAGTC 2 S syn10--------
    rs1392616271,2
    C--81624949(+) TCCGTA/GAGGGA 2 L syn10--------
    rs1156070371,2
    C,F--81624961(+) GGCTCG/TAACCT 2 L F mis11Minor allele frequency- T:0.01WA 118
    rs1997382441,2
    C--81624974(+) GCTTCC/TCTCTG 2 E G mis10--------
    rs1889562181,2
    C--81625006(+) TATTGG/TAAATT 2 L F mis10--------

    HapMap Linkage Disequilibrium report for TMC3 (81623558 - 81666554 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for TMC3:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv520339CNV Loss19592680

    Human Gene Mutation Database (HGMD): TMC3
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing TMC3
    DNA2.0 Custom Variant and Variant Library Synthesis for TMC3

    (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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    1 disease for TMC3:    
    About MalaCards
    epidermodysplasia verruciformis

    1 disease from the University of Copenhagen DISEASES database for TMC3:
    Epidermodysplasia verruciformis

    Find genes that share disorders with TMC3           About GenesLikeMe

    Genetic Association Database (GAD): TMC3

    Export disorders for TMC3 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 TMC3 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with TMC3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Characterization of the transmembrane channel-like (TMC) gene family: functional clues from hearing loss and epidermodysplasia verruciformis. (PubMed id 12906855)1, 2, 3, 9 Kurima K.... Griffith A.J. (Genomics 2003)
    2. TMC and EVER genes belong to a larger novel family, the TMC gene family encoding transmembrane proteins. (PubMed id 12812529)1, 2, 3 Keresztes G.... Heller S. (BMC Genomics 2003)
    3. Analysis of the DNA sequence and duplication history of human chromosome 15. (PubMed id 16572171)1, 2 Zody M.C....Nusbaum C. (Nature 2006)
    4. Parkinson disease loci in the mid-western Amish. (PubMed id 23793441)1 Davis M.F....Haines J.L. (Hum. Genet. 2013)
    5. A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. (PubMed id 17903299)4 Kathiresan S....Cupples L.A. (BMC Med. Genet. 2007)
    6. Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data. (PubMed id 17362836)4 Schymick J.C....Traynor B.J. (Lancet Neurol 2007)
    7. 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. (Genome Res. 2004)
    8. 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)

    (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: 342125 HGNC: 22995 AceView: TMC3 Ensembl:ENSG00000188869 euGenes: HUgn342125
    ECgene: TMC3 H-InvDB: TMC3

    (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 TMC3 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 TMC3 gene:
    Search GeneIP for patents involving TMC3

    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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    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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