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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

TMC3 Gene

protein-coding   GIFtS: 43
GCID: GC15M081624

Transmembrane Channel-Like 3

  See 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)
About This Section

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

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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000015.9  NT_010194.17  NC_018926.2  
Regulatory elements:
   SABiosciences 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 SABiosciences Chromatin IP Primers for TMC3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: TMC3_HUMAN, Q7Z5M5 (See protein sequence)
Recommended Name: Transmembrane channel-like protein 3  
Size: 1100 amino acids; 125685 Da
Subcellular location: Membrane; Multi-pass membrane protein (Potential)
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:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q7Z5M5

  • TMC3 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    TMC3 Protein Expression
    REFSEQ proteins: NP_001074001.1  
    ENSEMBL proteins: 
     ENSP00000452681   ENSP00000352413  

    Human Recombinant Protein Products for TMC3: 
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    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral to membrane IEA--

    TMC3 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    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


    TMC3 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,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

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

    Animal Models:

       inGenious Targeting Laboratory - Custom generated mouse model solutions for TMC3 
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    (Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for TMC3

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

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

    TMC3 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for TMC3

    Search CenterWatch for drugs/clinical trials and news about 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,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    About This Section

    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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      QIAGEN 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 BQ878522 AY263163 AI088153 AI272324 AI092720 
    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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    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


    See TMC3 Protein Expression from SPIRE MOPED and PaxDB
    SOURCE GeneReport for Unigene cluster: Hs.253489
        SABiosciences Custom PCR Arrays for TMC3
    Primer
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TMC3

    (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)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for TMC3 gene from 6/13 species (see all 13)    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 70.13(n)
    68.62(a)
      415470  NM_001005820.1  NP_001005820.1 
    lizard
    (Anolis carolinensis)
    Reptilia TMC36
    TMC36
    Uncharacterized protein
    88(a)
    46(a)
    1 ↔ 1
    possible ortholog
    AAWZ02038632(1033-10328)
    GL343894.1(17743-53762)
    zebrafish
    (Danio rerio)
    Actinopterygii TMC36
    transmembrane channel-like 3
    53(a)
    1 ↔ 1
    7(12442784-12490653)
    fruit fly
    (Drosophila melanogaster)
    Insecta CG32806
    --
    16(a)
    1 → many
    3L(9596701-9607009)
    worm
    (Caenorhabditis elegans)
    Secernentea tmc-16
    tmc-26
    TMC family membrane protein B0416.1
    28(a)
    25(a)
    many ↔ many
    many ↔ many
    X(1163153-1177160)
    X(9303724-9310483)


    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)
    About This Section
    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

    TMC3 for paralogs           About GeneDecksing



    (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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/1023 SNPs in TMC3 are shown (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
    SABiosciences Cancer Mutation 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, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    2 diseases for TMC3:    About MalaCards
    epidermodysplasia verruciformis    

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

    TMC3 for disorders           About GeneDecksing

    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)
    About This Section

    PubMed articles for TMC3 gene integrated from 9 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. (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. (2003)
    3. Analysis of the DNA sequence and duplication history of human chromosome 15. (PubMed id 16572171)1, 2 Zody M.C....Nusbaum C. (2006)
    4. 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. (2007)
    5. A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. (PubMed id 17903299)4 Kathiresan S....Cupples L.A. (2007)
    6. 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)
    7. 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. (2002)

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

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    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.)
    About This Section
    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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    Category
    (GIFtS: 73)
    transforming growth factor, beta 1
    GIFtS Group
    The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


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