Human Gene TMC6 (uc010wtq.1)
  Description: Homo sapiens transmembrane channel-like 6 (TMC6), transcript variant 1, mRNA.
RefSeq Summary (NM_001127198): Epidermodysplasia verruciformis (EV) is an autosomal recessive dermatosis characterized by abnormal susceptibility to human papillomaviruses (HPVs) and a high rate of progression to squamous cell carcinoma on sun-exposed skin. EV is caused by mutations in either of two adjacent genes located on chromosome 17q25.3. Both of these genes encode integral membrane proteins that localize to the endoplasmic reticulum and are predicted to form transmembrane channels. This gene encodes a transmembrane channel-like protein with 10 transmembrane domains and 2 leucine zipper motifs. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr17:76,121,807-76,124,861 Size: 3,055 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr17:76,122,260-76,122,913 Size: 654 Coding Exon Count: 3 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:76,121,807-76,124,861)mRNA (may differ from genome)Protein (122 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGeneCardsGeneNetworkH-INV
HGNCLynxMalacardsMGIPubMedTreefam
UniProtKBWikipedia

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TMC6
CDC HuGE Published Literature: TMC6

-  MalaCards Disease Associations
  MalaCards Gene Search: TMC6
Diseases sorted by gene-association score: epidermodysplasia verruciformis* (1006), superficial mycosis (12), pityriasis versicolor (7)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 53.04 RPKM in Spleen
Total median expression: 418.56 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -119.10243-0.490 Picture PostScript Text
3' UTR -208.44453-0.460 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  ModBase Predicted Comparative 3D Structure on B4E0Z0
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Cellular Component:
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AK074065 - Homo sapiens mRNA for FLJ00136 protein.
BC023597 - Homo sapiens transmembrane channel-like 6, mRNA (cDNA clone MGC:23241 IMAGE:4566166), complete cds.
AY099356 - Homo sapiens large EVER1 protein mRNA, complete cds.
AY099357 - Homo sapiens small EVER1 protein mRNA, complete cds.
AY236496 - Homo sapiens transmembrane channel-like protein 6 (TMC6) mRNA, complete cds.
AK310734 - Homo sapiens cDNA, FLJ17776.
DQ892316 - Synthetic construct clone IMAGE:100004946; FLH185194.01X; RZPDo839G05146D transmembrane channel-like 6 (TMC6) gene, encodes complete protein.
DQ895518 - Synthetic construct Homo sapiens clone IMAGE:100009978; FLH185190.01L; RZPDo839G05145D transmembrane channel-like 6 (TMC6) gene, encodes complete protein.
AY057379 - Homo sapiens EVIN1 (EVIN1) mRNA, complete cds.
AB384417 - Synthetic construct DNA, clone: pF1KSDF0136, Homo sapiens TMC6 gene for transmembrane channel-like protein 6, complete cds, without stop codon, in Flexi system.
BC007766 - Homo sapiens transmembrane channel-like 6, mRNA (cDNA clone IMAGE:4135187), complete cds.
AK096076 - Homo sapiens cDNA FLJ38757 fis, clone KIDNE2013158, highly similar to Transmembrane channel-like protein 6.
AK021738 - Homo sapiens cDNA FLJ11676 fis, clone HEMBA1004752, highly similar to Homo sapiens mRNA for LAK-4p.
AK303165 - Homo sapiens cDNA FLJ55825 complete cds, highly similar to Transmembrane channel-like protein 6.
AK303584 - Homo sapiens cDNA FLJ59111 complete cds, moderately similar to Transmembrane channel-like protein 6.

-  Other Names for This Gene
  Alternate Gene Symbols: AK303584, B4E0Z0, B4E0Z0_HUMAN
UCSC ID: uc010wtq.1
RefSeq Accession: NM_001127198
Protein: B4E0Z0

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK303584.1
exon count: 4CDS single in 3' UTR: no RNA size: 843
ORF size: 369CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 886.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.