Human Gene TMC6 (uc002juk.2)
  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 chr17:76,108,999-76,124,861 Size: 15,863 Total Exon Count: 20 Strand: -
Coding Region
   Position: hg19 chr17:76,109,229-76,122,913 Size: 13,685 Coding Exon Count: 19 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:76,108,999-76,124,861)mRNA (may differ from genome)Protein (805 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedReactomeTreefam
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TMC6_HUMAN
DESCRIPTION: RecName: Full=Transmembrane channel-like protein 6; AltName: Full=Epidermodysplasia verruciformis protein 1; AltName: Full=Protein LAK-4;
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Expressed in placenta, prostate, testis, activated T-lymphocytes and lymphokine-activated killer (LAK) lymphocytes.
DISEASE: Defects in TMC6 are a cause of epidermodysplasia verruciformis (EV) [MIM:226400]. It is a rare autosomal recessive genodermatosis associated with a high risk of skin carcinoma that results from an abnormal susceptibility to infection by specific human papillomaviruses. Infection leads to persistent wart-like or macular lesions.
SIMILARITY: Belongs to the TMC family.
SEQUENCE CAUTION: Sequence=AAH35648.1; Type=Erroneous initiation; Sequence=BAA24179.2; Type=Erroneous initiation; Sequence=BAB84891.1; Type=Erroneous initiation;
WEB RESOURCE: Name=TMC6base; Note=TMC6 mutation db; URL="http://bioinf.uta.fi/TMC6base/";

-  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 -84.20230-0.366 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
  InterPro Domains: Graphical view of domain structure
IPR012496 - TMC

Pfam Domains:
PF07810 - TMC domain

ModBase Predicted Comparative 3D Structure on Q7Z403
FrontTopSide
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
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0006811 ion transport
GO:0008150 biological_process
GO:0043312 neutrophil degranulation

Cellular Component:
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0031965 nuclear membrane
GO:0035579 specific granule membrane
GO:0070062 extracellular exosome
GO:0070821 tertiary granule membrane


-  Descriptions from all associated GenBank mRNAs
  KJ902227 - Synthetic construct Homo sapiens clone ccsbBroadEn_11621 TMC6 gene, encodes complete protein.
KJ902228 - Synthetic construct Homo sapiens clone ccsbBroadEn_11622 TMC6 gene, encodes complete protein.
AK074065 - Homo sapiens mRNA for FLJ00136 protein.
BC023597 - Homo sapiens transmembrane channel-like 6, mRNA (cDNA clone MGC:23241 IMAGE:4566166), complete cds.
BC035648 - Homo sapiens transmembrane channel-like 6, mRNA (cDNA clone MGC:46107 IMAGE:5575949), complete cds.
AB002405 - Homo sapiens mRNA for LAK-4p, complete cds.
BC018346 - Homo sapiens transmembrane channel-like 6, mRNA (cDNA clone IMAGE:3862414), partial 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.
JD341961 - Sequence 322985 from Patent EP1572962.
JD241988 - Sequence 223012 from Patent EP1572962.
JD200521 - Sequence 181545 from Patent EP1572962.
JD371863 - Sequence 352887 from Patent EP1572962.
JD187649 - Sequence 168673 from Patent EP1572962.
JD439849 - Sequence 420873 from Patent EP1572962.
AK310734 - Homo sapiens cDNA, FLJ17776.
JD392487 - Sequence 373511 from Patent EP1572962.
JD191879 - Sequence 172903 from Patent EP1572962.
JD317996 - Sequence 299020 from Patent EP1572962.
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.
DQ104440 - Homo sapiens expressed in activated T/LAK lymphocytes mRNA, complete cds, alternatively spliced.
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.
CU690150 - Synthetic construct Homo sapiens gateway clone IMAGE:100019427 5' read TMC6 mRNA.
JD283031 - Sequence 264055 from Patent EP1572962.
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.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q7Z403 (Reactome details) participates in the following event(s):

R-HSA-6799350 Exocytosis of specific granule membrane proteins
R-HSA-6798747 Exocytosis of tertiary granule membrane proteins
R-HSA-6798695 Neutrophil degranulation
R-HSA-168249 Innate Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: EVER1, EVIN1, NM_001127198, NP_009198, O43284, Q45VJ2, Q7Z403, Q8IU98, Q8IUI7, Q8IWU8, Q8TEQ7, Q9HAG5, TMC6_HUMAN
UCSC ID: uc002juk.2
RefSeq Accession: NM_001127198
Protein: Q7Z403 (aka TMC6_HUMAN)
CCDS: CCDS32748.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001127198.1
exon count: 20CDS single in 3' UTR: no RNA size: 2891
ORF size: 2418CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4562.00frame 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: no # 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.