Human Gene TMC5 (uc010var.2) Description and Page Index
  Description: Homo sapiens transmembrane channel-like 5 (TMC5), transcript variant 4, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr16:19,429,018-19,510,434 Size: 81,417 Total Exon Count: 22 Strand: +
Coding Region
   Position: hg19 chr16:19,451,361-19,509,288 Size: 57,928 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:19,429,018-19,510,434)mRNA (may differ from genome)Protein (1006 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMGIneXtProtOMIM
PubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: TMC5_HUMAN
DESCRIPTION: RecName: Full=Transmembrane channel-like protein 5;
FUNCTION: May function as ion channels, transporters or modulators of such.
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein (Potential).
SIMILARITY: Belongs to the TMC family.
SEQUENCE CAUTION: Sequence=BAB14629.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TMC5
CDC HuGE Published Literature: TMC5
Positive Disease Associations: Triglycerides
Related Studies:
  1. Triglycerides
    , , . [PubMed 0]

-  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: 19.94 RPKM in Small Intestine - Terminal Ileum
Total median expression: 73.24 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -218.02704-0.310 Picture PostScript Text
3' UTR -337.461146-0.294 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 Q6UXY8
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0006811 ion transport

Cellular Component:
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  AK299055 - Homo sapiens cDNA FLJ54454 complete cds, highly similar to Homo sapiens transmembrane channel-like 5 (TMC5), mRNA.
BC070101 - Homo sapiens cDNA clone IMAGE:30346457, partial cds.
AK304431 - Homo sapiens cDNA FLJ54906 complete cds, highly similar to Homo sapiens transmembrane channel-like 5 (TMC5), mRNA.
AK126270 - Homo sapiens cDNA FLJ44282 fis, clone TRACH2003516.
AY358155 - Homo sapiens clone DNA185189 SAYY8238 (UNQ8238) mRNA, complete cds.
CR749359 - Homo sapiens mRNA; cDNA DKFZp686E02211 (from clone DKFZp686E02211).
AY236494 - Homo sapiens transmembrane channel-like protein 5 (TMC5) mRNA, complete cds.
BC038118 - Homo sapiens transmembrane channel-like 5, mRNA (cDNA clone MGC:43308 IMAGE:5265527), complete cds.
AK097718 - Homo sapiens cDNA FLJ40399 fis, clone TESTI2037081, highly similar to Homo sapiens transmembrane channel-like 5 (TMC5), mRNA.
BC027602 - Homo sapiens transmembrane channel-like 5, mRNA (cDNA clone MGC:26648 IMAGE:4839111), complete cds.
AK131202 - Homo sapiens cDNA FLJ16059 fis, clone TESTI2029252, highly similar to Homo sapiens transmembrane channel-like 5 (TMC5), mRNA.
CU693274 - Synthetic construct Homo sapiens gateway clone IMAGE:100020066 5' read TMC5 mRNA.
AY263164 - Homo sapiens TMC5 protein (TMC5) mRNA, partial cds.
KJ904878 - Synthetic construct Homo sapiens clone ccsbBroadEn_14272 TMC5 gene, encodes complete protein.
KJ903234 - Synthetic construct Homo sapiens clone ccsbBroadEn_12628 TMC5 gene, encodes complete protein.
AK093944 - Homo sapiens cDNA FLJ36625 fis, clone TRACH2017368, highly similar to Homo sapiens transmembrane channel-like 5 (TMC5), mRNA.
AX748377 - Sequence 1902 from Patent EP1308459.
AK023655 - Homo sapiens cDNA FLJ13593 fis, clone PLACE1009493.
JD486206 - Sequence 467230 from Patent EP1572962.
JD102556 - Sequence 83580 from Patent EP1572962.
JD494728 - Sequence 475752 from Patent EP1572962.
JD238518 - Sequence 219542 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001261841, NP_001248770, Q68DK8, Q6UXY8, Q8IY20, Q8NHV6, Q9H8I7, TMC5_HUMAN, UNQ8238/PRO33604
UCSC ID: uc010var.2
RefSeq Accession: NM_001261841
Protein: Q6UXY8 (aka TMC5_HUMAN)
CCDS: CCDS45431.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001261841.1
exon count: 22CDS single in 3' UTR: no RNA size: 4872
ORF size: 3021CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5467.00frame shift in genome: no % Coverage: 99.98
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.