Human Gene KCNC3 (ENST00000376959.6) from GENCODE V44
  Description: Membrane; Multi-pass membrane protein (By similarity). (from UniProt E7ETH1)
RefSeq Summary (NM_004977): The Shaker gene family of Drosophila encodes components of voltage-gated potassium channels and is comprised of four subfamilies. Based on sequence similarity, this gene is similar to one of these subfamilies, namely the Shaw subfamily. The protein encoded by this gene belongs to the delayed rectifier class of channel proteins and is an integral membrane protein that mediates the voltage-dependent potassium ion permeability of excitable membranes. Alternate splicing results in several transcript variants. [provided by RefSeq, Mar 2014].
Gencode Transcript: ENST00000376959.6
Gencode Gene: ENSG00000131398.15
Transcript (Including UTRs)
   Position: hg38 chr19:50,311,937-50,329,246 Size: 17,310 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg38 chr19:50,316,075-50,329,082 Size: 13,008 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:50,311,937-50,329,246)mRNA (may differ from genome)Protein (728 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGencodeGeneCardsHGNC
LynxMalacardsMGIPubMedUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: E7ETH1_HUMAN
DESCRIPTION: SubName: Full=Potassium voltage-gated channel subfamily C member 3;
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein (By similarity).
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: KCNC3
Diseases sorted by gene-association score: spinocerebellar ataxia 13* (1611), spinocerebellar ataxia type13* (100), autosomal dominant cerebellar ataxia (10), cerebral palsy, ataxic, autosomal recessive (9), spinocerebellar ataxia 15 (9), ataxia (7), spinocerebellar ataxia 28 (7), encephalopathy, familial, with neuroserpin inclusion bodies (6), asphyxia neonatorum (5), cerebellar ataxia (4)
* = Manually curated disease association

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 31.14 RPKM in Brain - Cerebellum
Total median expression: 181.64 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 -13.40164-0.082 Picture PostScript Text
3' UTR -1208.003096-0.390 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
IPR000210 - BTB/POZ-like
IPR011333 - BTB/POZ_fold
IPR005821 - Ion_trans_dom
IPR003091 - K_chnl
IPR003968 - K_chnl_volt-dep_Kv
IPR003974 - K_chnl_volt-dep_Kv3
IPR005404 - K_chnl_volt-dep_Kv3.3
IPR021105 - K_chnl_volt-dep_Kv3_ID
IPR003131 - T1-type_BTB

Pfam Domains:
PF00520 - Ion transport protein
PF02214 - BTB/POZ domain
PF11404 - Potassium voltage-gated channel

ModBase Predicted Comparative 3D Structure on E7ETH1
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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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005216 ion channel activity
GO:0005244 voltage-gated ion channel activity
GO:0005249 voltage-gated potassium channel activity
GO:0005267 potassium channel activity

Biological Process:
GO:0006811 ion transport
GO:0006813 potassium ion transport
GO:0034765 regulation of ion transmembrane transport
GO:0051260 protein homooligomerization
GO:0055085 transmembrane transport
GO:0071805 potassium ion transmembrane transport

Cellular Component:
GO:0008076 voltage-gated potassium channel complex
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AK127492 - Homo sapiens cDNA FLJ45584 fis, clone BRTHA3013860.
AB208930 - Homo sapiens mRNA for Shaw-related voltage-gated potassium channel protein 3 variant protein.
DQ579801 - Homo sapiens piRNA piR-47913, complete sequence.
AF055989 - Homo sapiens Shaw type potassium channel Kv3.3 (KCNC3) mRNA, complete cds.
BC156302 - Synthetic construct Homo sapiens clone IMAGE:100061753, MGC:190091 potassium voltage-gated channel, Shaw-related subfamily, member 3 (KCNC3) mRNA, encodes complete protein.
JD458287 - Sequence 439311 from Patent EP1572962.
JD226480 - Sequence 207504 from Patent EP1572962.
JD226481 - Sequence 207505 from Patent EP1572962.
JD140286 - Sequence 121310 from Patent EP1572962.
JD129703 - Sequence 110727 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: AB208930, E7ETH1, E7ETH1_HUMAN, ENST00000376959.1, ENST00000376959.2, ENST00000376959.3, ENST00000376959.4, ENST00000376959.5, uc002prt.1, uc002prt.2
UCSC ID: ENST00000376959.6
RefSeq Accession: NM_004977
Protein: E7ETH1 CCDS: CCDS12793.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene KCNC3:
ataxias (Hereditary Ataxia Overview)
sca13 (Spinocerebellar Ataxia Type 13)

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