Human Gene KCNN3 (ENST00000271915.9_15) from GENCODE V47lift37
  Description: potassium calcium-activated channel subfamily N member 3, transcript variant 1 (from RefSeq NM_002249.6)
Gencode Transcript: ENST00000271915.9_15
Gencode Gene: ENSG00000143603.19_16
Transcript (Including UTRs)
   Position: hg19 chr1:154,669,931-154,842,757 Size: 172,827 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr1:154,680,452-154,842,440 Size: 161,989 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:154,669,931-154,842,757)mRNA (may differ from genome)Protein (731 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: KCNN3_HUMAN
DESCRIPTION: RecName: Full=Small conductance calcium-activated potassium channel protein 3; Short=SK3; Short=SKCa 3; Short=SKCa3; AltName: Full=KCa2.3;
FUNCTION: Forms a voltage-independent potassium channel activated by intracellular calcium. Activation is followed by membrane hyperpolarization. Thought to regulate neuronal excitability by contributing to the slow component of synaptic afterhyperpolarization. The channel is blocked by apamin.
SUBUNIT: Heterooligomer. The complex is composed of 4 channel subunits each of which binds to a calmodulin subunit which regulates the channel activity through calcium-binding (By similarity).
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein.
POLYMORPHISM: The second poly-Gln region of KCNN3 is highly polymorphic and the number of Gln varies from 12 to 28 in the population.
SIMILARITY: Belongs to the potassium channel KCNN family. KCa2.3/KCNN3 subfamily.

-  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: KCNN3
Diseases sorted by gene-association score: retinitis pigmentosa 19 (11), spinocerebellar ataxia 2 (11), bipolar disorder (10), retinitis pigmentosa 14 (8), hirschsprung disease 1 (5), schizophrenia (5)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 7.75 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 81.62 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 -113.70317-0.359 Picture PostScript Text
3' UTR -3099.5010521-0.295 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
IPR004178 - CaM-bd_dom
IPR013099 - Ion_trans_2
IPR015449 - K_chnl_Ca-activ_SK

Pfam Domains:
PF02888 - Calmodulin binding domain
PF03530 - Calcium-activated SK potassium channel
PF07885 - Ion channel

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases
81324 - Voltage-gated potassium channels
81327 - Small-conductance potassium channel

ModBase Predicted Comparative 3D Structure on Q9UGI6
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 DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005516 calmodulin binding
GO:0015269 calcium-activated potassium channel activity
GO:0016286 small conductance calcium-activated potassium channel activity

Biological Process:
GO:0006811 ion transport
GO:0006813 potassium ion transport
GO:0071805 potassium ion transmembrane transport

Cellular Component:
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0043025 neuronal cell body


-  Descriptions from all associated GenBank mRNAs
  AF438203 - Homo sapiens small conductance calcium-activated potassium channel mRNA, complete cds; alternatively spliced.
BC042147 - Homo sapiens potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3, mRNA (cDNA clone MGC:52352 IMAGE:3619576), complete cds.
AJ251016 - Homo sapiens mRNA for calcium-activated potassium channel SK3 (K3 (KCNN3) gene).
AY049734 - Homo sapiens small-conductance calcium-activated potassium channel SK3 (KCNN3) mRNA, complete cds.
AF031815 - Homo sapiens calcium-activated potassium channel (KCNN3) mRNA, complete cds.
AY138900 - Homo sapiens small conductance calcium-activated potassium channel subfamily N member 3 variant 1B (KCNN3) mRNA, complete cds; alternatively spliced.
AY258142 - Homo sapiens small-conductance calcium-activated potassium channel SK3 (SK3) mRNA, complete cds.
HQ448417 - Synthetic construct Homo sapiens clone IMAGE:100071845; CCSB013559_01 potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3 (KCNN3) gene, encodes complete protein.
CU692066 - Synthetic construct Homo sapiens gateway clone IMAGE:100022497 5' read KCNN3 mRNA.
Y08263 - H.sapiens mRNA for AAD14 protein, partial.
AK310077 - Homo sapiens cDNA, FLJ17119.
BC030100 - Homo sapiens cDNA clone IMAGE:4796595.
JD537334 - Sequence 518358 from Patent EP1572962.
JD478586 - Sequence 459610 from Patent EP1572962.
JD543272 - Sequence 524296 from Patent EP1572962.
JD537333 - Sequence 518357 from Patent EP1572962.
JD463832 - Sequence 444856 from Patent EP1572962.
JD407712 - Sequence 388736 from Patent EP1572962.
JD478587 - Sequence 459611 from Patent EP1572962.
JD095812 - Sequence 76836 from Patent EP1572962.
JD566167 - Sequence 547191 from Patent EP1572962.
JD219858 - Sequence 200882 from Patent EP1572962.
JD456183 - Sequence 437207 from Patent EP1572962.
JD108204 - Sequence 89228 from Patent EP1572962.
JD445559 - Sequence 426583 from Patent EP1572962.
JD085492 - Sequence 66516 from Patent EP1572962.
JD272447 - Sequence 253471 from Patent EP1572962.
JD470813 - Sequence 451837 from Patent EP1572962.
JD308400 - Sequence 289424 from Patent EP1572962.
DQ589198 - Homo sapiens piRNA piR-56310, complete sequence.
JD540632 - Sequence 521656 from Patent EP1572962.
JD205366 - Sequence 186390 from Patent EP1572962.
JD174619 - Sequence 155643 from Patent EP1572962.
JD339363 - Sequence 320387 from Patent EP1572962.
JD431303 - Sequence 412327 from Patent EP1572962.
JD157107 - Sequence 138131 from Patent EP1572962.
JD253572 - Sequence 234596 from Patent EP1572962.
JD148776 - Sequence 129800 from Patent EP1572962.
JD464380 - Sequence 445404 from Patent EP1572962.
JD289966 - Sequence 270990 from Patent EP1572962.
JD429997 - Sequence 411021 from Patent EP1572962.
JD175457 - Sequence 156481 from Patent EP1572962.
JD521034 - Sequence 502058 from Patent EP1572962.
JD106309 - Sequence 87333 from Patent EP1572962.

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

Protein Q9UGI6 (Reactome details) participates in the following event(s):

R-HSA-1296039 Activation of Ca2+ activated Potassium channels with small conductance
R-HSA-1296052 Ca2+ activated K+ channels
R-HSA-1296071 Potassium Channels
R-HSA-112316 Neuronal System

-  Other Names for This Gene
  Alternate Gene Symbols: B1ANX0, ENST00000271915.1, ENST00000271915.2, ENST00000271915.3, ENST00000271915.4, ENST00000271915.5, ENST00000271915.6, ENST00000271915.7, ENST00000271915.8, K3, KCNN3_HUMAN, NM_002249, O43517, Q86VF9, Q8WXG7, Q9UGI6, uc317ixf.1, uc317ixf.2
UCSC ID: ENST00000271915.9_15
RefSeq Accession: NM_002249.6
Protein: Q9UGI6 (aka KCNN3_HUMAN or KCN3_HUMAN)

-  Gene Model Information
  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.