Human Gene KCNN2 (uc010jcg.3)
  Description: Homo sapiens potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2 (KCNN2), transcript variant 4, non-coding RNA.
RefSeq Summary (NR_103458): Action potentials in vertebrate neurons are followed by an afterhyperpolarization (AHP) that may persist for several seconds and may have profound consequences for the firing pattern of the neuron. Each component of the AHP is kinetically distinct and is mediated by different calcium-activated potassium channels. The protein encoded by this gene is activated before membrane hyperpolarization and is thought to regulate neuronal excitability by contributing to the slow component of synaptic AHP. This gene is a member of the KCNN family of potassium channel genes. The encoded protein is an integral membrane protein that forms a voltage-independent calcium-activated channel with three other calmodulin-binding subunits. Alternate splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2013].
Transcript (Including UTRs)
   Position: hg19 chr5:113,769,227-113,832,197 Size: 62,971 Total Exon Count: 7 Strand: +


Page IndexSequence and LinksPrimersGenetic AssociationsCTDRNA-Seq Expression
Microarray ExpressionOther SpeciesmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:113,769,227-113,832,197)mRNA (may differ from genome)No protein
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSEnsemblExonPrimerHGNCLynxPubMed
Wikipedia

-  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): KCNN2
CDC HuGE Published Literature: KCNN2
Positive Disease Associations: Brain , Breath Tests , Cardiovascular Diseases , Central Nervous System , Cholesterol, HDL , Cholesterol, LDL , Lipoproteins, LDL
Related Studies:
  1. Brain
    Sudha Seshadri et al. BMC medical genetics 2007, Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study., BMC medical genetics. [PubMed 17903297]
    Our results suggest that genes associated with clinical neurological disease also have detectable effects on subclinical phenotypes. These hypothesis generating data illustrate the use of an unbiased approach to discover novel pathways that may be involved in brain aging, and could be used to replicate observations made in other studies.
  2. Brain
    Sudha Seshadri et al. BMC medical genetics 2007, Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study., BMC medical genetics. [PubMed 17903297]
    Our results suggest that genes associated with clinical neurological disease also have detectable effects on subclinical phenotypes. These hypothesis generating data illustrate the use of an unbiased approach to discover novel pathways that may be involved in brain aging, and could be used to replicate observations made in other studies.
  3. Brain
    Sudha Seshadri et al. BMC medical genetics 2007, Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study., BMC medical genetics. [PubMed 17903297]
    Our results suggest that genes associated with clinical neurological disease also have detectable effects on subclinical phenotypes. These hypothesis generating data illustrate the use of an unbiased approach to discover novel pathways that may be involved in brain aging, and could be used to replicate observations made in other studies.
           more ... click here to view the complete list

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D001030 Apamin
  • D014403 Tubocurarine
  • D001564 Benzo(a)pyrene
  • D013749 Tetrachlorodibenzodioxin
  • D013793 Thallium
  • C552889 cyclohexyl-(2-(3,5-dimethylpyrazol-1-yl)-6-methylpyrimidin-4-yl)amine
  • C056574 leiurotoxin I
  • C517041 (4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)
  • C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl
  • C028451 3,4,3',4'-tetrachlorobiphenyl
          more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 14.58 RPKM in Adrenal Gland
Total median expression: 66.58 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.

-  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
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AF239613 - Homo sapiens apamin-sensitive small-conductance Ca2+-activated potassium channel (KCNN2) mRNA, complete cds.
AK289948 - Homo sapiens cDNA FLJ75481 complete cds, highly similar to Homo sapiens potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2 (KCNN2), transcript variant 1, mRNA.
BC117454 - Homo sapiens potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2, mRNA (cDNA clone MGC:151063 IMAGE:40126005), complete cds.
BC117456 - Homo sapiens potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2, mRNA (cDNA clone MGC:151065 IMAGE:40126007), complete cds.
AF397175 - Homo sapiens small-conductance calcium-activated potassium channel (KCNN2) mRNA, complete cds.
AY258141 - Homo sapiens small-conductance calcium-activated potassium channel SK2 (SK2) mRNA, complete cds.
BC015371 - Homo sapiens potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2, mRNA (cDNA clone IMAGE:3917229), complete cds.
BC040722 - Homo sapiens potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2, mRNA (cDNA clone IMAGE:6064079), with apparent retained intron.
JD167928 - Sequence 148952 from Patent EP1572962.
JD361094 - Sequence 342118 from Patent EP1572962.
JD117385 - Sequence 98409 from Patent EP1572962.
JD051497 - Sequence 32521 from Patent EP1572962.
JD404571 - Sequence 385595 from Patent EP1572962.
JD404569 - Sequence 385593 from Patent EP1572962.
JD404570 - Sequence 385594 from Patent EP1572962.
JD214698 - Sequence 195722 from Patent EP1572962.
JD440659 - Sequence 421683 from Patent EP1572962.
JD062775 - Sequence 43799 from Patent EP1572962.
JD469232 - Sequence 450256 from Patent EP1572962.
JD535661 - Sequence 516685 from Patent EP1572962.
JD323358 - Sequence 304382 from Patent EP1572962.
JD077855 - Sequence 58879 from Patent EP1572962.
KJ891507 - Synthetic construct Homo sapiens clone ccsbBroadEn_00901 KCNN2 gene, encodes complete protein.
AK090521 - Homo sapiens cDNA FLJ33202 fis, clone ADRGL2006886, highly similar to Homo sapiens apamin-sensitive small-conductance Ca2+-activated potassium channel (KCNN2) mRNA.
JD326451 - Sequence 307475 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NR_103458
UCSC ID: uc010jcg.3
RefSeq Accession: NR_103458

-  Gene Model Information
 
category: nearCoding nonsense-mediated-decay: no RNA accession: NR_103458.1
exon count: 7CDS single in 3' UTR: no RNA size: 1579
ORF size: 0CDS single in intron: no Alignment % ID: 99.94
txCdsPredict score: 137.50frame shift in genome: no % Coverage: 98.99
has start codon: no stop codon in genome: no # of Alignments: 1
has end codon: no 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.