Human Gene KCNIP1 (uc003map.3) Description and Page Index
  Description: Homo sapiens Kv channel interacting protein 1 (KCNIP1), transcript variant 3, mRNA.
RefSeq Summary (NM_001034838): This gene encodes a member of the family of cytosolic voltage-gated potassium (Kv) channel-interacting proteins (KCNIPs), which belong to the neuronal calcium sensor (NCS) family of the calcium binding EF-hand proteins. They associate with Kv4 alpha subunits to form native Kv4 channel complexes. The encoded protein may regulate rapidly inactivating (A-type) currents, and hence neuronal membrane excitability, in response to changes in the concentration of intracellular calcium. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2013].
Transcript (Including UTRs)
   Position: hg19 chr5:169,780,881-170,163,636 Size: 382,756 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr5:169,780,881-170,162,810 Size: 381,930 Coding Exon Count: 8 

Page IndexSequence and LinksGenetic AssociationsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther Names
Model InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:169,780,881-170,163,636)mRNA (may differ from genome)Protein (225 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMGIOMIM
PubMedStanford SOURCETreefamUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): KCNIP1
CDC HuGE Published Literature: KCNIP1
Positive Disease Associations: Erythrocyte Count , Multiple Sclerosis , normalized brain volume, multiple sclerosis
Related Studies:
  1. Erythrocyte Count
    , , . [PubMed 0]
  2. Multiple Sclerosis
    Sergio E Baranzini et al. Human molecular genetics 2009, Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis., Human molecular genetics. [PubMed 19010793]
  3. normalized brain volume, multiple sclerosis
    Baranzini ,et al. 2008, Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis, Human molecular genetics 2009 18- 4 : 767-78. [PubMed 19010793]
           more ... click here to view the complete list

-  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: 16.98 RPKM in Brain - Nucleus accumbens (basal ganglia)
Total median expression: 121.31 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
3' UTR -222.60826-0.269 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
IPR011992 - EF-hand-like_dom
IPR018247 - EF_Hand_1_Ca_BS
IPR018249 - EF_HAND_2
IPR002048 - EF_hand_Ca-bd
IPR001125 - Recoverin

Pfam Domains:
PF00036 - EF hand
PF13202 - EF hand
PF13499 - EF-hand domain pair
PF13833 - EF-hand domain pair

SCOP Domains:
47473 - EF-hand

ModBase Predicted Comparative 3D Structure on Q3YAD3
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    

-  Descriptions from all associated GenBank mRNAs
  AK301775 - Homo sapiens cDNA FLJ52465 complete cds, highly similar to Homo sapiens Kv channel interacting protein 1 (KCNIP1), transcript variant 3, mRNA.
DQ148476 - Homo sapiens potassium channel interacting protein 1 mRNA, complete cds, alternatively spliced.
BC035032 - Homo sapiens Kv channel interacting protein 1, mRNA (cDNA clone IMAGE:5259689).
BC050375 - Homo sapiens Kv channel interacting protein 1, mRNA (cDNA clone MGC:51879 IMAGE:5752207), complete cds.
AY170821 - Homo sapiens vesicle APC-binding protein (VABP) mRNA, complete cds.
AY780424 - Homo sapiens Kv channel interacting protein 1 mRNA, complete cds.
AK074390 - Homo sapiens cDNA FLJ23810 fis, clone HRC08209, highly similar to Homo sapiens A-type potassium channel modulatory protein 1 (KCHIP1) mRNA.
AB527490 - Synthetic construct DNA, clone: pF1KB7936, Homo sapiens KCNIP1 gene for Kv channel interacting protein 1, without stop codon, in Flexi system.
KJ893743 - Synthetic construct Homo sapiens clone ccsbBroadEn_03137 KCNIP1 gene, encodes complete protein.
AF199597 - Homo sapiens A-type potassium channel modulatory protein 1 (KCHIP1) mRNA, complete cds.
DQ148477 - Homo sapiens potassium channel interacting protein 1 mRNA, complete cds, alternatively spliced.
DQ148478 - Homo sapiens potassium channel interacting protein 1 mRNA, complete cds, alternatively spliced.
DQ148479 - Homo sapiens potassium channel interacting protein 1 mRNA, complete cds, alternatively spliced.
JD041195 - Sequence 22219 from Patent EP1572962.
JD380370 - Sequence 361394 from Patent EP1572962.
JD429257 - Sequence 410281 from Patent EP1572962.
JD530868 - Sequence 511892 from Patent EP1572962.
JD177934 - Sequence 158958 from Patent EP1572962.
JD060009 - Sequence 41033 from Patent EP1572962.
JD251380 - Sequence 232404 from Patent EP1572962.
JD549904 - Sequence 530928 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001034838, NP_001030010, Q3YAD3, Q3YAD3_HUMAN
UCSC ID: uc003map.3
RefSeq Accession: NM_001034838
Protein: Q3YAD3 CCDS: CCDS34285.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001034838.1
exon count: 8CDS single in 3' UTR: no RNA size: 1518
ORF size: 678CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1456.00frame shift in genome: no % Coverage: 99.08
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.