Human Gene CACNA1E (uc009wxt.3) Description and Page Index
  Description: Homo sapiens calcium channel, voltage-dependent, R type, alpha 1E subunit (CACNA1E), transcript variant 1, mRNA.
RefSeq Summary (NM_001205293): Voltage-dependent calcium channels are multisubunit complexes consisting of alpha-1, alpha-2, beta, and delta subunits in a 1:1:1:1 ratio. These channels mediate the entry of calcium ions into excitable cells, and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death. This gene encodes the alpha-1E subunit of the R-type calcium channels, which belong to the 'high-voltage activated' group that maybe involved in the modulation of firing patterns of neurons important for information processing. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Apr 2011].
Transcript (Including UTRs)
   Position: hg19 chr1:181,452,686-181,775,921 Size: 323,236 Total Exon Count: 48 Strand: +
Coding Region
   Position: hg19 chr1:181,452,881-181,767,970 Size: 315,090 Coding Exon Count: 48 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:181,452,686-181,775,921)mRNA (may differ from genome)Protein (2313 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
HGNCHPRDLynxMGIneXtProtOMIM
PubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: CAC1E_HUMAN
DESCRIPTION: RecName: Full=Voltage-dependent R-type calcium channel subunit alpha-1E; AltName: Full=Brain calcium channel II; Short=BII; AltName: Full=Calcium channel, L type, alpha-1 polypeptide, isoform 6; AltName: Full=Voltage-gated calcium channel subunit alpha Cav2.3;
FUNCTION: Voltage-sensitive calcium channels (VSCC) mediate the entry of calcium ions into excitable cells and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death. The isoform alpha-1E gives rise to R-type calcium currents. R-type calcium channels belong to the 'high-voltage activated' (HVA) group and are blocked by nickel, and partially by omega-agatoxin-IIIA (omega-Aga-IIIA). They are however insensitive to dihydropyridines (DHP), omega- conotoxin-GVIA (omega-CTx-GVIA), and omega-agatoxin-IVA (omega- Aga-IVA). Calcium channels containing alpha-1E subunit could be involved in the modulation of firing patterns of neurons which is important for information processing.
SUBUNIT: Interacts with EFHC1. Voltage-dependent calcium channels are multisubunit complexes, consisting of alpha-1, alpha-2, beta and delta subunits in a 1:1:1:1 ratio. The channel activity is directed by the pore-forming and voltage-sensitive alpha-1 subunit. In many cases, this subunit is sufficient to generate voltage-sensitive calcium channel activity. The auxiliary subunits beta and alpha-2/delta linked by a disulfide bridge regulate the channel activity.
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Expressed in neuronal tissues and in kidney.
DOMAIN: Each of the four internal repeats contains five hydrophobic transmembrane segments (S1, S2, S3, S5, S6) and one positively charged transmembrane segment (S4). S4 segments probably represent the voltage-sensor and are characterized by a series of positively charged amino acids at every third position.
SIMILARITY: Belongs to the calcium channel alpha-1 subunit (TC 1.A.1.11) family. CACNA1E subfamily.
SIMILARITY: Contains 1 EF-hand domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CACNA1E
CDC HuGE Published Literature: CACNA1E
Positive Disease Associations: Echocardiography , Forced Expiratory Volume , Hip
Related Studies:
  1. Echocardiography
    Ramachandran S Vasan et al. BMC medical genetics 2007, Genome-wide association of echocardiographic dimensions, brachial artery endothelial function and treadmill exercise responses in the Framingham Heart Study., BMC medical genetics. [PubMed 17903301]
    In hypothesis-generating GWAS of echocardiography, ETT and BA vascular function in a moderate-sized community-based sample, we identified several SNPs that are candidates for replication attempts and we provide a web-based GWAS resource for the research community.
  2. Echocardiography
    Ramachandran S Vasan et al. BMC medical genetics 2007, Genome-wide association of echocardiographic dimensions, brachial artery endothelial function and treadmill exercise responses in the Framingham Heart Study., BMC medical genetics. [PubMed 17903301]
    In hypothesis-generating GWAS of echocardiography, ETT and BA vascular function in a moderate-sized community-based sample, we identified several SNPs that are candidates for replication attempts and we provide a web-based GWAS resource for the research community.
  3. Forced Expiratory Volume
    , , . [PubMed 0]
           more ... click here to view the complete list

-  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: 11.99 RPKM in Brain - Nucleus accumbens (basal ganglia)
Total median expression: 64.01 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 -69.90195-0.358 Picture PostScript Text
3' UTR -2582.117951-0.325 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
IPR018249 - EF_HAND_2
IPR005821 - Ion_trans_dom
IPR014873 - VDCC_a1su_IQ
IPR005449 - VDCC_R_a1su
IPR002077 - VDCCAlpha1

Pfam Domains:
PF00520 - Ion transport protein
PF08016 - Polycystin cation channel
PF08763 - Voltage gated calcium channel IQ domain
PF16905 - Voltage-dependent L-type calcium channel, IQ-associated

SCOP Domains:
81324 - Voltage-gated potassium channels

Protein Data Bank (PDB) 3-D Structure
MuPIT help

3BXL
- X-ray


ModBase Predicted Comparative 3D Structure on Q15878
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
  Molecular Function:
GO:0005216 ion channel activity
GO:0005244 voltage-gated ion channel activity
GO:0005245 voltage-gated calcium channel activity
GO:0005262 calcium channel activity
GO:0005509 calcium ion binding
GO:0008331 high voltage-gated calcium channel activity
GO:0046872 metal ion binding

Biological Process:
GO:0006811 ion transport
GO:0006816 calcium ion transport
GO:0007268 chemical synaptic transmission
GO:0034765 regulation of ion transmembrane transport
GO:0050796 regulation of insulin secretion
GO:0051899 membrane depolarization
GO:0055085 transmembrane transport
GO:0070588 calcium ion transmembrane transport
GO:0086010 membrane depolarization during action potential

Cellular Component:
GO:0005886 plasma membrane
GO:0005891 voltage-gated calcium channel complex
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AK309070 - Homo sapiens cDNA, FLJ99111.
L29384 - Homo sapiens (clone pcDNA-alpha1E-1) voltage-dependent calcium channel alpha-1E-1 subunit mRNA, complete cds.
L29385 - Homo sapiens (clone pcDNA-alpha1E-3) voltage-dependent calcium channel alpha-1E-3 subunit mRNA, complete cds.
BC172376 - Synthetic construct Homo sapiens clone IMAGE:100069070, MGC:199081 calcium channel, voltage-dependent, R type, alpha 1E subunit (CACNA1E) mRNA, encodes complete protein.
L27745 - Homo sapiens voltage-operated calcium channel, alpha-1 subunit mRNA, complete cds.
A22936 - H.sapiens mRNA fragment (pRR5-8).
JD200790 - Sequence 181814 from Patent EP1572962.
JD338012 - Sequence 319036 from Patent EP1572962.
JD144229 - Sequence 125253 from Patent EP1572962.
A22424 - H.sapiens mRNA fragment (p1247-5.1.2.1.1).
AB209499 - Homo sapiens mRNA for calcium channel, voltage-dependent, alpha 1E subunit variant protein.
JD103523 - Sequence 84547 from Patent EP1572962.
JD118743 - Sequence 99767 from Patent EP1572962.
JD127181 - Sequence 108205 from Patent EP1572962.
JD353914 - Sequence 334938 from Patent EP1572962.
JD290273 - Sequence 271297 from Patent EP1572962.
JD433796 - Sequence 414820 from Patent EP1572962.
JD129643 - Sequence 110667 from Patent EP1572962.
AK096563 - Homo sapiens cDNA FLJ39244 fis, clone OCBBF2008340.
JD186717 - Sequence 167741 from Patent EP1572962.
JD207165 - Sequence 188189 from Patent EP1572962.
JD455530 - Sequence 436554 from Patent EP1572962.
JD219506 - Sequence 200530 from Patent EP1572962.
JD194975 - Sequence 175999 from Patent EP1572962.
JD281380 - Sequence 262404 from Patent EP1572962.
JD361099 - Sequence 342123 from Patent EP1572962.
JD226969 - Sequence 207993 from Patent EP1572962.
JD364756 - Sequence 345780 from Patent EP1572962.
JD450292 - Sequence 431316 from Patent EP1572962.
JD254351 - Sequence 235375 from Patent EP1572962.
JD167849 - Sequence 148873 from Patent EP1572962.
JD186636 - Sequence 167660 from Patent EP1572962.
JD453131 - Sequence 434155 from Patent EP1572962.
JD275357 - Sequence 256381 from Patent EP1572962.
JD371468 - Sequence 352492 from Patent EP1572962.
JD297731 - Sequence 278755 from Patent EP1572962.
JD500404 - Sequence 481428 from Patent EP1572962.
JD555566 - Sequence 536590 from Patent EP1572962.
JD134449 - Sequence 115473 from Patent EP1572962.
JD267683 - Sequence 248707 from Patent EP1572962.
JD277833 - Sequence 258857 from Patent EP1572962.
JD410969 - Sequence 391993 from Patent EP1572962.
JD355208 - Sequence 336232 from Patent EP1572962.
JD493568 - Sequence 474592 from Patent EP1572962.
JD120686 - Sequence 101710 from Patent EP1572962.
JD444294 - Sequence 425318 from Patent EP1572962.
JD386625 - Sequence 367649 from Patent EP1572962.
JD231429 - Sequence 212453 from Patent EP1572962.
JD284216 - Sequence 265240 from Patent EP1572962.
JD454591 - Sequence 435615 from Patent EP1572962.
JD377932 - Sequence 358956 from Patent EP1572962.
JD538917 - Sequence 519941 from Patent EP1572962.
JD334916 - Sequence 315940 from Patent EP1572962.
JD065540 - Sequence 46564 from Patent EP1572962.
JD315459 - Sequence 296483 from Patent EP1572962.
JD563962 - Sequence 544986 from Patent EP1572962.
BC037800 - Homo sapiens cDNA clone IMAGE:4796172.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04010 - MAPK signaling pathway
hsa04020 - Calcium signaling pathway
hsa04930 - Type II diabetes mellitus

Reactome (by CSHL, EBI, and GO)

Protein Q15878 (Reactome details) participates in the following event(s):

R-HSA-210420 Ca2+ influx through voltage gated Ca2+ channels
R-HSA-265645 Calcium Influx through Voltage-gated Calcium Channels
R-HSA-112308 Presynaptic depolarization and calcium channel opening
R-HSA-422356 Regulation of insulin secretion
R-HSA-112315 Transmission across Chemical Synapses
R-HSA-163685 Energy Metabolism
R-HSA-112316 Neuronal System
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: B1AM12, B1AM13, B1AM14, CAC1E_HUMAN, CACH6, CACNL1A6, NM_001205293, NP_001192222, Q14580, Q14581, Q15878
UCSC ID: uc009wxt.3
RefSeq Accession: NM_001205293
Protein: Q15878 (aka CAC1E_HUMAN or CCAE_HUMAN)
CCDS: CCDS53443.1, CCDS55664.1, CCDS55665.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001205293.1
exon count: 48CDS single in 3' UTR: no RNA size: 15101
ORF size: 6942CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 14029.00frame shift in genome: no % Coverage: 99.91
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 1
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.