Human Gene CACNA1D (uc011bes.2)
  Description: Homo sapiens calcium channel, voltage-dependent, L type, alpha 1D subunit (CACNA1D), transcript variant 2, mRNA.
RefSeq Summary (NM_001128840): Voltage-dependent calcium 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, and gene expression. Calcium channels are multisubunit complexes composed of alpha-1, beta, alpha-2/delta, and gamma subunits. The channel activity is directed by the pore-forming alpha-1 subunit, whereas the others act as auxiliary subunits regulating this activity. The distinctive properties of the calcium channel types are related primarily to the expression of a variety of alpha-1 isoforms, namely alpha-1A, B, C, D, E, and S. This gene encodes the alpha-1D subunit. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012].
Transcript (Including UTRs)
   Position: hg19 chr3:53,830,149-53,846,492 Size: 16,344 Total Exon Count: 9 Strand: +


Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionOther SpeciesmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:53,830,149-53,846,492)mRNA (may differ from genome)No protein
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSEnsemblExonPrimerHGNCHuman Cortex Gene ExpressionLynx
MalacardsPubMedTreefamWikipedia

-  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): CACNA1D
CDC HuGE Published Literature: CACNA1D
Positive Disease Associations: Bone Density , Cholesterol, HDL , Hip , Insulin Resistance , Metabolism , Triglycerides
Related Studies:
  1. Bone Density
    Douglas P Kiel et al. BMC medical genetics 2007, Genome-wide association with bone mass and geometry in the Framingham Heart Study., BMC medical genetics. [PubMed 17903296]
    The FHS 100K SNP project offers an unbiased genome-wide strategy to identify new candidate loci and to replicate previously suggested candidate genes for osteoporosis.
  2. Cholesterol, HDL
    Sekar Kathiresan et al. BMC medical genetics 2007, A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study., BMC medical genetics. [PubMed 17903299]
    Using a 100K genome-wide scan, we have generated a set of putative associations for common sequence variants and lipid phenotypes. Validation of selected hypotheses in additional samples did not identify any new loci underlying variability in blood lipids. Lack of replication may be due to inadequate statistical power to detect modest quantitative trait locus effects (i.e., <1% of trait variance explained) or reduced genomic coverage of the 100K array. GWAS in FHS using a denser genome-wide genotyping platform and a better-powered replication strategy may identify novel loci underlying blood lipids.
  3. Hip
    Douglas P Kiel et al. BMC medical genetics 2007, Genome-wide association with bone mass and geometry in the Framingham Heart Study., BMC medical genetics. [PubMed 17903296]
    The FHS 100K SNP project offers an unbiased genome-wide strategy to identify new candidate loci and to replicate previously suggested candidate genes for osteoporosis.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: CACNA1D
Diseases sorted by gene-association score: sinoatrial node dysfunction and deafness* (1369), primary aldosteronism, seizures, and neurologic abnormalities* (1280), aldosterone-producing adenoma (11), congenital stationary night blindness (5), usher syndrome, type 2d (4), endocrine organ benign neoplasm (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: 4.89 RPKM in Pituitary
Total median expression: 43.51 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
  M76558 - Human neuronal DHP-sensitive, voltage-dependent, calcium channel alpha-1D subunit mRNA, complete cds.
M83566 - Human neuroendocrine/beta-cell-type calcium channel alpha-1 subunit mRNA, complete cds.
EU363339 - Homo sapiens calcium channel voltage-dependent L type alpha 1D subunit (CACNA1D) mRNA, complete cds.
AB209171 - Homo sapiens mRNA for calcium channel, voltage-dependent, L type, alpha 1D subunit variant protein.
A22940 - H.sapiens mRNA fragment (pCA3).
AK294397 - Homo sapiens cDNA FLJ50754 complete cds, highly similar to Voltage-dependent L-type calcium channel subunit alpha-1D.
JD330272 - Sequence 311296 from Patent EP1572962.
JD526792 - Sequence 507816 from Patent EP1572962.
JD372926 - Sequence 353950 from Patent EP1572962.
JD210372 - Sequence 191396 from Patent EP1572962.
JD178423 - Sequence 159447 from Patent EP1572962.
JD124283 - Sequence 105307 from Patent EP1572962.
JD120180 - Sequence 101204 from Patent EP1572962.
JD108560 - Sequence 89584 from Patent EP1572962.
JD095680 - Sequence 76704 from Patent EP1572962.
JD059132 - Sequence 40156 from Patent EP1572962.
JD538429 - Sequence 519453 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04010 - MAPK signaling pathway
hsa04020 - Calcium signaling pathway
hsa04260 - Cardiac muscle contraction
hsa04270 - Vascular smooth muscle contraction
hsa04912 - GnRH signaling pathway
hsa04930 - Type II diabetes mellitus
hsa05010 - Alzheimer's disease
hsa05410 - Hypertrophic cardiomyopathy (HCM)
hsa05412 - Arrhythmogenic right ventricular cardiomyopathy (ARVC)
hsa05414 - Dilated cardiomyopathy

-  Other Names for This Gene
  Alternate Gene Symbols: AK294397
UCSC ID: uc011bes.2
RefSeq Accession: NM_001128840

-  Gene Model Information
 
category: nearCoding nonsense-mediated-decay: yes RNA accession: AK294397.1
exon count: 9CDS single in 3' UTR: no RNA size: 1749
ORF size: 0CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1568.00frame shift in genome: no % Coverage: 100.00
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.