Cacna1d calcium voltage-gated channel subunit alpha1 D [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Cacna1dprovided by RGD
Official Full Name: calcium voltage-gated channel subunit alpha1 Dprovided by RGD
Primary source: RGD:70973
See related: Ensembl:ENSRNOG00000013147 AllianceGenome:RGD:70973
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables PDZ domain binding activity; ankyrin binding activity; and high voltage-gated calcium channel activity. Involved in several processes, including cellular response to amyloid-beta; positive regulation of CREB transcription factor activity; and positive regulation of transport. Located in several cellular components, including apical plasma membrane; dendrite membrane; and sarcolemma. Biomarker of sciatic neuropathy. Human ortholog(s) of this gene implicated in type 2 diabetes mellitus. Orthologous to human CACNA1D (calcium voltage-gated channel subunit alpha1 D). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Adrenal (RPKM 52.2), Brain (RPKM 48.0) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 16p16

Exon count:: 52

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	16	NC_086034.1 (5233682..5527549, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	16	NC_051351.1 (5227157..5521163, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	16	NC_005115.4 (6110294..6405022, complement)

Chromosome 16 - NC_086034.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Dominant role of CACNA1D exon mutations for blood pressure regulation.
Title: Dominant role of CACNA1D exon mutations for blood pressure regulation.
Snapin Specifically Up-Regulates Cav1.3 Ca(2+) Channel Variant with a Long Carboxyl Terminus.
Title: Snapin Specifically Up-Regulates Ca(v)1.3 Ca(2+) Channel Variant with a Long Carboxyl Terminus.
Cav 1.3 damages the osteogenic differentiation in osteoporotic rats by negatively regulating Spred 2-mediated autophagy-induced cell senescence.
Title: Cav 1.3 damages the osteogenic differentiation in osteoporotic rats by negatively regulating Spred 2-mediated autophagy-induced cell senescence.
Cdk5 phosphorylates CaV1.3 channels and regulates GABAA-mediated miniature inhibitory post-synaptic currents in striato-nigral terminals.
Title: Cdk5 phosphorylates Ca(V)1.3 channels and regulates GABA(A)-mediated miniature inhibitory post-synaptic currents in striato-nigral terminals.
CaV1.2 and CaV1.3 voltage-gated L-type Ca2+ channels in rat white fat adipocytes.
Title: CaV1.2 and CaV1.3 voltage-gated L-type Ca2+ channels in rat white fat adipocytes.
Study have showned a significant effect of the autism-associated mutation A760G on the gating of CaV1.3 such that channel activation is significantly left-shifted, Ca(2+)-dependent inactivation is decreased, and deactivation is slowed, resulting in excess Ca2+ entry. However, these effects are mitigated by an increase in voltage-dependent inactivation. Also, A760G mutation differentially affects CaV1.3 splice variants.
Title: An autism-associated mutation in CaV1.3 channels has opposing effects on voltage- and Ca(2+)-dependent regulation.
L-type channels in insulin-secreting cells are directly targeted by cGMP signaling through PKG.
Title: Regulation of L-type Ca(V)1.3 channel activity and insulin secretion by the cGMP-PKG signaling pathway.
In addition, single-molecule localization microscopy revealed striking clusters of CaV1.3 channels surrounding clusters of BK channels and forming a multi-channel complex both in a heterologous system and in rat hippocampal and sympathetic neurons.
Title: Proximal clustering between BK and Ca(V)1.3 channels promotes functional coupling and BK channel activation at low voltage.
Data indicate that in rats, central L-type calcium Cav1.2 channels, rather than Cav1.3, mediate alcohol-seeking behavior.
Title: Differential Roles for L-Type Calcium Channel Subtypes in Alcohol Dependence.
activated Ca(2+)/calmodulin-dependent protein kinase II (CaMKII) strongly interacts with a novel binding motif in the N-terminal domain of CaV1 LTCC alpha1 subunits that is not conserved in CaV2 or CaV3 voltage-gated Ca(2+) channel subunits. Mutations in the CaV1.3 alpha1 subunit N-terminal domain or in the CaMKII catalytic domain that largely prevent the in vitro interaction also disrupt CaMKII association with intact...
Title: A novel mechanism for Ca(2+)/calmodulin-dependent protein kinase II targeting to L-type Ca(2+) channels that initiates long-range signaling to the nucleus.

Submit: New GeneRIF Correction See all GeneRIFs (42)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AI555146 (e-PCR)
- UniSTS:239933

PMC18246P1 (e-PCR)
- UniSTS:271680

Cacna1d (e-PCR), detects polymorphism
- UniSTS:461908

BE113526 (e-PCR)
- UniSTS:246692

RH143397 (e-PCR)
- UniSTS:232644

RH94500 (e-PCR)
- UniSTS:119748

BE113723 (e-PCR)
- UniSTS:246778

AU028122 (e-PCR)
- UniSTS:112637

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables PDZ domain binding	IDA Inferred from Direct Assay more info	PubMed
enables alpha-actinin binding	IEA Inferred from Electronic Annotation more info
enables alpha-actinin binding	ISO Inferred from Sequence Orthology more info
enables ankyrin binding	IPI Inferred from Physical Interaction more info	PubMed
enables ankyrin binding	ISO Inferred from Sequence Orthology more info
enables calcium channel activity	ISO Inferred from Sequence Orthology more info
enables high voltage-gated calcium channel activity	IBA Inferred from Biological aspect of Ancestor more info
enables high voltage-gated calcium channel activity	IDA Inferred from Direct Assay more info	PubMed
enables high voltage-gated calcium channel activity	IEA Inferred from Electronic Annotation more info
contributes_to high voltage-gated calcium channel activity	ISO Inferred from Sequence Orthology more info
enables high voltage-gated calcium channel activity	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables voltage-gated calcium channel activity	IDA Inferred from Direct Assay more info	PubMed
enables voltage-gated calcium channel activity	IEA Inferred from Electronic Annotation more info
enables voltage-gated calcium channel activity	ISO Inferred from Sequence Orthology more info
enables voltage-gated calcium channel activity involved SA node cell action potential	IEA Inferred from Electronic Annotation more info
enables voltage-gated calcium channel activity involved SA node cell action potential	ISO Inferred from Sequence Orthology more info
enables voltage-gated calcium channel activity involved in cardiac muscle cell action potential	IC Inferred by Curator more info	PubMed
enables voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within adenylate cyclase-modulating G protein-coupled receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in calcium ion import	IEA Inferred from Electronic Annotation more info
involved_in calcium ion import	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in calcium ion import	ISO Inferred from Sequence Orthology more info
involved_in calcium ion import across plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
involved_in calcium ion transmembrane transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within calcium ion transmembrane transport	ISO Inferred from Sequence Orthology more info
involved_in calcium ion transport	IDA Inferred from Direct Assay more info	PubMed
involved_in calcium ion transport	ISO Inferred from Sequence Orthology more info
involved_in calcium-mediated signaling	IDA Inferred from Direct Assay more info	PubMed
involved_in cardiac muscle cell action potential involved in contraction	IEA Inferred from Electronic Annotation more info
involved_in cardiac muscle cell action potential involved in contraction	ISO Inferred from Sequence Orthology more info
involved_in cellular response to amyloid-beta	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within establishment of localization in cell	ISO Inferred from Sequence Orthology more info
involved_in heart development	IEP Inferred from Expression Pattern more info	PubMed
involved_in membrane depolarization during SA node cell action potential	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within membrane depolarization during SA node cell action potential	ISO Inferred from Sequence Orthology more info
involved_in membrane depolarization during SA node cell action potential	ISO Inferred from Sequence Orthology more info
involved_in membrane depolarization during cardiac muscle cell action potential	IC Inferred by Curator more info	PubMed
involved_in memory	IEP Inferred from Expression Pattern more info	PubMed
involved_in metal ion transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in optic nerve development	IEP Inferred from Expression Pattern more info	PubMed
involved_in positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of calcium ion transport	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of calcium ion transport	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of insulin secretion involved in cellular response to glucose stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of membrane depolarization	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of atrial cardiac muscle cell membrane repolarization	ISO Inferred from Sequence Orthology more info
involved_in regulation of calcium ion transport	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of heart rate by cardiac conduction	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of heart rate by cardiac conduction	ISO Inferred from Sequence Orthology more info
involved_in regulation of heart rate by cardiac conduction	ISO Inferred from Sequence Orthology more info
involved_in regulation of potassium ion transmembrane transport	ISO Inferred from Sequence Orthology more info
involved_in regulation of presynaptic cytosolic calcium ion concentration	IEA Inferred from Electronic Annotation more info
involved_in response to estradiol	IEP Inferred from Expression Pattern more info	PubMed
involved_in sensory perception of sound	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within sensory perception of sound	ISO Inferred from Sequence Orthology more info
involved_in sensory perception of sound	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of L-type voltage-gated calcium channel complex	IEA Inferred from Electronic Annotation more info
part_of L-type voltage-gated calcium channel complex	ISO Inferred from Sequence Orthology more info
located_in Z disc	ISO Inferred from Sequence Orthology more info
located_in apical plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in basolateral plasma membrane	ISO Inferred from Sequence Orthology more info
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
is_active_in cochlear hair cell ribbon synapse	ISO Inferred from Sequence Orthology more info
located_in dendrite	ISO Inferred from Sequence Orthology more info
located_in dendrite membrane	IDA Inferred from Direct Assay more info	PubMed
located_in neuron projection terminus	ISO Inferred from Sequence Orthology more info
located_in neuronal cell body	ISO Inferred from Sequence Orthology more info
located_in perikaryon	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
is_active_in postsynaptic membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in presynaptic active zone membrane	ISO Inferred from Sequence Orthology more info
located_in primary dendrite	IDA Inferred from Direct Assay more info	PubMed
located_in sarcolemma	IDA Inferred from Direct Assay more info	PubMed
located_in somatodendritic compartment	IEA Inferred from Electronic Annotation more info
part_of voltage-gated calcium channel complex	IBA Inferred from Biological aspect of Ancestor more info
part_of voltage-gated calcium channel complex	IEA Inferred from Electronic Annotation more info
part_of voltage-gated calcium channel complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: voltage-dependent L-type calcium channel subunit alpha-1D

Names: CaV1.3alpha1; RBD; brain class D; calcium channel alpha-1 subunit; calcium channel, L type, alpha-1 polypeptide; calcium channel, voltage-dependent, L type, alpha 1D subunit; voltage-dependent calcium channel subunit alpha1D; voltage-gated calcium channel pore forming subunit CaV1.3alpha1 IVS3-IVS4 extracellular linker; voltage-gated calcium channel subunit alpha Cav1.3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001389225.2 → NP_001376154.1 voltage-dependent L-type calcium channel subunit alpha-1D

Status: VALIDATED

Source sequence(s)

JAXUCZ010000016

UniProtKB/TrEMBL

F1LNB7

Related

ENSRNOP00000041766.4, ENSRNOT00000040759.5

Conserved Domains (4) summary

pfam00520
Location:125 → 417

Ion_trans; Ion transport protein

pfam08763
Location:1553 → 1624

Ca_chan_IQ; Voltage gated calcium channel IQ domain

pfam16885
Location:1647 → 2161

CAC1F_C; Voltage-gated calcium channel subunit alpha, C-term

pfam16905
Location:1489 → 1542

GPHH; Voltage-dependent L-type calcium channel, IQ-associated

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086034.1 Reference GRCr8

Range

5233682..5527549 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063275281.1 → XP_063131351.1 voltage-dependent L-type calcium channel subunit alpha-1D isoform X23
XM_006252595.5 → XP_006252657.1 voltage-dependent L-type calcium channel subunit alpha-1D isoform X14

UniProtKB/TrEMBL

F1LNB7

Related

ENSRNOP00000051407.4

Conserved Domains (4) summary

pfam00520
Location:1222 → 1460

Ion_trans; Ion transport protein

pfam08763
Location:1533 → 1604

Ca_chan_IQ; Voltage gated calcium channel IQ domain

pfam16885
Location:1628 → 2141

CAC1F_C; Voltage-gated calcium channel subunit alpha, C-term

pfam16905
Location:1468 → 1531

GPHH; Voltage-dependent L-type calcium channel, IQ-associated
XM_063275280.1 → XP_063131350.1 voltage-dependent L-type calcium channel subunit alpha-1D isoform X22
XM_017600059.3 → XP_017455548.1 voltage-dependent L-type calcium channel subunit alpha-1D isoform X6

UniProtKB/TrEMBL

E9PTK1

Related

ENSRNOP00000084179.1
XM_039094434.2 → XP_038950362.1 voltage-dependent L-type calcium channel subunit alpha-1D isoform X3

UniProtKB/TrEMBL

E9PTK1

Conserved Domains (4) summary

pfam00520
Location:125 → 417

Ion_trans; Ion transport protein

pfam08763
Location:1595 → 1666

Ca_chan_IQ; Voltage gated calcium channel IQ domain

pfam16885
Location:1689 → 2203

CAC1F_C; Voltage-gated calcium channel subunit alpha, C-term

pfam16905
Location:1531 → 1584

GPHH; Voltage-dependent L-type calcium channel, IQ-associated
XM_017600065.3 → XP_017455554.1 voltage-dependent L-type calcium channel subunit alpha-1D isoform X15

UniProtKB/TrEMBL

F1LNB7
XM_017600064.3 → XP_017455553.1 voltage-dependent L-type calcium channel subunit alpha-1D isoform X10

UniProtKB/TrEMBL

F1LNB7
XM_063275274.1 → XP_063131344.1 voltage-dependent L-type calcium channel subunit alpha-1D isoform X13
XM_006252590.5 → XP_006252652.1 voltage-dependent L-type calcium channel subunit alpha-1D isoform X8

UniProtKB/TrEMBL

F1LNB7

Conserved Domains (4) summary

pfam00520
Location:1242 → 1495

Ion_trans; Ion transport protein

pfam08763
Location:1568 → 1639

Ca_chan_IQ; Voltage gated calcium channel IQ domain

pfam16885
Location:1663 → 2176

CAC1F_C; Voltage-gated calcium channel subunit alpha, C-term

pfam16905
Location:1503 → 1566

GPHH; Voltage-dependent L-type calcium channel, IQ-associated
XM_017600058.3 → XP_017455547.1 voltage-dependent L-type calcium channel subunit alpha-1D isoform X5

UniProtKB/TrEMBL

E9PTK1
XM_017600057.3 → XP_017455546.1 voltage-dependent L-type calcium channel subunit alpha-1D isoform X4

UniProtKB/TrEMBL

E9PTK1
XM_063275273.1 → XP_063131343.1 voltage-dependent L-type calcium channel subunit alpha-1D isoform X11
XM_017600055.3 → XP_017455544.1 voltage-dependent L-type calcium channel subunit alpha-1D isoform X1

UniProtKB/TrEMBL

E9PTK1
XM_063275282.1 → XP_063131352.1 voltage-dependent L-type calcium channel subunit alpha-1D isoform X24
XM_006252597.5 → XP_006252659.1 voltage-dependent L-type calcium channel subunit alpha-1D isoform X16

UniProtKB/TrEMBL

F1LNB7

Related

ENSRNOP00000043046.4

Conserved Domains (4) summary

pfam00520
Location:1222 → 1460

Ion_trans; Ion transport protein

pfam08763
Location:1533 → 1604

Ca_chan_IQ; Voltage gated calcium channel IQ domain

pfam16885
Location:1628 → 2132

CAC1F_C; Voltage-gated calcium channel subunit alpha, C-term

pfam16905
Location:1468 → 1531

GPHH; Voltage-dependent L-type calcium channel, IQ-associated
XM_006252594.5 → XP_006252656.1 voltage-dependent L-type calcium channel subunit alpha-1D isoform X12

UniProtKB/TrEMBL

A0A8I5ZX89

Conserved Domains (4) summary

pfam00520
Location:1222 → 1475

Ion_trans; Ion transport protein

pfam08763
Location:1548 → 1619

Ca_chan_IQ; Voltage gated calcium channel IQ domain

pfam16885
Location:1643 → 2156

CAC1F_C; Voltage-gated calcium channel subunit alpha, C-term

pfam16905
Location:1483 → 1546

GPHH; Voltage-dependent L-type calcium channel, IQ-associated
XM_017600060.3 → XP_017455549.1 voltage-dependent L-type calcium channel subunit alpha-1D isoform X7

UniProtKB/TrEMBL

E9PTK1
XM_017600062.3 → XP_017455551.1 voltage-dependent L-type calcium channel subunit alpha-1D isoform X9

UniProtKB/TrEMBL

F1LNB7
XM_017600056.3 → XP_017455545.1 voltage-dependent L-type calcium channel subunit alpha-1D isoform X2

UniProtKB/TrEMBL

E9PTK1

Related

ENSRNOP00000042492.5
XM_017600066.3 → XP_017455555.1 voltage-dependent L-type calcium channel subunit alpha-1D isoform X17

UniProtKB/TrEMBL

Q91WX9
XM_063275279.1 → XP_063131349.1 voltage-dependent L-type calcium channel subunit alpha-1D isoform X21

UniProtKB/TrEMBL

A6KG45
XM_063275277.1 → XP_063131347.1 voltage-dependent L-type calcium channel subunit alpha-1D isoform X19
XM_063275278.1 → XP_063131348.1 voltage-dependent L-type calcium channel subunit alpha-1D isoform X20

UniProtKB/TrEMBL

A6KG44
XM_063275276.1 → XP_063131346.1 voltage-dependent L-type calcium channel subunit alpha-1D isoform X18

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_017298.1: Suppressed sequence

Description

NM_017298.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.