Detailed information of evm.model.HiC_scaffold_27.263 in Chrysaora quinquecirrha

Genomic Location: HiC_scaffold_27:3609312...3656975
NR annotation: CAH3118679.1, unnamed protein product [Pocillopora meandrina]
Species Chrysaora quinquecirrha · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q01815Voltage-dependent L-type calcium channel subunit alpha-1C OS=Mus musculus OX=10090 GN=Cacna1c PE=1 SV=1
P15381Voltage-dependent L-type calcium channel subunit alpha-1C OS=Oryctolagus cuniculus OX=9986 GN=CACNA1C PE=1 SV=1
O35505Voltage-dependent L-type calcium channel subunit alpha-1C OS=Cavia porcellus OX=10141 GN=CACNA1C PE=1 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0000418 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF16905
all species →
GPHHVoltage-dependent L-type calcium channel, IQ-associatedFamilyInterproscan
PF00520
all species →
Ion_transIon transport proteinFamilyInterproscan
PF08763
all species →
Ca_chan_IQVoltage gated calcium channel IQ domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR031649
all species →
DomainVoltage-dependent L-type calcium channel, IQ-associated domainInterproscan
IPR002077
all species →
FamilyVoltage-dependent calcium channel, alpha-1 subunitInterproscan
IPR005821
all species →
DomainIon transport domainInterproscan
IPR050599
all species →
FamilyVoltage-dependent calcium channel alpha-1 subunitInterproscan
IPR027359
all species →
Homologous_superfamilyVoltage-dependent channel domain superfamilyInterproscan
IPR014873
all species →
DomainVoltage-dependent calcium channel, alpha-1 subunit, IQ domainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR45628
all species →
VOLTAGE-DEPENDENT CALCIUM CHANNEL TYPE A SUBUNIT ALPHA-1Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005245
all species →
Molecular Functionvoltage-gated calcium channel activityInterproscan
GO:0005891
all species →
Cellular Componentvoltage-gated calcium channel complexInterproscan
GO:0070588
all species →
Biological Processcalcium ion transmembrane transportInterproscan
GO:0005216
all species →
Molecular Functionmonoatomic ion channel activityInterproscan
GO:0006811
all species →
Biological Processmonoatomic ion transportInterproscan
GO:0016020
all species →
Cellular ComponentmembraneInterproscan
GO:0055085
all species →
Biological Processtransmembrane transportInterproscan
GO:0008331
all species →
Molecular Functionhigh voltage-gated calcium channel activityInterproscan
GO:0098703
all species →
Biological Processcalcium ion import across plasma membraneInterproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.
 KEGG pathway
No KEGG orthology assignment for evm.model.HiC_scaffold_27.263.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Co-expression network

Genes whose expression across the transcriptome samples of Chrysaora quinquecirrha tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Chrysaora quinquecirrha, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

AnalysisWhat it doesStatus
Primer designDesign PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.template foundopen →
BLASTSearch this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.template foundopen →
Expression heatmapDraw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.no expression matrix
Gene family / orthogroupLook this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.open →
Gene set analysisStart a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.open →
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