Detailed information of g13535.t1 in Montipora capitata

Genomic Location: Sc0000467:125391...139920
NR annotation: XP_029204312.2, sodium/calcium exchanger 2-like isoform X2 [Acropora millepora]
Species Montipora capitata · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
S4R2P9Sodium/calcium exchanger 3 OS=Mus musculus OX=10090 GN=Slc8a3 PE=1 SV=1
Q8K596Sodium/calcium exchanger 2 OS=Mus musculus OX=10090 GN=Slc8a2 PE=1 SV=1
P70549Sodium/calcium exchanger 3 OS=Rattus norvegicus OX=10116 GN=Slc8a3 PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0001091 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF03160
all species →		Calx-betaCalx-beta domainDomainInterproscan
PF01699
all species →		Na_Ca_exSodium/calcium exchanger proteinFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR038081
all species →		Homologous_superfamilyCalX-like domain superfamilyInterproscan
IPR044880
all species →		Homologous_superfamilyNCX, central ion-binding domain superfamilyInterproscan
IPR003644
all species →		DomainNa-Ca exchanger/integrin-beta4Interproscan
IPR004837
all species →		DomainSodium/calcium exchanger membrane regionInterproscan
IPR004836
all species →		FamilySodium/calcium exchanger proteinInterproscan
IPR051171
all species →		FamilyCalcium/Cation AntiporterInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR11878
all species →		SODIUM/CALCIUM EXCHANGERInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0007154
all species →		Biological Processcell communicationInterproscan
GO:0016020
all species →		Cellular ComponentmembraneInterproscan
GO:0055085
all species →		Biological Processtransmembrane transportInterproscan
GO:0005432
all species →		Molecular Functioncalcium:sodium antiporter activityInterproscan
GO:0006816
all species →		Biological Processcalcium ion transportInterproscan
GO:0005887
all species →		Cellular Componentplasma membraneInterproscan
GO:0015491
all species →		Molecular Functionobsolete cation:cation antiporter activityInterproscan
GO:0030001
all species →		Biological Processmetal ion transportInterproscan
GO:0030424
all species →		Cellular ComponentaxonInterproscan
GO:0035725
all species →		Biological Processsodium ion transmembrane transportInterproscan
GO:0042383
all species →		Cellular ComponentsarcolemmaInterproscan
GO:0098703
all species →		Biological Processcalcium ion import across plasma membraneInterproscan
GO:0098794
all species →		Cellular ComponentpostsynapseInterproscan

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 g13535.t1.

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

Expression pattern (RNA-seq)

Transcript abundance of g13535.t1 across 48 RNA-seq samples of Montipora capitata. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

48Samples
44TPM > 0
3Conditions
81.3Max TPM
18.8Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole organisms · ambient pH treatment 21 21 19.61 81.30
whole organisms · low pH treatment 15 13 15.55 61.98
whole organisms · extra low pH treatment pH treatment 12 10 21.63 77.17

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR11452222 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 81.30
SRR11452228 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 80.06
SRR11452230 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 76.26
SRR11452232 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 41.45
SRR11452231 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 27.50
SRR11452233 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 20.96
SRR11452234 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 18.45
SRR11452242 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 10.98
SRR11452263 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 7.58
SRR11452240 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 6.86
SRR11452262 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 6.65
SRR11452251 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 5.83
SRR11452243 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 5.71
SRR11452237 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 5.41
SRR11452260 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 3.57
SRR11452259 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 3.35
SRR11452250 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 2.65
SRR11452217 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 2.61
SRR11452252 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 2.47
SRR11452246 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 1.67
SRR11452254 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 0.56
SRR11452221 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 61.98
SRR11452224 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 61.30
SRR11452223 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 56.93
SRR11452241 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 12.04
SRR11452236 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 7.92
SRR11452229 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 7.79
SRR11452238 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 7.09
SRR11452218 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 3.88
SRR11452253 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 3.76
SRR11452247 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 2.95
SRR11452245 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 2.91
SRR11452216 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 2.44
SRR11452249 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 2.29
SRR11452255 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 0.00
SRR11452258 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 0.00
SRR11452227 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 77.17
SRR11452225 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 75.73
SRR11452226 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 72.70
SRR11452235 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 8.80
SRR11452239 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 7.55
SRR11452219 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 6.50
SRR11452257 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 3.64
SRR11452256 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 3.16
SRR11452261 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 2.23
SRR11452248 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 2.12
SRR11452220 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 0.00
SRR11452244 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 0.00

Source: CnidoSite RNA-seq expression matrices (MCAPI_TPM, StringTie quantification over 48 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.

Co-expression network

Genes whose expression across the transcriptome samples of Montipora capitata 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.

DirectionPartnersMost correlated partnerPCC
Positively correlated29g27514.t10.992487653789658
Negatively correlated3g6649.t1-0.932044511501314

Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Montipora capitata, 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.readyopen →
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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