Detailed information of g11627.t1 in Montipora capitata

Genomic Location: Sc0000353:97442...101130
NR annotation: XP_020603976.1, cadmium/zinc-transporting ATPase HMA3-like [Orbicella faveolata]
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
A3BF39Cadmium/zinc-transporting ATPase HMA2 OS=Oryza sativa subsp. japonica OX=39947 GN=HMA2 PE=1 SV=1
Q9SZW4Cadmium/zinc-transporting ATPase HMA2 OS=Arabidopsis thaliana OX=3702 GN=HMA2 PE=2 SV=1
O64474Putative cadmium/zinc-transporting ATPase HMA4 OS=Arabidopsis thaliana OX=3702 GN=HMA4 PE=1 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0001634 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00702
all species →		Hydrolasehaloacid dehalogenase-like hydrolaseDomainInterproscan
PF00122
all species →		E1-E2_ATPaseE1-E2 ATPaseFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR036412
all species →		Homologous_superfamilyHAD-like superfamilyInterproscan
IPR023214
all species →		Homologous_superfamilyHAD superfamilyInterproscan
IPR051014
all species →		FamilyCation Transport ATPase Type IBInterproscan
IPR023298
all species →		Homologous_superfamilyP-type ATPase, transmembrane domain superfamilyInterproscan
IPR018303
all species →		PTMP-type ATPase, phosphorylation siteInterproscan
IPR023299
all species →		Homologous_superfamilyP-type ATPase, cytoplasmic domain NInterproscan
IPR036163
all species →		Homologous_superfamilyHeavy metal-associated domain superfamilyInterproscan
IPR008250
all species →		Homologous_superfamilyP-type ATPase, A domain superfamilyInterproscan
IPR027256
all species →		FamilyP-type ATPase, subfamily IBInterproscan
IPR006121
all species →		DomainHeavy metal-associated domain, HMAInterproscan
IPR001757
all species →		FamilyP-type ATPaseInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR48085
all species →		CADMIUM/ZINC-TRANSPORTING ATPASE HMA2-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0016020
all species →		Cellular ComponentmembraneInterproscan
GO:0022857
all species →		Molecular Functiontransmembrane transporter activityInterproscan
GO:0055085
all species →		Biological Processtransmembrane transportInterproscan
GO:0000166
all species →		Molecular Functionnucleotide bindingInterproscan
GO:0046872
all species →		Molecular Functionmetal ion bindingInterproscan
GO:0006812
all species →		Biological Processmonoatomic cation transportInterproscan
GO:0019829
all species →		Molecular FunctionATPase-coupled monoatomic cation transmembrane transporter activityInterproscan
GO:0005215
all species →		Molecular Functiontransporter activityInterproscan
GO:0005524
all species →		Molecular FunctionATP bindingInterproscan
GO:0016887
all species →		Molecular FunctionATP hydrolysis activityInterproscan

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
KOEnzymeEnzyme IDPathwayMap IDSource
K01534zntA; Zn2+/Cd2+-exporting ATPaseEC:7.2.2.12
EC:7.2.2.21
Enzymes with EC numbers-deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g11627.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
48TPM > 0
3Conditions
40.5Max TPM
18.1Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole organisms · ambient pH treatment 21 21 18.74 39.88
whole organisms · low pH treatment 15 15 17.03 31.65
whole organisms · extra low pH treatment pH treatment 12 12 18.49 40.47

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 39.88
SRR11452230 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 38.76
SRR11452232 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 36.57
SRR11452228 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 33.97
SRR11452242 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 27.63
SRR11452234 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 27.30
SRR11452250 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 19.73
SRR11452243 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 19.63
SRR11452233 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 19.29
SRR11452246 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 18.35
SRR11452237 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 18.08
SRR11452252 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 18.01
SRR11452259 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 14.62
SRR11452231 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 14.21
SRR11452262 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 9.62
SRR11452260 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 8.54
SRR11452254 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 8.47
SRR11452263 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 7.15
SRR11452251 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 5.32
SRR11452217 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 4.25
SRR11452240 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 4.24
SRR11452241 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 31.65
SRR11452223 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 23.92
SRR11452221 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 22.94
SRR11452249 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 22.86
SRR11452245 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 21.16
SRR11452224 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 21.03
SRR11452247 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 21.01
SRR11452236 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 20.65
SRR11452238 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 17.14
SRR11452255 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 11.79
SRR11452258 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 11.06
SRR11452253 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 9.61
SRR11452218 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 8.87
SRR11452216 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 6.42
SRR11452229 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 5.34
SRR11452227 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 40.47
SRR11452225 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 33.29
SRR11452239 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 32.84
SRR11452226 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 21.79
SRR11452248 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 21.19
SRR11452235 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 20.25
SRR11452244 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 14.98
SRR11452256 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 10.71
SRR11452257 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 10.70
SRR11452219 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 8.01
SRR11452261 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 3.89
SRR11452220 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 3.78

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 correlated26g4695.t10.955621003942012
Negatively correlated3g20756.t1-0.872250318990407

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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