Detailed information of g11625.t1 in Montipora capitata

Genomic Location: Sc0000353:71715...78565
NR annotation: XP_029212106.1, syntaxin-6-like [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
Q5ZL19Syntaxin-6 OS=Gallus gallus OX=9031 GN=STX6 PE=2 SV=1
Q9JKK1Syntaxin-6 OS=Mus musculus OX=10090 GN=Stx6 PE=1 SV=1
Q63635Syntaxin-6 OS=Rattus norvegicus OX=10116 GN=Stx6 PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0008025 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF09177
all species →		Syntaxin-6_NSyntaxin 6, N-terminalDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR000727
all species →		DomainTarget SNARE coiled-coil homology domainInterproscan
IPR015260
all species →		DomainSyntaxin 6, N-terminalInterproscan
IPR045242
all species →		FamilySyntaxinInterproscan
IPR010989
all species →		Homologous_superfamilySNAREInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR19957
all species →		SYNTAXINInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0016020
all species →		Cellular ComponentmembraneInterproscan
GO:0048193
all species →		Biological ProcessGolgi vesicle transportInterproscan
GO:0000149
all species →		Molecular FunctionSNARE bindingInterproscan
GO:0005484
all species →		Molecular FunctionSNAP receptor activityInterproscan
GO:0006886
all species →		Biological Processintracellular protein transportInterproscan
GO:0006906
all species →		Biological Processvesicle fusionInterproscan
GO:0012505
all species →		Cellular Componentendomembrane systemInterproscan
GO:0016021
all species →		Cellular ComponentmembraneInterproscan
GO:0031201
all species →		Cellular ComponentSNARE complexInterproscan
GO:0042147
all species →		Biological Processretrograde transport, endosome to GolgiInterproscan
GO:0048278
all species →		Biological Processvesicle dockingInterproscan
GO:0016192
all species →		Biological Processvesicle-mediated transportInterproscan

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
K08498STX6; syntaxin 6-Membrane traffickingko04131deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g11625.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
511.3Max TPM
250.7Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole organisms · ambient pH treatment 21 21 241.27 460.50
whole organisms · low pH treatment 15 15 259.44 511.35
whole organisms · extra low pH treatment pH treatment 12 12 256.16 455.35

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR11452254 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 460.50
SRR11452259 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 455.69
SRR11452263 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 430.67
SRR11452262 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 408.41
SRR11452260 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 404.70
SRR11452251 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 387.94
SRR11452217 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 379.27
SRR11452252 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 356.48
SRR11452250 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 325.35
SRR11452246 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 322.75
SRR11452240 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 303.39
SRR11452243 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 170.11
SRR11452237 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 145.54
SRR11452242 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 145.51
SRR11452234 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 86.48
SRR11452233 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 71.50
SRR11452232 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 49.96
SRR11452230 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 49.15
SRR11452222 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 47.07
SRR11452228 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 36.25
SRR11452231 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 29.96
SRR11452258 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 511.35
SRR11452253 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 489.78
SRR11452216 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 398.98
SRR11452255 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 359.86
SRR11452218 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 351.22
SRR11452247 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 340.69
SRR11452229 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 311.97
SRR11452249 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 272.16
SRR11452245 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 270.39
SRR11452241 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 153.00
SRR11452238 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 150.94
SRR11452236 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 141.03
SRR11452221 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 51.04
SRR11452223 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 50.05
SRR11452224 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 39.14
SRR11452261 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 455.35
SRR11452257 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 405.78
SRR11452256 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 392.47
SRR11452220 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 373.83
SRR11452244 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 345.32
SRR11452219 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 338.86
SRR11452248 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 294.45
SRR11452239 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 180.55
SRR11452235 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 159.97
SRR11452225 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 48.67
SRR11452227 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 41.32
SRR11452226 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 37.33

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 correlated40g11683.t10.980474761533394
Negatively correlated41g2455.t1-0.952244848069102

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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