Detailed information of ENSBQFP00000041803.1 in Heliopora coerulea

Genomic Location: JASJOG010000185.1:528015...538822
NR annotation: CAB4002375.1, calsyntenin-1 isoform X4 [Paramuricea clavata]
Species Heliopora coerulea · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q6Q0N0Calsyntenin-1 OS=Rattus norvegicus OX=10116 GN=Clstn1 PE=1 SV=1
F1R520Calsyntenin-1 OS=Danio rerio OX=7955 GN=clstn1 PE=1 SV=1
Q9EPL2Calsyntenin-1 OS=Mus musculus OX=10090 GN=Clstn1 PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0007397 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF13385
all species →		Laminin_G_3Concanavalin A-like lectin/glucanases superfamilyDomainInterproscan
PF19699
all species →		CLSTN_CCalsyntenin C-terminalFamilyInterproscan
PF00028
all species →		CadherinCadherin domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR015919
all species →		Homologous_superfamilyCadherin-like superfamilyInterproscan
IPR013320
all species →		Homologous_superfamilyConcanavalin A-like lectin/glucanase domain superfamilyInterproscan
IPR002126
all species →		DomainCadherin-likeInterproscan
IPR045588
all species →		DomainCalsyntenin, C-terminalInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR14139
all species →		CALSYNTENINInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0009986
all species →		Cellular Componentcell surfaceInterproscan
GO:0045211
all species →		Cellular Componentpostsynaptic membraneInterproscan
GO:0050806
all species →		Biological Processpositive regulation of synaptic transmissionInterproscan
GO:0051965
all species →		Biological Processpositive regulation of synapse assemblyInterproscan
GO:0005509
all species →		Molecular Functioncalcium ion bindingInterproscan
GO:0016020
all species →		Cellular ComponentmembraneInterproscan
GO:0007156
all species →		Biological Processhomophilic cell adhesion via plasma membrane adhesion moleculesInterproscan

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 ENSBQFP00000041803.1.

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

Expression pattern (RNA-seq)

Transcript abundance of ENSBQFP00000041803.1 across 37 RNA-seq samples of Heliopora coerulea. 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.

37Samples
37TPM > 0
6Conditions
1,020.0Max TPM
458.7Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Whole coral 17 17 480.59 652.45
polyp and skeleton · 31C, 3week 6 6 300.69 454.20
polyp and skeleton · 28C, 3week 6 6 526.03 762.09
polyp and skeleton · 26C, 3week 4 4 614.44 1,019.97
polyp and skeleton · 28C, 24hr 2 2 350.64 363.60
polyp and skeleton · 31C, 24hr 2 2 341.59 383.82

Per sample · hover a bar for the full sample record

Show the sample table (37 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
ERR6178781 Whole coral Whole coral not recorded not recorded ERP120267 652.45
ERR6178775 Whole coral Whole coral not recorded not recorded ERP120267 649.00
ERR6178780 Whole coral Whole coral not recorded not recorded ERP120267 587.74
ERR6178773 Whole coral Whole coral not recorded not recorded ERP120267 538.68
ERR6178771 Whole coral Whole coral not recorded not recorded ERP120267 532.58
ERR6178778 Whole coral Whole coral not recorded not recorded ERP120267 497.66
ERR6178783 Whole coral Whole coral not recorded not recorded ERP120267 484.37
ERR6178772 Whole coral Whole coral not recorded not recorded ERP120267 475.90
ERR6178774 Whole coral Whole coral not recorded not recorded ERP120267 471.10
ERR6178388 Whole coral Whole coral not recorded not recorded ERP120267 460.02
ERR6178782 Whole coral Whole coral not recorded not recorded ERP120267 438.83
ERR6178387 Whole coral Whole coral not recorded not recorded ERP120267 436.09
ERR6178776 Whole coral Whole coral not recorded not recorded ERP120267 418.34
ERR6178770 Whole coral Whole coral not recorded not recorded ERP120267 408.04
ERR6178389 Whole coral Whole coral not recorded not recorded ERP120267 406.80
ERR6178777 Whole coral Whole coral not recorded not recorded ERP120267 384.46
ERR6178779 Whole coral Whole coral not recorded not recorded ERP120267 328.05
SRR12578065 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 454.20
SRR12578068 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 352.69
SRR12587804 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 352.65
SRR12587800 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 291.94
SRR12587799 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 201.59
SRR12578066 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 151.07
SRR12587803 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 762.09
SRR12587808 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 650.92
SRR12587802 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 597.33
SRR5949849 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 582.78
SRR12578067 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 311.19
SRR12587807 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 251.87
SRR12587806 polyp and skeleton · 26C, 3week polyp and skeleton not recorded 26C, 3week SRP115860 1,019.97
SRR12587801 polyp and skeleton · 26C, 3week polyp and skeleton not recorded 26C, 3week SRP115860 525.19
SRR12587798 polyp and skeleton · 26C, 3week polyp and skeleton not recorded 26C, 3week SRP115860 501.41
SRR12587805 polyp and skeleton · 26C, 3week polyp and skeleton not recorded 26C, 3week SRP115860 411.19
SRR12578063 polyp and skeleton · 28C, 24hr polyp and skeleton not recorded 28C, 24hr SRP115860 363.60
SRR5949850 polyp and skeleton · 28C, 24hr polyp and skeleton not recorded 28C, 24hr SRP115860 337.69
SRR5949848 polyp and skeleton · 31C, 24hr polyp and skeleton not recorded 31C, 24hr SRP115860 383.82
SRR12578064 polyp and skeleton · 31C, 24hr polyp and skeleton not recorded 31C, 24hr SRP115860 299.36

Source: CnidoSite RNA-seq expression matrices (HCOER_TPM, StringTie quantification over 37 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 Heliopora coerulea 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 correlated5ENSBQFP000000056570.794346299857878
Negatively correlated43ENSBQFP00000030823-0.583338905867613

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. Partner counts were matched on ENSBQFP00000041803, the spelling this network uses.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Heliopora coerulea, 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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