Detailed information of ENSBQFP00000039769 in Heliopora coerulea

Genomic Location: JASJOG010000196.1:159850...166276
NR annotation: XP_028402521.1, mothers against decapentaplegic homolog 4-like [Dendronephthya gigantea]
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
P97471Mothers against decapentaplegic homolog 4 OS=Mus musculus OX=10090 GN=Smad4 PE=1 SV=2
Q9GKQ9Mothers against decapentaplegic homolog 4 OS=Sus scrofa OX=9823 GN=SMAD4 PE=2 SV=1
Q1HE26Mothers against decapentaplegic homolog 4 OS=Bos taurus OX=9913 GN=SMAD4 PE=2 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0005653 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF03165
all species →		MH1MH1 domainDomainInterproscan
PF03166
all species →		MH2MH2 domainFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR003619
all species →		DomainMAD homology 1, Dwarfin-typeInterproscan
IPR036578
all species →		Homologous_superfamilySMAD MH1 domain superfamilyInterproscan
IPR001132
all species →		DomainSMAD domain, Dwarfin-typeInterproscan
IPR017855
all species →		Homologous_superfamilySMAD-like domain superfamilyInterproscan
IPR013790
all species →		FamilyDwarfinInterproscan
IPR008984
all species →		Homologous_superfamilySMAD/FHA domain superfamilyInterproscan
IPR013019
all species →		DomainMAD homology, MH1Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR13703
all species →		SMADInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0006355
all species →		Biological Processregulation of DNA-templated transcriptionInterproscan
GO:0000978
all species →		Molecular FunctionRNA polymerase II cis-regulatory region sequence-specific DNA bindingInterproscan
GO:0000981
all species →		Molecular FunctionDNA-binding transcription factor activity, RNA polymerase II-specificInterproscan
GO:0006357
all species →		Biological Processregulation of transcription by RNA polymerase IIInterproscan
GO:0007179
all species →		Biological Processtransforming growth factor beta receptor signaling pathwayInterproscan
GO:0009653
all species →		Biological Processanatomical structure morphogenesisInterproscan
GO:0030154
all species →		Biological Processcell differentiationInterproscan
GO:0030509
all species →		Biological ProcessBMP signaling pathwayInterproscan
GO:0060395
all species →		Biological ProcessSMAD protein signal transductionInterproscan
GO:0070411
all species →		Molecular FunctionI-SMAD bindingInterproscan
GO:0071144
all species →		Cellular Componentheteromeric SMAD protein complexInterproscan
GO:0005515
all species →		Molecular Functionprotein bindingInterproscan
GO:0005667
all species →		Cellular Componenttranscription regulator complexInterproscan

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
K04501SMAD4; mothers against decapentaplegic homolog 4-AGE-RAGE signaling pathway in diabetic complicationsko04933deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of ENSBQFP00000039769 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
36TPM > 0
6Conditions
131.8Max TPM
69.9Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Whole coral 17 17 81.19 100.37
polyp and skeleton · 31C, 3week 6 6 57.49 73.48
polyp and skeleton · 28C, 3week 6 6 68.29 131.81
polyp and skeleton · 26C, 3week 4 4 71.58 113.25
polyp and skeleton · 28C, 24hr 2 2 52.78 56.00
polyp and skeleton · 31C, 24hr 2 1 30.57 61.14

Per sample · hover a bar for the full sample record

Show the sample table (37 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
ERR6178387 Whole coral Whole coral not recorded not recorded ERP120267 100.37
ERR6178777 Whole coral Whole coral not recorded not recorded ERP120267 99.80
ERR6178779 Whole coral Whole coral not recorded not recorded ERP120267 98.66
ERR6178781 Whole coral Whole coral not recorded not recorded ERP120267 91.74
ERR6178775 Whole coral Whole coral not recorded not recorded ERP120267 91.03
ERR6178780 Whole coral Whole coral not recorded not recorded ERP120267 84.82
ERR6178772 Whole coral Whole coral not recorded not recorded ERP120267 84.42
ERR6178771 Whole coral Whole coral not recorded not recorded ERP120267 83.88
ERR6178783 Whole coral Whole coral not recorded not recorded ERP120267 78.06
ERR6178776 Whole coral Whole coral not recorded not recorded ERP120267 77.51
ERR6178770 Whole coral Whole coral not recorded not recorded ERP120267 76.71
ERR6178388 Whole coral Whole coral not recorded not recorded ERP120267 72.98
ERR6178782 Whole coral Whole coral not recorded not recorded ERP120267 72.70
ERR6178773 Whole coral Whole coral not recorded not recorded ERP120267 72.34
ERR6178389 Whole coral Whole coral not recorded not recorded ERP120267 70.53
ERR6178778 Whole coral Whole coral not recorded not recorded ERP120267 64.44
ERR6178774 Whole coral Whole coral not recorded not recorded ERP120267 60.23
SRR12578066 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 73.48
SRR12587804 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 63.84
SRR12587800 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 56.13
SRR12578065 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 54.28
SRR12578068 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 50.11
SRR12587799 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 47.11
SRR5949849 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 131.81
SRR12578067 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 79.58
SRR12587802 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 64.35
SRR12587807 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 49.67
SRR12587808 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 49.23
SRR12587803 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 35.10
SRR12587801 polyp and skeleton · 26C, 3week polyp and skeleton not recorded 26C, 3week SRP115860 113.25
SRR12587805 polyp and skeleton · 26C, 3week polyp and skeleton not recorded 26C, 3week SRP115860 58.19
SRR12587798 polyp and skeleton · 26C, 3week polyp and skeleton not recorded 26C, 3week SRP115860 58.05
SRR12587806 polyp and skeleton · 26C, 3week polyp and skeleton not recorded 26C, 3week SRP115860 56.84
SRR5949850 polyp and skeleton · 28C, 24hr polyp and skeleton not recorded 28C, 24hr SRP115860 56.00
SRR12578063 polyp and skeleton · 28C, 24hr polyp and skeleton not recorded 28C, 24hr SRP115860 49.56
SRR12578064 polyp and skeleton · 31C, 24hr polyp and skeleton not recorded 31C, 24hr SRP115860 61.14
SRR5949848 polyp and skeleton · 31C, 24hr polyp and skeleton not recorded 31C, 24hr SRP115860 0.00

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 correlated20ENSBQFP000000454920.817583140205263
Negatively correlated129ENSBQFP00000007688-0.807556634286576

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 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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