Detailed information of g7663.t1 in Acropora digitifera

Genomic Location: chr3Alt:33729998...33738800
NR annotation: XP_015758467.1, PREDICTED: mothers against decapentaplegic homolog 3-like [Acropora digitifera]
Species Acropora digitifera · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
P84023Mothers against decapentaplegic homolog 3 OS=Gallus gallus OX=9031 GN=SMAD3 PE=2 SV=1
P84022Mothers against decapentaplegic homolog 3 OS=Homo sapiens OX=9606 GN=SMAD3 PE=1 SV=1
Q8BUN5Mothers against decapentaplegic homolog 3 OS=Mus musculus OX=10090 GN=Smad3 PE=1 SV=2
 Gene family
Family typeMembership / link
Transcription factor familyMH1 · all TF in this species

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

 PANTHER
PANTHER termDescriptionSource
PTHR13703
all species →		SMADInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0006355
all species →		Biological Processregulation of DNA-templated transcriptionInterproscan
GO:0005515
all species →		Molecular Functionprotein bindingInterproscan
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:0032924
all species →		Biological Processactivin receptor signaling pathwayInterproscan
GO:0045944
all species →		Biological Processpositive regulation of transcription by RNA polymerase IIInterproscan
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: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
K23605SMAD3; mothers against decapentaplegic homolog 3-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 g7663.t1 across 39 RNA-seq samples of Acropora digitifera. 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.

39Samples
39TPM > 0
1Conditions
164.4Max TPM
111.6Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Coral branch 39 39 111.57 164.43

Per sample · hover a bar for the full sample record

Show the sample table (39 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR23047221 Coral branch Coral branch adult not recorded SRP416931 164.43
SRR23047243 Coral branch Coral branch adult not recorded SRP416931 150.98
SRR23047220 Coral branch Coral branch adult not recorded SRP416931 150.64
SRR23047222 Coral branch Coral branch adult not recorded SRP416931 145.41
SRR23047210 Coral branch Coral branch adult not recorded SRP416931 141.70
SRR23047208 Coral branch Coral branch adult not recorded SRP416931 137.38
SRR23047219 Coral branch Coral branch adult not recorded SRP416931 129.22
SRR23047227 Coral branch Coral branch adult not recorded SRP416931 129.21
SRR23047231 Coral branch Coral branch adult not recorded SRP416931 125.08
SRR23047225 Coral branch Coral branch adult not recorded SRP416931 122.45
SRR23047226 Coral branch Coral branch adult not recorded SRP416931 120.79
SRR23047241 Coral branch Coral branch adult not recorded SRP416931 118.66
SRR23047223 Coral branch Coral branch adult not recorded SRP416931 118.50
SRR23047215 Coral branch Coral branch adult not recorded SRP416931 118.44
SRR23047209 Coral branch Coral branch adult not recorded SRP416931 117.83
SRR23047207 Coral branch Coral branch adult not recorded SRP416931 117.01
SRR23047224 Coral branch Coral branch adult not recorded SRP416931 116.02
SRR23047234 Coral branch Coral branch adult not recorded SRP416931 113.17
SRR23047232 Coral branch Coral branch adult not recorded SRP416931 110.04
SRR23047237 Coral branch Coral branch adult not recorded SRP416931 109.95
SRR23047212 Coral branch Coral branch adult not recorded SRP416931 106.91
SRR23047211 Coral branch Coral branch adult not recorded SRP416931 105.80
SRR23047233 Coral branch Coral branch adult not recorded SRP416931 103.60
SRR23047235 Coral branch Coral branch adult not recorded SRP416931 100.58
SRR23047217 Coral branch Coral branch adult not recorded SRP416931 99.86
SRR23047228 Coral branch Coral branch adult not recorded SRP416931 99.73
SRR23047214 Coral branch Coral branch adult not recorded SRP416931 97.74
SRR23047213 Coral branch Coral branch adult not recorded SRP416931 97.63
SRR23047216 Coral branch Coral branch adult not recorded SRP416931 97.09
SRR23047238 Coral branch Coral branch adult not recorded SRP416931 95.34
SRR23047229 Coral branch Coral branch adult not recorded SRP416931 92.81
SRR23047239 Coral branch Coral branch adult not recorded SRP416931 91.65
SRR23047206 Coral branch Coral branch adult not recorded SRP416931 91.42
SRR23047242 Coral branch Coral branch adult not recorded SRP416931 91.07
SRR23047230 Coral branch Coral branch adult not recorded SRP416931 90.31
SRR23047218 Coral branch Coral branch adult not recorded SRP416931 86.15
SRR23047240 Coral branch Coral branch adult not recorded SRP416931 86.02
SRR23047236 Coral branch Coral branch adult not recorded SRP416931 81.42
SRR23047244 Coral branch Coral branch adult not recorded SRP416931 79.13

Source: CnidoSite RNA-seq expression matrices (ADIGI_TPM, StringTie quantification over 39 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 Acropora digitifera 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 correlated13g10461.t10.874281773733419
Negatively correlated11g7539.t1-0.722415980534701

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 Acropora digitifera, 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.

Peak calls overlapping this gene

AssaySamplePeaksRegion

No called peak overlaps this gene in 1 available assay. Either the gene is not near an accessible or marked region in those samples, or it is not represented in the peak caller’s annotation.

Browse the full epigenomic landscape of this species: DNase-seq (DHS).

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 →
TOP