Detailed information of g16794.t1 in Acropora digitifera

Genomic Location: chr8Alt:1394956...1418799
NR annotation: XP_029179571.1, uncharacterized protein LOC114947054 [Acropora millepora]
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
Q13485Mothers against decapentaplegic homolog 4 OS=Homo sapiens OX=9606 GN=SMAD4 PE=1 SV=1
Q1HE26Mothers against decapentaplegic homolog 4 OS=Bos taurus OX=9913 GN=SMAD4 PE=2 SV=1
P97471Mothers against decapentaplegic homolog 4 OS=Mus musculus OX=10090 GN=Smad4 PE=1 SV=2
 Gene family
Family typeMembership / link
Ubiquitin familyE3|E3 activity RING|PHD · all ubiquitin genes in this species

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00628
all species →		PHDPHD-fingerDomainInterproscan
PF03165
all species →		MH1MH1 domainDomainInterproscan
PF13771
all species →		zf-HC5HC2HPHD-like zinc-binding domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR036578
all species →		Homologous_superfamilySMAD MH1 domain superfamilyInterproscan
IPR019787
all species →		DomainZinc finger, PHD-fingerInterproscan
IPR013083
all species →		Homologous_superfamilyZinc finger, RING/FYVE/PHD-typeInterproscan
IPR034732
all species →		DomainExtended PHD (ePHD) domainInterproscan
IPR011011
all species →		Homologous_superfamilyZinc finger, FYVE/PHD-typeInterproscan
IPR013790
all species →		FamilyDwarfinInterproscan
IPR003619
all species →		DomainMAD homology 1, Dwarfin-typeInterproscan
IPR013019
all species →		DomainMAD homology, MH1Interproscan
IPR001965
all species →		DomainZinc finger, PHD-typeInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR13703
all species →		SMADInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
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:0006355
all species →		Biological Processregulation of DNA-templated transcriptionInterproscan
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: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
No KEGG orthology assignment for g16794.t1.

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

Expression pattern (RNA-seq)

Transcript abundance of g16794.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
30.6Max TPM
11.1Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Coral branch 39 39 11.13 30.62

Per sample · hover a bar for the full sample record

Show the sample table (39 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR23047226 Coral branch Coral branch adult not recorded SRP416931 30.62
SRR23047243 Coral branch Coral branch adult not recorded SRP416931 19.71
SRR23047229 Coral branch Coral branch adult not recorded SRP416931 19.16
SRR23047227 Coral branch Coral branch adult not recorded SRP416931 18.48
SRR23047222 Coral branch Coral branch adult not recorded SRP416931 17.85
SRR23047239 Coral branch Coral branch adult not recorded SRP416931 17.55
SRR23047234 Coral branch Coral branch adult not recorded SRP416931 16.91
SRR23047242 Coral branch Coral branch adult not recorded SRP416931 15.80
SRR23047220 Coral branch Coral branch adult not recorded SRP416931 14.80
SRR23047221 Coral branch Coral branch adult not recorded SRP416931 14.03
SRR23047241 Coral branch Coral branch adult not recorded SRP416931 13.58
SRR23047213 Coral branch Coral branch adult not recorded SRP416931 13.18
SRR23047208 Coral branch Coral branch adult not recorded SRP416931 13.12
SRR23047217 Coral branch Coral branch adult not recorded SRP416931 12.50
SRR23047206 Coral branch Coral branch adult not recorded SRP416931 12.07
SRR23047233 Coral branch Coral branch adult not recorded SRP416931 11.02
SRR23047240 Coral branch Coral branch adult not recorded SRP416931 10.80
SRR23047216 Coral branch Coral branch adult not recorded SRP416931 10.28
SRR23047207 Coral branch Coral branch adult not recorded SRP416931 10.18
SRR23047214 Coral branch Coral branch adult not recorded SRP416931 9.90
SRR23047223 Coral branch Coral branch adult not recorded SRP416931 9.73
SRR23047231 Coral branch Coral branch adult not recorded SRP416931 9.66
SRR23047228 Coral branch Coral branch adult not recorded SRP416931 9.48
SRR23047210 Coral branch Coral branch adult not recorded SRP416931 9.40
SRR23047211 Coral branch Coral branch adult not recorded SRP416931 8.60
SRR23047212 Coral branch Coral branch adult not recorded SRP416931 8.50
SRR23047230 Coral branch Coral branch adult not recorded SRP416931 8.40
SRR23047225 Coral branch Coral branch adult not recorded SRP416931 8.28
SRR23047209 Coral branch Coral branch adult not recorded SRP416931 8.11
SRR23047238 Coral branch Coral branch adult not recorded SRP416931 7.72
SRR23047224 Coral branch Coral branch adult not recorded SRP416931 7.00
SRR23047215 Coral branch Coral branch adult not recorded SRP416931 6.95
SRR23047235 Coral branch Coral branch adult not recorded SRP416931 5.93
SRR23047244 Coral branch Coral branch adult not recorded SRP416931 5.85
SRR23047232 Coral branch Coral branch adult not recorded SRP416931 4.29
SRR23047219 Coral branch Coral branch adult not recorded SRP416931 4.27
SRR23047236 Coral branch Coral branch adult not recorded SRP416931 3.76
SRR23047218 Coral branch Coral branch adult not recorded SRP416931 3.41
SRR23047237 Coral branch Coral branch adult not recorded SRP416931 3.31

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 correlated38g6962.t10.900707800369849
Negatively correlated33g13410.t1-0.802418049606792

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 →
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