Detailed information of g14490.t1 in Acropora digitifera

Genomic Location: chr6Alt:33207969...33219053
NR annotation: XP_015761851.1, PREDICTED: tumor necrosis factor receptor superfamily member 4-like isoform X2 [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)
No Swiss-Prot hit above the reporting threshold for this gene.
 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00020
all species →		TNFR_c6TNFR/NGFR cysteine-rich regionDomainInterproscan
PF00531
all species →		DeathDeath domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR001368
all species →		DomainTNFR/NGFR cysteine-rich regionInterproscan
IPR011029
all species →		Homologous_superfamilyDeath-like domain superfamilyInterproscan
IPR000488
all species →		DomainDeath domainInterproscan
IPR052302
all species →		FamilyNeurotrophin receptor-related death domain-containing proteinInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR46605
all species →		TUMOR NECROSIS FACTOR RECEPTORInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005515
all species →		Molecular Functionprotein bindingInterproscan
GO:0007165
all species →		Biological Processsignal transductionInterproscan
GO:0005035
all species →		Molecular Functiondeath receptor activityInterproscan
GO:0005886
all species →		Cellular Componentplasma membraneInterproscan
GO:0007266
all species →		Biological ProcessRho protein signal transductionInterproscan
GO:0009986
all species →		Cellular Componentcell surfaceInterproscan
GO:0015026
all species →		Molecular Functioncoreceptor activityInterproscan
GO:0048406
all species →		Molecular Functionnerve growth factor bindingInterproscan

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 g14490.t1.

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

Expression pattern (RNA-seq)

Transcript abundance of g14490.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
33.6Max TPM
17.4Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Coral branch 39 39 17.35 33.60

Per sample · hover a bar for the full sample record

Show the sample table (39 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR23047219 Coral branch Coral branch adult not recorded SRP416931 33.60
SRR23047236 Coral branch Coral branch adult not recorded SRP416931 32.10
SRR23047244 Coral branch Coral branch adult not recorded SRP416931 31.25
SRR23047222 Coral branch Coral branch adult not recorded SRP416931 30.57
SRR23047226 Coral branch Coral branch adult not recorded SRP416931 29.58
SRR23047232 Coral branch Coral branch adult not recorded SRP416931 25.23
SRR23047216 Coral branch Coral branch adult not recorded SRP416931 25.19
SRR23047223 Coral branch Coral branch adult not recorded SRP416931 24.24
SRR23047229 Coral branch Coral branch adult not recorded SRP416931 23.61
SRR23047242 Coral branch Coral branch adult not recorded SRP416931 23.61
SRR23047227 Coral branch Coral branch adult not recorded SRP416931 22.44
SRR23047207 Coral branch Coral branch adult not recorded SRP416931 21.73
SRR23047220 Coral branch Coral branch adult not recorded SRP416931 21.41
SRR23047213 Coral branch Coral branch adult not recorded SRP416931 21.40
SRR23047217 Coral branch Coral branch adult not recorded SRP416931 20.81
SRR23047233 Coral branch Coral branch adult not recorded SRP416931 20.36
SRR23047239 Coral branch Coral branch adult not recorded SRP416931 20.31
SRR23047234 Coral branch Coral branch adult not recorded SRP416931 19.93
SRR23047206 Coral branch Coral branch adult not recorded SRP416931 19.89
SRR23047209 Coral branch Coral branch adult not recorded SRP416931 19.18
SRR23047214 Coral branch Coral branch adult not recorded SRP416931 18.54
SRR23047237 Coral branch Coral branch adult not recorded SRP416931 17.48
SRR23047224 Coral branch Coral branch adult not recorded SRP416931 17.00
SRR23047230 Coral branch Coral branch adult not recorded SRP416931 16.42
SRR23047243 Coral branch Coral branch adult not recorded SRP416931 16.32
SRR23047211 Coral branch Coral branch adult not recorded SRP416931 15.32
SRR23047221 Coral branch Coral branch adult not recorded SRP416931 14.49
SRR23047210 Coral branch Coral branch adult not recorded SRP416931 14.26
SRR23047208 Coral branch Coral branch adult not recorded SRP416931 14.19
SRR23047240 Coral branch Coral branch adult not recorded SRP416931 13.70
SRR23047235 Coral branch Coral branch adult not recorded SRP416931 6.30
SRR23047218 Coral branch Coral branch adult not recorded SRP416931 4.53
SRR23047215 Coral branch Coral branch adult not recorded SRP416931 4.33
SRR23047241 Coral branch Coral branch adult not recorded SRP416931 3.28
SRR23047228 Coral branch Coral branch adult not recorded SRP416931 3.09
SRR23047238 Coral branch Coral branch adult not recorded SRP416931 2.96
SRR23047225 Coral branch Coral branch adult not recorded SRP416931 2.86
SRR23047212 Coral branch Coral branch adult not recorded SRP416931 2.84
SRR23047231 Coral branch Coral branch adult not recorded SRP416931 2.33

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 correlated8g24294.t10.800099940073578
Negatively correlated86g13947.t1-0.802682442099133

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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