Genomic Location: sc0000245_pilon:230395...286955
NR annotation: XP_044166613.1, LOW QUALITY PROTEIN: cAMP-specific 3',5'-cyclic phosphodiesterase 4C-like [Acropora millepora]
Species Acropora gemmifera · all data for this species · gene families
| CDS |
| agem_s0245.g16.t1 |
| Transcript |
| agem_s0245.g16.t1 |
| Protein |
| agem_s0245.g16.t1 |
| UniProt accession | Description |
|---|---|
| Q01063 | 3',5'-cyclic-AMP phosphodiesterase 4D OS=Mus musculus OX=10090 GN=Pde4d PE=1 SV=2 |
| Q08499 | 3',5'-cyclic-AMP phosphodiesterase 4D OS=Homo sapiens OX=9606 GN=PDE4D PE=1 SV=2 |
| P14270 | 3',5'-cyclic-AMP phosphodiesterase 4D OS=Rattus norvegicus OX=10116 GN=Pde4d PE=1 SV=4 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0001674 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF18100 all species → | PDE4_UCR | Phosphodiesterase 4 upstream conserved regions (UCR) | Domain | Interproscan |
| PF00233 all species → | PDEase_I | 3'5'-cyclic nucleotide phosphodiesterase | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR003607 all species → | Domain | HD/PDEase domain | Interproscan |
| IPR036971 all species → | Homologous_superfamily | 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily | Interproscan |
| IPR040844 all species → | Domain | Phosphodiesterase 4 upstream conserved regions (UCR) | Interproscan |
| IPR023088 all species → | Family | 3'5'-cyclic nucleotide phosphodiesterase | Interproscan |
| IPR002073 all species → | Domain | 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain | Interproscan |
| IPR023174 all species → | Conserved_site | 3'5'-cyclic nucleotide phosphodiesterase, conserved site | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR11347 all species → | CYCLIC NUCLEOTIDE PHOSPHODIESTERASE | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0004114 all species → | Molecular Function | 3',5'-cyclic-nucleotide phosphodiesterase activity | Interproscan |
| GO:0004115 all species → | Molecular Function | 3',5'-cyclic-AMP phosphodiesterase activity | Interproscan |
| GO:0005634 all species → | Cellular Component | nucleus | Interproscan |
| GO:0005829 all species → | Cellular Component | cytosol | Interproscan |
| GO:0007165 all species → | Biological Process | signal transduction | Interproscan |
| GO:0048471 all species → | Cellular Component | perinuclear region of cytoplasm | Interproscan |
| GO:0008081 all species → | Molecular Function | phosphoric diester hydrolase activity | Interproscan |
agem_s0245.g16.t1.Transcript abundance of agem_s0245.g16.t1 across 48 RNA-seq samples of Acropora gemmifera. 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.
| Condition | Samples | TPM > 0 | Mean TPM | Max TPM | Mean, relative to max |
|---|---|---|---|---|---|
| branch tip | 48 | 3 | 1.22 | 23.44 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR3223317 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 23.44 |
| SRR2169558 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 21.40 |
| SRR3223319 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 13.92 |
| SRR3169421 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169422 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169423 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169425 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169426 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169518 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169527 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169528 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169529 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169530 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169531 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169532 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169533 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169534 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169535 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169536 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169537 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169538 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169539 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169540 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169541 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182410 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182448 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182557 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182684 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182685 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182686 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182775 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182776 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182777 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182778 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182779 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182780 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182781 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182784 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182785 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182786 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182787 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182788 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182789 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182790 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182791 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182792 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182793 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182794 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (AGEMM_TPM,
StringTie quantification over 48 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.
Genes whose expression across the transcriptome samples of Acropora gemmifera 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.
| Direction | Partners | Most correlated partner | PCC |
|---|---|---|---|
| Positively correlated | 8 | agem_s0220.g17.t1 | 0.999996272227323 |
| Negatively correlated | 3 | agem_s0028.g73.t1 | -0.606032981511079 |
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.
Whether this gene can be visualised in the single-cell atlases of Acropora gemmifera, 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.
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.
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.
| Analysis | What it does | Status | |
|---|---|---|---|
| Primer design | Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed. | template found | open → |
| BLAST | Search 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 found | open → |
| Expression heatmap | Draw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it. | ready | open → |
| Gene family / orthogroup | Look 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 analysis | Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it. | open → |
