Genomic Location: chr4:15758479...15759689
NR annotation: CAB3994125.1, E3 ubiquitin- ligase NRDP1-like [Paramuricea clavata]
Species Eunicella verrucosa · all data for this species · gene families
| CDS |
| ENSNOVT00005033036 |
| Transcript |
| ENSNOVT00005033036 |
| Protein |
| ENSNOVP00005029167.1 |
| UniProt accession | Description |
|---|---|
| Q9UPQ7 | E3 ubiquitin-protein ligase PDZRN3 OS=Homo sapiens OX=9606 GN=PDZRN3 PE=1 SV=2 |
| P68907 | E3 ubiquitin-protein ligase PDZRN3 OS=Rattus norvegicus OX=10116 GN=Pdzrn3 PE=1 SV=1 |
| Q69ZS0 | E3 ubiquitin-protein ligase PDZRN3 OS=Mus musculus OX=10090 GN=Pdzrn3 PE=1 SV=3 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0001310 (this species only) · gene tree & orthology |
| Ubiquitin family | E3|E3 activity RING|U-box · all ubiquitin genes in this species |
ENSNOVP00005029167.1 in Eunicella verrucosa.| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR001293 all species → | Domain | Zinc finger, TRAF-type | Interproscan |
| IPR051438 all species → | Family | RNF E3 ubiquitin-protein ligase | Interproscan |
| IPR001841 all species → | Domain | Zinc finger, RING-type | Interproscan |
| IPR013083 all species → | Homologous_superfamily | Zinc finger, RING/FYVE/PHD-type | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR46016 all species → | ZINC FINGER, RING/FYVE/PHD-TYPE | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0008270 all species → | Molecular Function | zinc ion binding | Interproscan |
| GO:0000209 all species → | Biological Process | protein polyubiquitination | Interproscan |
| GO:0006511 all species → | Biological Process | ubiquitin-dependent protein catabolic process | Interproscan |
| GO:0061630 all species → | Molecular Function | ubiquitin protein ligase activity | Interproscan |
ENSNOVP00005029167.1.Transcript abundance of ENSNOVP00005029167.1 across 21 RNA-seq samples of Eunicella verrucosa. 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 |
|---|---|---|---|---|---|
| whole tissue | 21 | 1 | 0.45 | 9.42 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| ERR11252253 | whole tissue | whole tissue | polyp | not recorded | ERP146504 | 9.42 |
| ERR11252240 | whole tissue | whole tissue | polyp | not recorded | ERP146504 | 0.00 |
| ERR11252242 | whole tissue | whole tissue | polyp | not recorded | ERP146504 | 0.00 |
| ERR11252243 | whole tissue | whole tissue | polyp | not recorded | ERP146504 | 0.00 |
| ERR11252244 | whole tissue | whole tissue | polyp | not recorded | ERP146504 | 0.00 |
| ERR11252245 | whole tissue | whole tissue | polyp | not recorded | ERP146504 | 0.00 |
| ERR11252246 | whole tissue | whole tissue | polyp | not recorded | ERP146504 | 0.00 |
| ERR11252248 | whole tissue | whole tissue | polyp | not recorded | ERP146504 | 0.00 |
| ERR11252249 | whole tissue | whole tissue | polyp | not recorded | ERP146504 | 0.00 |
| ERR11252250 | whole tissue | whole tissue | polyp | not recorded | ERP146504 | 0.00 |
| ERR11252251 | whole tissue | whole tissue | polyp | not recorded | ERP146504 | 0.00 |
| ERR11252252 | whole tissue | whole tissue | polyp | not recorded | ERP146504 | 0.00 |
| ERR11252254 | whole tissue | whole tissue | polyp | not recorded | ERP146504 | 0.00 |
| ERR11252255 | whole tissue | whole tissue | polyp | not recorded | ERP146504 | 0.00 |
| ERR11252256 | whole tissue | whole tissue | polyp | not recorded | ERP146504 | 0.00 |
| ERR11252257 | whole tissue | whole tissue | polyp | not recorded | ERP146504 | 0.00 |
| ERR11252258 | whole tissue | whole tissue | polyp | not recorded | ERP146504 | 0.00 |
| ERR11252259 | whole tissue | whole tissue | polyp | not recorded | ERP146504 | 0.00 |
| ERR11252260 | whole tissue | whole tissue | polyp | not recorded | ERP146504 | 0.00 |
| ERR11252261 | whole tissue | whole tissue | polyp | not recorded | ERP146504 | 0.00 |
| ERR11252262 | whole tissue | whole tissue | polyp | not recorded | ERP146504 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (EVERR_TPM,
StringTie quantification over 21 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 Eunicella verrucosa 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 | 50 | ENSNOVP00005016921.1 | 1 |
| Negatively correlated | 3 | ENSNOVP00005019896.1 | -0.550756138916537 |
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 Eunicella verrucosa, 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 → |
