Genomic Location: chr21:13362312...13364849
NR annotation: XP_047244536.1, E3 ubiquitin-protein ligase rnf146-like [Girardinichthys multiradiatus]
Species Aurelia coerulea · all data for this species · gene families
| CDS |
| evm.model.ptg000028l.921 |
| Transcript |
| evm.model.ptg000028l.921 |
| Protein |
| evm.model.ptg000028l.921 |
| UniProt accession | Description |
|---|---|
| C0HBT3 | E3 ubiquitin-protein ligase rnf146 OS=Salmo salar OX=8030 GN=rnf146 PE=2 SV=1 |
| Q6GQD5 | E3 ubiquitin-protein ligase rnf146 OS=Xenopus laevis OX=8355 GN=rnf146 PE=2 SV=1 |
| Q66JE4 | E3 ubiquitin-protein ligase rnf146 OS=Xenopus tropicalis OX=8364 GN=rnf146 PE=2 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0006731 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF13920 all species → | zf-C3HC4_3 | Zinc finger, C3HC4 type (RING finger) | Domain | Interproscan |
| PF02825 all species → | WWE | WWE domain | Family | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR018123 all species → | Domain | WWE domain, subgroup | Interproscan |
| IPR033509 all species → | Family | E3 ubiquitin-protein ligase RNF146 | Interproscan |
| IPR037197 all species → | Homologous_superfamily | WWE domain superfamily | Interproscan |
| IPR001841 all species → | Domain | Zinc finger, RING-type | Interproscan |
| IPR017907 all species → | Conserved_site | Zinc finger, RING-type, conserved site | Interproscan |
| IPR004170 all species → | Domain | WWE domain | Interproscan |
| IPR044110 all species → | Domain | RNF146, RING finger, HC subclass | Interproscan |
| IPR013083 all species → | Homologous_superfamily | Zinc finger, RING/FYVE/PHD-type | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR13417 all species → | UNCHARACTERIZED | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0008270 all species → | Molecular Function | zinc ion binding | Interproscan |
| GO:0004842 all species → | Molecular Function | ubiquitin-protein transferase activity | Interproscan |
| GO:0005634 all species → | Cellular Component | nucleus | Interproscan |
| GO:0005737 all species → | Cellular Component | cytoplasm | Interproscan |
| GO:0006511 all species → | Biological Process | ubiquitin-dependent protein catabolic process | Interproscan |
| GO:0016055 all species → | Biological Process | Wnt signaling pathway | Interproscan |
| GO:0061630 all species → | Molecular Function | ubiquitin protein ligase activity | Interproscan |
| GO:0072572 all species → | Molecular Function | poly-ADP-D-ribose binding | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K15700 | RNF146; E3 ubiquitin-protein ligase RNF146 | EC:2.3.2.27 | Ubiquitin system | ko04121 | deepkoala |
Transcript abundance of evm.model.ptg000028l.921 across 30 RNA-seq samples of Aurelia coerulea. 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.
Every sample in this dataset carries its own condition — the source metadata gives each run a distinct treatment label — so this table is effectively a sample list. The per-sample chart below is the informative view here.
| Condition | Samples | TPM > 0 | Mean TPM | Max TPM | Mean, relative to max |
|---|---|---|---|---|---|
| whole organism · T_A1ES | 1 | 1 | 25.63 | 25.63 | |
| whole organism · T_C3E | 1 | 1 | 37.73 | 37.73 | |
| whole organism · T_C2P | 1 | 1 | 25.40 | 25.40 | |
| whole organism · T_A2ES | 1 | 1 | 26.67 | 26.67 | |
| whole organism · T_A3ES | 1 | 1 | 33.59 | 33.59 | |
| whole organism · T_C1AS | 1 | 1 | 18.58 | 18.58 | |
| whole organism · T_C2AS | 1 | 1 | 28.62 | 28.62 | |
| whole organism · T_C3AS | 1 | 1 | 22.39 | 22.39 | |
| whole organism · T_A1AS | 1 | 1 | 31.21 | 31.21 | |
| whole organism · T_A2AS | 1 | 1 | 41.13 | 41.13 | |
| whole organism · T_A3AS | 1 | 1 | 36.98 | 36.98 | |
| whole organism · T_C1E | 1 | 1 | 34.61 | 34.61 | |
| whole organism · T_C2E | 1 | 1 | 31.05 | 31.05 | |
| whole organism · T_C3P | 1 | 1 | 24.98 | 24.98 | |
| whole organism · T_AE1 | 1 | 1 | 49.84 | 49.84 | |
| whole organism · T_C3ES | 1 | 1 | 28.58 | 28.58 | |
| whole organism · T_AE2 | 1 | 1 | 50.20 | 50.20 | |
| whole organism · T_AE3 | 1 | 1 | 39.01 | 39.01 | |
| whole organism · T_AES1 | 1 | 1 | 53.66 | 53.66 | |
| whole organism · T_AES2 | 1 | 1 | 79.93 | 79.93 | |
| whole organism · T_AES3 | 1 | 1 | 45.78 | 45.78 | |
| whole organism · T_AAS1 | 1 | 1 | 40.04 | 40.04 | |
| whole organism · T_AAS2 | 1 | 1 | 45.92 | 45.92 | |
| whole organism · T_AAS3 | 1 | 1 | 43.17 | 43.17 | |
| whole organism · T_A1P | 1 | 1 | 17.44 | 17.44 | |
| whole organism · T_A2P | 1 | 1 | 8.87 | 8.87 | |
| whole organism · T_A3P | 1 | 1 | 13.12 | 13.12 | |
| whole organism · T_C1ES | 1 | 1 | 27.48 | 27.48 | |
| whole organism · T_C2ES | 1 | 1 | 26.18 | 26.18 | |
| whole organism · T_C1P | 1 | 1 | 11.76 | 11.76 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR25982246 | whole organism · T_A1ES | whole organism | not recorded | T_A1ES | SRP459341 | 25.63 |
| SRR25982262 | whole organism · T_C3E | whole organism | not recorded | T_C3E | SRP459341 | 37.73 |
| SRR25982274 | whole organism · T_C2P | whole organism | not recorded | T_C2P | SRP459341 | 25.40 |
| SRR25982273 | whole organism · T_A2ES | whole organism | not recorded | T_A2ES | SRP459341 | 26.67 |
| SRR25982272 | whole organism · T_A3ES | whole organism | not recorded | T_A3ES | SRP459341 | 33.59 |
| SRR25982271 | whole organism · T_C1AS | whole organism | not recorded | T_C1AS | SRP459341 | 18.58 |
| SRR25982270 | whole organism · T_C2AS | whole organism | not recorded | T_C2AS | SRP459341 | 28.62 |
| SRR25982269 | whole organism · T_C3AS | whole organism | not recorded | T_C3AS | SRP459341 | 22.39 |
| SRR25982268 | whole organism · T_A1AS | whole organism | not recorded | T_A1AS | SRP459341 | 31.21 |
| SRR25982267 | whole organism · T_A2AS | whole organism | not recorded | T_A2AS | SRP459341 | 41.13 |
| SRR25982266 | whole organism · T_A3AS | whole organism | not recorded | T_A3AS | SRP459341 | 36.98 |
| SRR25982265 | whole organism · T_C1E | whole organism | not recorded | T_C1E | SRP459341 | 34.61 |
| SRR25982264 | whole organism · T_C2E | whole organism | not recorded | T_C2E | SRP459341 | 31.05 |
| SRR25982263 | whole organism · T_C3P | whole organism | not recorded | T_C3P | SRP459341 | 24.98 |
| SRR25982261 | whole organism · T_AE1 | whole organism | not recorded | T_AE1 | SRP459341 | 49.84 |
| SRR25982247 | whole organism · T_C3ES | whole organism | not recorded | T_C3ES | SRP459341 | 28.58 |
| SRR25982260 | whole organism · T_AE2 | whole organism | not recorded | T_AE2 | SRP459341 | 50.20 |
| SRR25982259 | whole organism · T_AE3 | whole organism | not recorded | T_AE3 | SRP459341 | 39.01 |
| SRR25982258 | whole organism · T_AES1 | whole organism | not recorded | T_AES1 | SRP459341 | 53.66 |
| SRR25982257 | whole organism · T_AES2 | whole organism | not recorded | T_AES2 | SRP459341 | 79.93 |
| SRR25982256 | whole organism · T_AES3 | whole organism | not recorded | T_AES3 | SRP459341 | 45.78 |
| SRR25982255 | whole organism · T_AAS1 | whole organism | not recorded | T_AAS1 | SRP459341 | 40.04 |
| SRR25982254 | whole organism · T_AAS2 | whole organism | not recorded | T_AAS2 | SRP459341 | 45.92 |
| SRR25982253 | whole organism · T_AAS3 | whole organism | not recorded | T_AAS3 | SRP459341 | 43.17 |
| SRR25982252 | whole organism · T_A1P | whole organism | not recorded | T_A1P | SRP459341 | 17.44 |
| SRR25982251 | whole organism · T_A2P | whole organism | not recorded | T_A2P | SRP459341 | 8.87 |
| SRR25982250 | whole organism · T_A3P | whole organism | not recorded | T_A3P | SRP459341 | 13.12 |
| SRR25982249 | whole organism · T_C1ES | whole organism | not recorded | T_C1ES | SRP459341 | 27.48 |
| SRR25982248 | whole organism · T_C2ES | whole organism | not recorded | T_C2ES | SRP459341 | 26.18 |
| SRR25982275 | whole organism · T_C1P | whole organism | not recorded | T_C1P | SRP459341 | 11.76 |
Source: CnidoSite RNA-seq expression matrices (ACOER_TPM,
StringTie quantification over 30 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 Aurelia coerulea 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 | 12 | evm.model.ptg000002l.3 | 0.958429715028305 |
| Negatively correlated | 3 | evm.model.ptg000007l.783 | -0.819508533239419 |
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 Aurelia coerulea, 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 → |
