Genomic Location: pcla8_s029738:1896...3552
NR annotation: CAB4039530.1, E3 ubiquitin- ligase PDZRN3-like [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families
| CDS |
| PACLA_8A055220 |
| Transcript |
| rna-PACLA_8A055220 |
| Protein |
| CAB4039530.1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0000376 (this species only) · gene tree & orthology |
| Ubiquitin family | E3|E3 activity RING|U-box · all ubiquitin genes in this species |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF01344 all species → | Kelch_1 | Kelch motif | Repeat | Interproscan |
| PF13923 all species → | zf-C3HC4_2 | Zinc finger, C3HC4 type (RING finger) | Domain | Interproscan |
| PF13418 all species → | Kelch_4 | Galactose oxidase, central domain | Repeat | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR013083 all species → | Homologous_superfamily | Zinc finger, RING/FYVE/PHD-type | Interproscan |
| IPR006652 all species → | Repeat | Kelch repeat type 1 | Interproscan |
| IPR001841 all species → | Domain | Zinc finger, RING-type | Interproscan |
| IPR015915 all species → | Homologous_superfamily | Kelch-type beta propeller | Interproscan |
| IPR001293 all species → | Domain | Zinc finger, TRAF-type | Interproscan |
| IPR051746 all species → | Family | Kelch domain-containing protein 8 | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR46260 all species → | RING-TYPE DOMAIN-CONTAINING PROTEIN | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0005515 all species → | Molecular Function | protein binding | Interproscan |
| GO:0008270 all species → | Molecular Function | zinc ion binding | Interproscan |
CAB4039530.1.Transcript abundance of CAB4039530.1 across 21 RNA-seq samples of Paramuricea clavata. 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 |
|---|---|---|---|---|---|
| apical branchlet · Control at T25 | 6 | 5 | 6.52 | 26.68 | |
| apical branchlet · Temperature treatment at T0 | 6 | 3 | 1.14 | 5.19 | |
| apical branchlet · Temperature treatment at T25 | 5 | 3 | 4.02 | 16.23 | |
| apical branchlet · Control at T0 | 4 | 3 | 11.14 | 37.42 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR19977440 | apical branchlet · Control at T25 | apical branchlet | not recorded | Control at T25 | SRP384900 | 26.68 |
| SRR19977433 | apical branchlet · Control at T25 | apical branchlet | not recorded | Control at T25 | SRP384900 | 9.68 |
| SRR19977441 | apical branchlet · Control at T25 | apical branchlet | not recorded | Control at T25 | SRP384900 | 1.39 |
| SRR19977455 | apical branchlet · Control at T25 | apical branchlet | not recorded | Control at T25 | SRP384900 | 0.87 |
| SRR19977444 | apical branchlet · Control at T25 | apical branchlet | not recorded | Control at T25 | SRP384900 | 0.47 |
| SRR19977439 | apical branchlet · Control at T25 | apical branchlet | not recorded | Control at T25 | SRP384900 | 0.00 |
| SRR19977437 | apical branchlet · Temperature treatment at T0 | apical branchlet | not recorded | Temperature treatment at T0 | SRP384900 | 5.19 |
| SRR19977427 | apical branchlet · Temperature treatment at T0 | apical branchlet | not recorded | Temperature treatment at T0 | SRP384900 | 0.98 |
| SRR19977438 | apical branchlet · Temperature treatment at T0 | apical branchlet | not recorded | Temperature treatment at T0 | SRP384900 | 0.69 |
| SRR19977426 | apical branchlet · Temperature treatment at T0 | apical branchlet | not recorded | Temperature treatment at T0 | SRP384900 | 0.00 |
| SRR19977428 | apical branchlet · Temperature treatment at T0 | apical branchlet | not recorded | Temperature treatment at T0 | SRP384900 | 0.00 |
| SRR19977436 | apical branchlet · Temperature treatment at T0 | apical branchlet | not recorded | Temperature treatment at T0 | SRP384900 | 0.00 |
| SRR19977434 | apical branchlet · Temperature treatment at T25 | apical branchlet | not recorded | Temperature treatment at T25 | SRP384900 | 16.23 |
| SRR19977425 | apical branchlet · Temperature treatment at T25 | apical branchlet | not recorded | Temperature treatment at T25 | SRP384900 | 2.45 |
| SRR19977435 | apical branchlet · Temperature treatment at T25 | apical branchlet | not recorded | Temperature treatment at T25 | SRP384900 | 1.42 |
| SRR19977432 | apical branchlet · Temperature treatment at T25 | apical branchlet | not recorded | Temperature treatment at T25 | SRP384900 | 0.00 |
| SRR19977463 | apical branchlet · Temperature treatment at T25 | apical branchlet | not recorded | Temperature treatment at T25 | SRP384900 | 0.00 |
| SRR19977445 | apical branchlet · Control at T0 | apical branchlet | not recorded | Control at T0 | SRP384900 | 37.42 |
| SRR19977446 | apical branchlet · Control at T0 | apical branchlet | not recorded | Control at T0 | SRP384900 | 6.13 |
| SRR19977443 | apical branchlet · Control at T0 | apical branchlet | not recorded | Control at T0 | SRP384900 | 1.01 |
| SRR19977442 | apical branchlet · Control at T0 | apical branchlet | not recorded | Control at T0 | SRP384900 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (PCLAV_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 Paramuricea clavata 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 | 4 | CAB3985850.1 | 0.895334954398375 |
| Negatively correlated | 14 | CAB4005014.1 | -0.530284726317257 |
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 Paramuricea clavata, 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 → |
