Genomic Location: JASJOG010000072.1:424086...429009
NR annotation: XP_028407789.1, exosome complex component RRP4-like [Dendronephthya gigantea]
Species Heliopora coerulea · all data for this species · gene families
| CDS |
| ENSBQFT00000029663 |
| Protein |
| ENSBQFP00000026505.1 |
| UniProt accession | Description |
|---|---|
| Q8VBV3 | Exosome complex component RRP4 OS=Mus musculus OX=10090 GN=Exosc2 PE=1 SV=1 |
| Q2KID0 | Exosome complex component RRP4 OS=Bos taurus OX=9913 GN=EXOSC2 PE=2 SV=1 |
| Q13868 | Exosome complex component RRP4 OS=Homo sapiens OX=9606 GN=EXOSC2 PE=1 SV=2 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0006464 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF14382 all species → | ECR1_N | Exosome complex exonuclease RRP4 N-terminal region | Domain | Interproscan |
| PF15985 all species → | KH_6 | KH domain | Domain | Interproscan |
| PF21266 all species → | RRP4_S1 | RRP4, S1 domain | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR026699 all species → | Family | Exosome complex RNA-binding protein 1/RRP40/RRP4 | Interproscan |
| IPR025721 all species → | Domain | Exosome complex component, N-terminal domain | Interproscan |
| IPR036612 all species → | Homologous_superfamily | K Homology domain, type 1 superfamily | Interproscan |
| IPR048565 all species → | Domain | RRP4, S1 domain | Interproscan |
| IPR012340 all species → | Homologous_superfamily | Nucleic acid-binding, OB-fold | Interproscan |
| IPR004088 all species → | Domain | K Homology domain, type 1 | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR21321 all species → | PNAS-3 RELATED | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0000176 all species → | Cellular Component | nuclear exosome (RNase complex) | Interproscan |
| GO:0000177 all species → | Cellular Component | cytoplasmic exosome (RNase complex) | Interproscan |
| GO:0000178 all species → | Cellular Component | exosome (RNase complex) | Interproscan |
| GO:0000467 all species → | Biological Process | exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) | Interproscan |
| GO:0003723 all species → | Molecular Function | RNA binding | Interproscan |
| GO:0034427 all species → | Biological Process | obsolete nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' | Interproscan |
| GO:0034475 all species → | Biological Process | U4 snRNA 3'-end processing | Interproscan |
| GO:0043928 all species → | Biological Process | obsolete exonucleolytic catabolism of deadenylated mRNA | Interproscan |
| GO:0071034 all species → | Biological Process | CUT catabolic process | Interproscan |
| GO:0071035 all species → | Biological Process | nuclear polyadenylation-dependent rRNA catabolic process | Interproscan |
| GO:0071038 all species → | Biological Process | TRAMP-dependent tRNA surveillance pathway | Interproscan |
| GO:0071051 all species → | Biological Process | poly(A)-dependent snoRNA 3'-end processing | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K03679 | RRP4, EXOSC2; exosome complex component RRP4 | - | Messenger RNA biogenesis | ko03019 | deepkoala |
Transcript abundance of ENSBQFP00000026505.1 across 37 RNA-seq samples of Heliopora coerulea. This gene has no row in the species' RNA-seq expression matrix, so every value below is shown as zero — the matrix simply does not cover this transcript. 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 coral | 17 | 0 | 0.00 | 0.00 | |
| polyp and skeleton · 31C, 3week | 6 | 0 | 0.00 | 0.00 | |
| polyp and skeleton · 28C, 3week | 6 | 0 | 0.00 | 0.00 | |
| polyp and skeleton · 26C, 3week | 4 | 0 | 0.00 | 0.00 | |
| polyp and skeleton · 28C, 24hr | 2 | 0 | 0.00 | 0.00 | |
| polyp and skeleton · 31C, 24hr | 2 | 0 | 0.00 | 0.00 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| ERR6178387 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178388 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178389 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178770 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178771 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178772 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178773 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178774 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178775 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178776 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178777 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178778 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178779 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178780 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178781 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178782 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178783 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| SRR12578065 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 0.00 |
| SRR12578066 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 0.00 |
| SRR12578068 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 0.00 |
| SRR12587799 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 0.00 |
| SRR12587800 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 0.00 |
| SRR12587804 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 0.00 |
| SRR12578067 | polyp and skeleton · 28C, 3week | polyp and skeleton | not recorded | 28C, 3week | SRP115860 | 0.00 |
| SRR12587802 | polyp and skeleton · 28C, 3week | polyp and skeleton | not recorded | 28C, 3week | SRP115860 | 0.00 |
| SRR12587803 | polyp and skeleton · 28C, 3week | polyp and skeleton | not recorded | 28C, 3week | SRP115860 | 0.00 |
| SRR12587807 | polyp and skeleton · 28C, 3week | polyp and skeleton | not recorded | 28C, 3week | SRP115860 | 0.00 |
| SRR12587808 | polyp and skeleton · 28C, 3week | polyp and skeleton | not recorded | 28C, 3week | SRP115860 | 0.00 |
| SRR5949849 | polyp and skeleton · 28C, 3week | polyp and skeleton | not recorded | 28C, 3week | SRP115860 | 0.00 |
| SRR12587798 | polyp and skeleton · 26C, 3week | polyp and skeleton | not recorded | 26C, 3week | SRP115860 | 0.00 |
| SRR12587801 | polyp and skeleton · 26C, 3week | polyp and skeleton | not recorded | 26C, 3week | SRP115860 | 0.00 |
| SRR12587805 | polyp and skeleton · 26C, 3week | polyp and skeleton | not recorded | 26C, 3week | SRP115860 | 0.00 |
| SRR12587806 | polyp and skeleton · 26C, 3week | polyp and skeleton | not recorded | 26C, 3week | SRP115860 | 0.00 |
| SRR12578063 | polyp and skeleton · 28C, 24hr | polyp and skeleton | not recorded | 28C, 24hr | SRP115860 | 0.00 |
| SRR5949850 | polyp and skeleton · 28C, 24hr | polyp and skeleton | not recorded | 28C, 24hr | SRP115860 | 0.00 |
| SRR12578064 | polyp and skeleton · 31C, 24hr | polyp and skeleton | not recorded | 31C, 24hr | SRP115860 | 0.00 |
| SRR5949848 | polyp and skeleton · 31C, 24hr | polyp and skeleton | not recorded | 31C, 24hr | SRP115860 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (HCOER_TPM,
StringTie quantification over 37 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 Heliopora 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 | 0 | not in this network | - |
| Negatively correlated | 0 | not in this network | - |
This gene has no edge at all in the Heliopora coerulea network, in either direction — it is not one of the genes the network was built from (the network covers genes with enough expression variation across the transcriptome samples). The counts above are a property of the network, not a failed lookup.
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 Heliopora 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. | no expression matrix | – |
| 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 → |
