Genomic Location: sc0000324_pilon:286776...288668
NR annotation: XP_029182467.2, putative exosome complex component rrp40 [Acropora millepora]
Species Acropora gemmifera · all data for this species · gene families
| CDS |
| agem_s0324.g22.t1 |
| Transcript |
| agem_s0324.g22.t1 |
| Protein |
| agem_s0324.g22.t1 |
| UniProt accession | Description |
|---|---|
| Q7KWX9 | Putative exosome complex component rrp40 OS=Dictyostelium discoideum OX=44689 GN=exosc3 PE=3 SV=1 |
| Q7TQK4 | Exosome complex component RRP40 OS=Mus musculus OX=10090 GN=Exosc3 PE=1 SV=3 |
| Q9NQT5 | Exosome complex component RRP40 OS=Homo sapiens OX=9606 GN=EXOSC3 PE=1 SV=3 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0006678 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF21262 all species → | RRP40_S1 | Exosome complex component RRP40, S1 domain | Domain | Interproscan |
| PF15985 all species → | KH_6 | KH domain | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR037319 all species → | Domain | Rrp40, S1 domain | Interproscan |
| IPR012340 all species → | Homologous_superfamily | Nucleic acid-binding, OB-fold | Interproscan |
| IPR036612 all species → | Homologous_superfamily | K Homology domain, type 1 superfamily | Interproscan |
| IPR026699 all species → | Family | Exosome complex RNA-binding protein 1/RRP40/RRP4 | Interproscan |
| IPR049469 all species → | Domain | Exosome complex component RRP40, type I KH domain | 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:0003723 all species → | Molecular Function | RNA binding | Interproscan |
| 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: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 |
|---|---|---|---|---|---|
| K03681 | RRP40, EXOSC3; exosome complex component RRP40 | - | Messenger RNA biogenesis | ko03019 | deepkoala |
Transcript abundance of agem_s0324.g22.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 | 15 | 148.59 | 940.57 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR3169535 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 940.57 |
| SRR3182789 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 891.39 |
| SRR3182793 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 833.62 |
| SRR3169532 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 725.69 |
| SRR3182787 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 640.67 |
| SRR3169422 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 566.35 |
| SRR3169518 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 557.90 |
| SRR3169426 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 428.72 |
| SRR3169527 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 392.03 |
| SRR3169537 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 331.55 |
| SRR3169528 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 322.27 |
| SRR3169425 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 269.60 |
| SRR3182788 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 206.42 |
| SRR3223319 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 18.12 |
| SRR3223317 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 7.45 |
| SRR2169558 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169421 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169423 | 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 |
| SRR3169533 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169534 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169536 | 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 |
| 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 |
| 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 | 0 | not in this network | - |
| Negatively correlated | 11 | agem_s0176.g11.t1 | -0.302277750291412 |
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 → |
