Genomic Location: chr4:10776817...10786567
NR annotation: XP_015753495.1, PREDICTED: regulator of nonsense transcripts 3B-like [Acropora digitifera]
Species Mastigias papua · all data for this species · gene families
| CDS |
| BRAKERKYLT00000018926 |
| Transcript |
| BRAKERKYLT00000018926 |
| Protein |
| BRAKERKYLP00000018926.1 |
| UniProt accession | Description |
|---|---|
| B0S733 | Regulator of nonsense transcripts 3A OS=Danio rerio OX=7955 GN=upf3a PE=1 SV=2 |
| F1QNX7 | Regulator of nonsense transcripts 3B OS=Danio rerio OX=7955 GN=upf3b PE=2 SV=1 |
| Q9BZI7 | Regulator of nonsense transcripts 3B OS=Homo sapiens OX=9606 GN=UPF3B PE=1 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0005524 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF03467 all species → | Smg4_UPF3 | Smg-4/UPF3 family | Family | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR005120 all species → | Domain | UPF3 domain | Interproscan |
| IPR035979 all species → | Homologous_superfamily | RNA-binding domain superfamily | Interproscan |
| IPR039722 all species → | Family | Nonsense-mediated mRNA decay protein 3 | Interproscan |
| IPR012677 all species → | Homologous_superfamily | Nucleotide-binding alpha-beta plait domain superfamily | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR13112 all species → | UPF3 REGULATOR OF NONSENSE TRANSCRIPTS-LIKE PROTEIN | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0003676 all species → | Molecular Function | nucleic acid binding | Interproscan |
| GO:0000184 all species → | Biological Process | nuclear-transcribed mRNA catabolic process, nonsense-mediated decay | Interproscan |
| GO:0003729 all species → | Molecular Function | mRNA binding | Interproscan |
| GO:0005730 all species → | Cellular Component | nucleolus | Interproscan |
| GO:0005737 all species → | Cellular Component | cytoplasm | Interproscan |
| GO:0045727 all species → | Biological Process | positive regulation of translation | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K14328 | UPF3, RENT3; regulator of nonsense transcripts 3 | - | Messenger RNA biogenesis | ko03019 | deepkoala |
Genes whose expression across the transcriptome samples of Mastigias papua 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.
No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.
Whether this gene can be visualised in the single-cell atlases of Mastigias papua, 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. | not in the sequence table | 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. | not in the sequence table | 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 → |
