Genomic Location: chr2:17853623...17863234
NR annotation: RXN20472.1, roquin-1 isoform X1 [Labeo rohita]
Species Pelagia noctiluca · all data for this species · gene families
| CDS |
| ENSXLYT00000025808 |
| Transcript |
| ENSXLYT00000025808 |
| Protein |
| ENSXLYP00000024724.1 |
| UniProt accession | Description |
|---|---|
| Q6NUC6 | Roquin-1 OS=Xenopus laevis OX=8355 GN=rc3h1 PE=2 SV=1 |
| Q4VGL6 | Roquin-1 OS=Mus musculus OX=10090 GN=Rc3h1 PE=1 SV=1 |
| Q5TC82 | Roquin-1 OS=Homo sapiens OX=9606 GN=RC3H1 PE=1 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0003562 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF18386 all species → | ROQ_II | Roquin II domain | Domain | Interproscan |
| PF00642 all species → | zf-CCCH | Zinc finger C-x8-C-x5-C-x3-H type (and similar) | Family | Interproscan |
| PF14634 all species → | zf-RING_5 | zinc-RING finger domain | Domain | Interproscan |
| PF21206 all species → | Roquin_1_2-like_ROQ | Roquin 1/2-like, ROQ domain | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR036855 all species → | Homologous_superfamily | Zinc finger, CCCH-type superfamily | Interproscan |
| IPR000571 all species → | Domain | Zinc finger, CCCH-type | Interproscan |
| IPR017907 all species → | Conserved_site | Zinc finger, RING-type, conserved site | Interproscan |
| IPR041523 all species → | Domain | Roquin II | Interproscan |
| IPR001841 all species → | Domain | Zinc finger, RING-type | Interproscan |
| IPR052249 all species → | Family | Roquin domain-containing protein | Interproscan |
| IPR048575 all species → | Domain | Roquin 1/2-like, ROQ domain | Interproscan |
| IPR013083 all species → | Homologous_superfamily | Zinc finger, RING/FYVE/PHD-type | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR13139 all species → | RING FINGER AND CCCH-TYPE ZINC FINGER DOMAIN-CONTAINING PROTEIN | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0046872 all species → | Molecular Function | metal ion binding | Interproscan |
| GO:0000209 all species → | Biological Process | protein polyubiquitination | Interproscan |
| GO:0000288 all species → | Biological Process | nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay | Interproscan |
| GO:0003725 all species → | Molecular Function | double-stranded RNA binding | Interproscan |
| GO:0003729 all species → | Molecular Function | mRNA binding | Interproscan |
| GO:0006511 all species → | Biological Process | ubiquitin-dependent protein catabolic process | Interproscan |
| GO:0010494 all species → | Cellular Component | cytoplasmic stress granule | Interproscan |
| GO:0035613 all species → | Molecular Function | RNA stem-loop binding | Interproscan |
| GO:0061630 all species → | Molecular Function | ubiquitin protein ligase activity | Interproscan |
ENSXLYP00000024724.1.Genes whose expression across the transcriptome samples of Pelagia noctiluca 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 Pelagia noctiluca, 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 → |
