Genomic Location: not available for this species
NR annotation: WP_170326394.1, transcription antitermination factor NusB [Ruegeria arenilitoris]
Species Cassiopea xamachana · all data for this species · gene families
| UniProt accession | Description |
|---|---|
| Q9KVU5 | Ribosomal RNA small subunit methyltransferase B OS=Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) OX=243277 GN=rsmB PE=3 SV=1 |
| B2VK95 | Ribosomal RNA small subunit methyltransferase B OS=Erwinia tasmaniensis (strain DSM 17950 / CFBP 7177 / CIP 109463 / NCPPB 4357 / Et1/99) OX=465817 GN=rsmB PE=3 SV=1 |
| Q87KD3 | Ribosomal RNA small subunit methyltransferase B OS=Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) OX=223926 GN=rsmB PE=3 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0030275 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF01029 all species → | NusB | NusB family | Domain | Interproscan |
| PF01189 all species → | Methyltr_RsmB-F | 16S rRNA methyltransferase RsmB/F | Family | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR006027 all species → | Domain | NusB/RsmB/TIM44 | Interproscan |
| IPR023267 all species → | Family | RNA (C5-cytosine) methyltransferase | Interproscan |
| IPR035926 all species → | Homologous_superfamily | NusB-like superfamily | Interproscan |
| IPR001678 all species → | Domain | SAM-dependent methyltransferase RsmB-F/NOP2-type domain | Interproscan |
| IPR049560 all species → | Domain | SAM-dependent methyltransferase RsmB-F/NOP2-type, catalytic core | Interproscan |
| IPR029063 all species → | Homologous_superfamily | S-adenosyl-L-methionine-dependent methyltransferase superfamily | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR22807 all species → | NOP2 YEAST -RELATED NOL1/NOP2/FMU SUN DOMAIN-CONTAINING | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0003723 all species → | Molecular Function | RNA binding | Interproscan |
| GO:0006355 all species → | Biological Process | regulation of DNA-templated transcription | Interproscan |
| GO:0001510 all species → | Biological Process | RNA methylation | Interproscan |
| GO:0008173 all species → | Molecular Function | RNA methyltransferase activity | Interproscan |
| GO:0008168 all species → | Molecular Function | methyltransferase activity | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K03500 | rsmB, sun; 16S rRNA (cytosine967-C5)-methyltransferase | EC:2.1.1.176 | Ribosome biogenesis | ko03009 | deepkoala |
Genes whose expression across the transcriptome samples of Cassiopea xamachana 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 Cassiopea xamachana, 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. | sequence table not available | – |
| 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. | sequence table not available | – |
| 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 → |
