Genomic Location: HOLI00299:199398...200593
NR annotation: WP_208932844.1, RNA polymerase factor sigma-54 [Rheinheimera sp. F8]
Species Hydra oligactis · all data for this species · gene families
| CDS |
| HOLI00299.g46669.t1 |
| Transcript |
| HOLI00299.g46669.t1 |
| Protein |
| HOLI00299.G46669 |
| UniProt accession | Description |
|---|---|
| Q9S0L2 | RNA polymerase sigma-54 factor OS=Shewanella violacea (strain JCM 10179 / CIP 106290 / LMG 19151 / DSS12) OX=637905 GN=rpoN PE=3 SV=1 |
| P06223 | RNA polymerase sigma-54 factor OS=Klebsiella oxytoca OX=571 GN=rpoN PE=1 SV=1 |
| P26979 | RNA polymerase sigma-54 factor OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) OX=99287 GN=rpoN PE=3 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0009864 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF00309 all species → | Sigma54_AID | Sigma-54 factor, Activator interacting domain (AID) | Family | Interproscan |
| PF04963 all species → | Sigma54_CBD | Sigma-54 factor, core binding domain | Domain | Interproscan |
| PF04552 all species → | Sigma54_DBD | Sigma-54, DNA binding domain | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR000394 all species → | Family | RNA polymerase sigma factor 54 | Interproscan |
| IPR007046 all species → | Domain | RNA polymerase sigma factor 54, core-binding domain | Interproscan |
| IPR038709 all species → | Homologous_superfamily | RNA polymerase sigma-54 factor, core-binding domain superfamily | Interproscan |
| IPR007634 all species → | Domain | RNA polymerase sigma factor 54, DNA-binding | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR32248 all species → | RNA POLYMERASE SIGMA-54 FACTOR | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0001216 all species → | Molecular Function | DNA-binding transcription activator activity | Interproscan |
| GO:0016987 all species → | Molecular Function | sigma factor activity | Interproscan |
| GO:0003677 all species → | Molecular Function | DNA binding | Interproscan |
| GO:0006352 all species → | Biological Process | DNA-templated transcription initiation | Interproscan |
HOLI00299.G46669.Genes whose expression across the transcriptome samples of Hydra oligactis 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 Hydra oligactis, 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 → |
