Genomic Location: HOLI00002:5130528...5131064
NR annotation: MBA4240844.1, RNA polymerase sigma-54 factor [Sphingobacteriaceae bacterium]
Species Hydra oligactis · all data for this species · gene families
| CDS |
| HOLI00002.g21576.t1 |
| Transcript |
| HOLI00002.g21576.t1 |
| Protein |
| HOLI00002.G21576 |
| UniProt accession | Description |
|---|---|
| P28615 | RNA polymerase sigma-54 factor OS=Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337) OX=381666 GN=rpoN PE=3 SV=2 |
| P0A171 | RNA polymerase sigma-54 factor OS=Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440) OX=160488 GN=rpoN PE=1 SV=1 |
| P0A172 | RNA polymerase sigma-54 factor OS=Pseudomonas putida OX=303 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 |
|---|---|---|---|---|
| PF04552 all species → | Sigma54_DBD | Sigma-54, DNA binding domain | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR007634 all species → | Domain | RNA polymerase sigma factor 54, DNA-binding | Interproscan |
| IPR000394 all species → | Family | RNA polymerase sigma factor 54 | 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 |
HOLI00002.G21576.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 → |
