Genomic Location: HOLI00002:3239863...3240726
NR annotation: MBA4240022.1, RNA polymerase subunit sigma [Sphingobacteriaceae bacterium]
Species Hydra oligactis · all data for this species · gene families
| CDS |
| HOLI00002.g20008.t1 |
| Transcript |
| HOLI00002.g20008.t1 |
| Protein |
| HOLI00002.G20008 |
| UniProt accession | Description |
|---|---|
| P33656 | RNA polymerase sigma factor SigA OS=Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W) OX=272562 GN=sigA PE=3 SV=1 |
| O66381 | RNA polymerase sigma factor SigA OS=Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125) OX=272558 GN=sigA PE=3 SV=2 |
| P52329 | RNA polymerase sigma factor SigA OS=Enterococcus faecalis (strain ATCC 700802 / V583) OX=226185 GN=sigA PE=3 SV=2 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0013255 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF04542 all species → | Sigma70_r2 | Sigma-70 region 2 | Domain | Interproscan |
| PF00140 all species → | Sigma70_r1_2 | Sigma-70 factor, region 1.2 | Family | Interproscan |
| PF04545 all species → | Sigma70_r4 | Sigma-70, region 4 | Domain | Interproscan |
| PF04539 all species → | Sigma70_r3 | Sigma-70 region 3 | Family | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR036388 all species → | Homologous_superfamily | Winged helix-like DNA-binding domain superfamily | Interproscan |
| IPR007627 all species → | Domain | RNA polymerase sigma-70 region 2 | Interproscan |
| IPR050239 all species → | Family | Sigma-70 factor family, RNA polymerase initiation factors | Interproscan |
| IPR013324 all species → | Homologous_superfamily | RNA polymerase sigma factor, region 3/4-like | Interproscan |
| IPR013325 all species → | Homologous_superfamily | RNA polymerase sigma factor, region 2 | Interproscan |
| IPR009042 all species → | Domain | RNA polymerase sigma-70 region 1.2 | Interproscan |
| IPR014284 all species → | Domain | RNA polymerase sigma-70 like domain | Interproscan |
| IPR007630 all species → | Domain | RNA polymerase sigma-70 region 4 | Interproscan |
| IPR007624 all species → | Domain | RNA polymerase sigma-70 region 3 | Interproscan |
| IPR000943 all species → | Domain | RNA polymerase sigma-70 | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR30603 all species → | RNA POLYMERASE SIGMA FACTOR RPO | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0003700 all species → | Molecular Function | DNA-binding transcription factor activity | Interproscan |
| GO:0006352 all species → | Biological Process | DNA-templated transcription initiation | Interproscan |
| GO:0006355 all species → | Biological Process | regulation of DNA-templated transcription | Interproscan |
| GO:0003677 all species → | Molecular Function | DNA binding | Interproscan |
| GO:0016987 all species → | Molecular Function | sigma factor activity | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K03086 | rpoD; RNA polymerase primary sigma factor | - | Transcription machinery | ko03021 | deepkoala |
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 → |
