Genomic Location: not available for this species
NR annotation: MBN2490102.1, RNA polymerase sigma factor RpoD [Planctomycetota bacterium]
Species Cassiopea xamachana · all data for this species · gene families
| UniProt accession | Description |
|---|---|
| P56835 | RNA polymerase sigma factor SigA OS=Chlamydia muridarum (strain MoPn / Nigg) OX=243161 GN=sigA PE=3 SV=1 |
| P18333 | RNA polymerase sigma factor SigA OS=Chlamydia trachomatis serovar D (strain ATCC VR-885 / DSM 19411 / UW-3/Cx) OX=272561 GN=sigA PE=1 SV=2 |
| Q9Z7F0 | RNA polymerase sigma factor SigA OS=Chlamydia pneumoniae OX=83558 GN=sigA PE=3 SV=1 |
| 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 |
| PF04545 all species → | Sigma70_r4 | Sigma-70, region 4 | Domain | Interproscan |
| PF04539 all species → | Sigma70_r3 | Sigma-70 region 3 | Family | Interproscan |
| PF00140 all species → | Sigma70_r1_2 | Sigma-70 factor, region 1.2 | Family | Interproscan |
| PF03979 all species → | Sigma70_r1_1 | Sigma-70 factor, region 1.1 | Family | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR014284 all species → | Domain | RNA polymerase sigma-70 like domain | Interproscan |
| IPR000943 all species → | Domain | RNA polymerase sigma-70 | Interproscan |
| IPR028630 all species → | Family | RNA polymerase sigma factor RpoD | Interproscan |
| IPR007627 all species → | Domain | RNA polymerase sigma-70 region 2 | Interproscan |
| IPR007630 all species → | Domain | RNA polymerase sigma-70 region 4 | Interproscan |
| IPR007624 all species → | Domain | RNA polymerase sigma-70 region 3 | Interproscan |
| IPR009042 all species → | Domain | RNA polymerase sigma-70 region 1.2 | Interproscan |
| IPR013325 all species → | Homologous_superfamily | RNA polymerase sigma factor, region 2 | Interproscan |
| IPR013324 all species → | Homologous_superfamily | RNA polymerase sigma factor, region 3/4-like | Interproscan |
| IPR012760 all species → | Domain | RNA polymerase sigma factor RpoD, C-terminal | Interproscan |
| IPR036388 all species → | Homologous_superfamily | Winged helix-like DNA-binding domain superfamily | Interproscan |
| IPR042189 all species → | Homologous_superfamily | Sigma-70 factor, region 1.1 superfamily | Interproscan |
| IPR050239 all species → | Family | Sigma-70 factor family, RNA polymerase initiation factors | Interproscan |
| IPR007127 all species → | Domain | RNA polymerase sigma factor 70, region 1.1 | 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:0016987 all species → | Molecular Function | sigma factor activity | Interproscan |
| GO:0003677 all species → | Molecular Function | DNA binding | 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 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 → |
