Genomic Location: not available for this species
NR annotation: WP_170334470.1, LysR family transcriptional regulator [Ruegeria arenilitoris]
Species Cassiopea xamachana · all data for this species · gene families
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0014281 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF00126 all species → | HTH_1 | Bacterial regulatory helix-turn-helix protein, lysR family | Domain | Interproscan |
| PF03466 all species → | LysR_substrate | LysR substrate binding domain | Family | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR036388 all species → | Homologous_superfamily | Winged helix-like DNA-binding domain superfamily | Interproscan |
| IPR000847 all species → | Domain | Transcription regulator HTH, LysR | Interproscan |
| IPR036390 all species → | Homologous_superfamily | Winged helix DNA-binding domain superfamily | Interproscan |
| IPR005119 all species → | Domain | LysR, substrate-binding | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR30537 all species → | HTH-TYPE TRANSCRIPTIONAL REGULATOR | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0003700 all species → | Molecular Function | DNA-binding transcription factor activity | Interproscan |
| GO:0006351 all species → | Biological Process | DNA-templated transcription | Interproscan |
| GO:0043565 all species → | Molecular Function | sequence-specific DNA binding | Interproscan |
| GO:0006355 all species → | Biological Process | regulation of DNA-templated transcription | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K03566 | gcvA; LysR family transcriptional regulator, glycine cleavage system transcriptional activator | - | Transcription factors | ko03000 | 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 → |
