Genomic Location: Chr11:9188900...9190779
NR annotation: CAB3989767.1, transcription factor Sox-9-like [Paramuricea clavata]
Species Hemicorallium imperiale · all data for this species · gene families
evm.model.Chr11.472 in HIMPE (the gene ID may belong to a different isoform naming scheme). Try the gene search.| UniProt accession | Description |
|---|---|
| Q6DFF5 | Transcription factor Sox-9-B OS=Xenopus laevis OX=8355 GN=sox9-b PE=2 SV=1 |
| B7ZR65 | Transcription factor Sox-9-A OS=Xenopus laevis OX=8355 GN=sox9-a PE=1 SV=1 |
| Q6F2E7 | Transcription factor Sox-9 OS=Xenopus tropicalis OX=8364 GN=sox9 PE=1 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0005988 (this species only) · gene tree & orthology |
| Transcription factor family | HMG · all TF in this species |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF00505 all species → | HMG_box | HMG (high mobility group) box | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR009071 all species → | Domain | High mobility group box domain | Interproscan |
| IPR036910 all species → | Homologous_superfamily | High mobility group box domain superfamily | Interproscan |
| IPR050917 all species → | Family | SOX Transcription Factors | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR45803 all species → | SOX100B | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0000978 all species → | Molecular Function | RNA polymerase II cis-regulatory region sequence-specific DNA binding | Interproscan |
| GO:0000981 all species → | Molecular Function | DNA-binding transcription factor activity, RNA polymerase II-specific | Interproscan |
| GO:0005634 all species → | Cellular Component | nucleus | Interproscan |
| GO:0006357 all species → | Biological Process | regulation of transcription by RNA polymerase II | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K18435 | SOX9; transcription factor SOX9 (SOX group E) | - | Transcription factors | ko03000 | deepkoala |
Genes whose expression across the transcriptome samples of Hemicorallium imperiale 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 Hemicorallium imperiale, 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. | not in the sequence table | 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. | not in the sequence table | 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 → |
