Genomic Location: Chr09:23793000...23797655
NR annotation: CAB3989749.1, visual system homeobox 1 isoform X1 [Paramuricea clavata]
Species Hemicorallium imperiale · all data for this species · gene families
evm.model.Chr09.1443 in HIMPE (the gene ID may belong to a different isoform naming scheme). Try the gene search.| UniProt accession | Description |
|---|---|
| Q90277 | Visual system homeobox 1 OS=Carassius auratus OX=7957 GN=vsx1 PE=1 SV=1 |
| P41935 | Homeobox protein ceh-10 OS=Caenorhabditis elegans OX=6239 GN=ceh-10 PE=1 SV=1 |
| O42250 | Visual system homeobox 1 OS=Danio rerio OX=7955 GN=vsx1 PE=1 SV=2 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0000263 (this species only) · gene tree & orthology |
| Transcription factor family | Homeobox · all TF in this species |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF00046 all species → | Homeodomain | Homeodomain | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR017970 all species → | Conserved_site | Homeobox, conserved site | Interproscan |
| IPR001356 all species → | Domain | Homeobox domain | Interproscan |
| IPR052294 all species → | Family | Visual system homeobox transcriptional regulators | Interproscan |
| IPR009057 all species → | Homologous_superfamily | Homeobox-like domain superfamily | Interproscan |
| IPR023339 all species → | Domain | CVC domain | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR46892 all species → | VISUAL SYSTEM HOMEOBOX 2 | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0000981 all species → | Molecular Function | DNA-binding transcription factor activity, RNA polymerase II-specific | Interproscan |
| GO:0006355 all species → | Biological Process | regulation of DNA-templated transcription | Interproscan |
| GO:0003677 all species → | Molecular Function | DNA binding | Interproscan |
| GO:0005634 all species → | Cellular Component | nucleus | Interproscan |
| GO:0006357 all species → | Biological Process | regulation of transcription by RNA polymerase II | Interproscan |
| GO:1990837 all species → | Molecular Function | sequence-specific double-stranded DNA binding | Interproscan |
evm.model.Chr09.1443.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 → |
