Genomic Location: JASJOG010000034.1:1344682...1348087
NR annotation: CAB3989749.1, visual system homeobox 1 isoform X1 [Paramuricea clavata]
Species Heliopora coerulea · all data for this species · gene families
| CDS |
| ENSBQFT00000018032 |
| Protein |
| ENSBQFP00000016140.1 |
| UniProt accession | Description |
|---|---|
| O42250 | Visual system homeobox 1 OS=Danio rerio OX=7955 GN=vsx1 PE=1 SV=2 |
| Q90277 | Visual system homeobox 1 OS=Carassius auratus OX=7957 GN=vsx1 PE=1 SV=1 |
| Q9IAL1 | Visual system homeobox 2 OS=Gallus gallus OX=9031 GN=VSX2 PE=2 SV=1 |
| 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 |
|---|---|---|---|
| IPR001356 all species → | Domain | Homeobox domain | Interproscan |
| IPR009057 all species → | Homologous_superfamily | Homeobox-like domain superfamily | Interproscan |
| IPR052294 all species → | Family | Visual system homeobox transcriptional regulators | Interproscan |
| IPR023339 all species → | Domain | CVC domain | Interproscan |
| IPR017970 all species → | Conserved_site | Homeobox, conserved site | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR46892 all species → | VISUAL SYSTEM HOMEOBOX 2 | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| 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 |
| 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 |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K24841 | IQCG, DRC9; dynein regulatory complex subunit 9 | - | Domain-containing proteins not elsewhere classified | ko04990 | deepkoala |
Transcript abundance of ENSBQFP00000016140.1 across 37 RNA-seq samples of Heliopora coerulea. This gene has no row in the species' RNA-seq expression matrix, so every value below is shown as zero — the matrix simply does not cover this transcript. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.
| Condition | Samples | TPM > 0 | Mean TPM | Max TPM | Mean, relative to max |
|---|---|---|---|---|---|
| Whole coral | 17 | 0 | 0.00 | 0.00 | |
| polyp and skeleton · 31C, 3week | 6 | 0 | 0.00 | 0.00 | |
| polyp and skeleton · 28C, 3week | 6 | 0 | 0.00 | 0.00 | |
| polyp and skeleton · 26C, 3week | 4 | 0 | 0.00 | 0.00 | |
| polyp and skeleton · 28C, 24hr | 2 | 0 | 0.00 | 0.00 | |
| polyp and skeleton · 31C, 24hr | 2 | 0 | 0.00 | 0.00 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| ERR6178387 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178388 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178389 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178770 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178771 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178772 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178773 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178774 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178775 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178776 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178777 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178778 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178779 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178780 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178781 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178782 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178783 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| SRR12578065 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 0.00 |
| SRR12578066 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 0.00 |
| SRR12578068 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 0.00 |
| SRR12587799 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 0.00 |
| SRR12587800 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 0.00 |
| SRR12587804 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 0.00 |
| SRR12578067 | polyp and skeleton · 28C, 3week | polyp and skeleton | not recorded | 28C, 3week | SRP115860 | 0.00 |
| SRR12587802 | polyp and skeleton · 28C, 3week | polyp and skeleton | not recorded | 28C, 3week | SRP115860 | 0.00 |
| SRR12587803 | polyp and skeleton · 28C, 3week | polyp and skeleton | not recorded | 28C, 3week | SRP115860 | 0.00 |
| SRR12587807 | polyp and skeleton · 28C, 3week | polyp and skeleton | not recorded | 28C, 3week | SRP115860 | 0.00 |
| SRR12587808 | polyp and skeleton · 28C, 3week | polyp and skeleton | not recorded | 28C, 3week | SRP115860 | 0.00 |
| SRR5949849 | polyp and skeleton · 28C, 3week | polyp and skeleton | not recorded | 28C, 3week | SRP115860 | 0.00 |
| SRR12587798 | polyp and skeleton · 26C, 3week | polyp and skeleton | not recorded | 26C, 3week | SRP115860 | 0.00 |
| SRR12587801 | polyp and skeleton · 26C, 3week | polyp and skeleton | not recorded | 26C, 3week | SRP115860 | 0.00 |
| SRR12587805 | polyp and skeleton · 26C, 3week | polyp and skeleton | not recorded | 26C, 3week | SRP115860 | 0.00 |
| SRR12587806 | polyp and skeleton · 26C, 3week | polyp and skeleton | not recorded | 26C, 3week | SRP115860 | 0.00 |
| SRR12578063 | polyp and skeleton · 28C, 24hr | polyp and skeleton | not recorded | 28C, 24hr | SRP115860 | 0.00 |
| SRR5949850 | polyp and skeleton · 28C, 24hr | polyp and skeleton | not recorded | 28C, 24hr | SRP115860 | 0.00 |
| SRR12578064 | polyp and skeleton · 31C, 24hr | polyp and skeleton | not recorded | 31C, 24hr | SRP115860 | 0.00 |
| SRR5949848 | polyp and skeleton · 31C, 24hr | polyp and skeleton | not recorded | 31C, 24hr | SRP115860 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (HCOER_TPM,
StringTie quantification over 37 runs), joined to SRA sample
metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped
by the descriptor carried in the expression matrix itself.
Genes whose expression across the transcriptome samples of Heliopora coerulea 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.
| Direction | Partners | Most correlated partner | PCC |
|---|---|---|---|
| Positively correlated | 0 | not in this network | - |
| Negatively correlated | 0 | not in this network | - |
This gene has no edge at all in the Heliopora coerulea network, in either direction — it is not one of the genes the network was built from (the network covers genes with enough expression variation across the transcriptome samples). The counts above are a property of the network, not a failed lookup.
Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.
Whether this gene can be visualised in the single-cell atlases of Heliopora coerulea, 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 → |
