Genomic Location: JASJOG010000259.1:118857...121274
NR annotation: CAB3983589.1, Transcription elongation factor SPT4 [Paramuricea clavata]
Species Heliopora coerulea · all data for this species · gene families
| CDS |
| ENSBQFT00000050313 |
| Protein |
| ENSBQFP00000044638.1 |
| UniProt accession | Description |
|---|---|
| P63271 | Transcription elongation factor SPT4-A OS=Mus musculus OX=10090 GN=Supt4h1a PE=2 SV=1 |
| Q3SYX6 | Transcription elongation factor SPT4 OS=Bos taurus OX=9913 GN=SUPT4H1 PE=3 SV=1 |
| P63272 | Transcription elongation factor SPT4 OS=Homo sapiens OX=9606 GN=SUPT4H1 PE=1 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0009348 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF06093 all species → | Spt4 | Spt4/RpoE2 zinc finger | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR022800 all species → | Domain | Spt4/RpoE2 zinc finger | Interproscan |
| IPR009287 all species → | Family | Transcription initiation Spt4 | Interproscan |
| IPR038510 all species → | Homologous_superfamily | Spt4 superfamily | Interproscan |
| IPR029040 all species → | Homologous_superfamily | RNA polymerase subunit RPABC4/transcription elongation factor Spt4 | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR12882 all species → | SUPPRESSOR OF TY 4 | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0000993 all species → | Molecular Function | RNA polymerase II complex binding | Interproscan |
| GO:0005634 all species → | Cellular Component | nucleus | Interproscan |
| GO:0006325 all species → | Biological Process | chromatin organization | Interproscan |
| GO:0006355 all species → | Biological Process | regulation of DNA-templated transcription | Interproscan |
| GO:0008270 all species → | Molecular Function | zinc ion binding | Interproscan |
| GO:0032044 all species → | Cellular Component | DSIF complex | Interproscan |
| GO:0034243 all species → | Biological Process | regulation of transcription elongation by RNA polymerase II | Interproscan |
| GO:0140673 all species → | Biological Process | transcription elongation-coupled chromatin remodeling | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K15171 | SUPT4H1, SPT4; transcription elongation factor SPT4 | - | Messenger RNA biogenesis | ko03019 | deepkoala |
Transcript abundance of ENSBQFP00000044638.1 across 37 RNA-seq samples of Heliopora coerulea. 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 | 13 | 7.82 | 15.62 | |
| polyp and skeleton · 31C, 3week | 6 | 6 | 16.25 | 24.62 | |
| polyp and skeleton · 28C, 3week | 6 | 4 | 11.97 | 24.78 | |
| polyp and skeleton · 26C, 3week | 4 | 2 | 9.41 | 23.27 | |
| polyp and skeleton · 28C, 24hr | 2 | 2 | 13.85 | 19.54 | |
| polyp and skeleton · 31C, 24hr | 2 | 1 | 5.38 | 10.77 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| ERR6178772 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 15.62 |
| ERR6178387 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 14.77 |
| ERR6178388 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 14.06 |
| ERR6178779 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 13.71 |
| ERR6178780 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 12.04 |
| ERR6178782 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 10.30 |
| ERR6178781 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 10.30 |
| ERR6178389 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 9.81 |
| ERR6178770 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 8.99 |
| ERR6178776 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 8.39 |
| ERR6178783 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 7.85 |
| ERR6178778 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 4.12 |
| ERR6178773 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 2.96 |
| ERR6178771 | 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 |
| ERR6178777 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| SRR12578066 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 24.62 |
| SRR12587800 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 23.88 |
| SRR12587804 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 19.06 |
| SRR12587799 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 13.18 |
| SRR12578065 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 9.76 |
| SRR12578068 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 6.97 |
| SRR12587807 | polyp and skeleton · 28C, 3week | polyp and skeleton | not recorded | 28C, 3week | SRP115860 | 24.78 |
| SRR12587808 | polyp and skeleton · 28C, 3week | polyp and skeleton | not recorded | 28C, 3week | SRP115860 | 19.48 |
| SRR12587802 | polyp and skeleton · 28C, 3week | polyp and skeleton | not recorded | 28C, 3week | SRP115860 | 17.00 |
| SRR12587803 | polyp and skeleton · 28C, 3week | polyp and skeleton | not recorded | 28C, 3week | SRP115860 | 10.56 |
| SRR12578067 | 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 | 23.27 |
| SRR12587805 | polyp and skeleton · 26C, 3week | polyp and skeleton | not recorded | 26C, 3week | SRP115860 | 14.36 |
| SRR12587801 | 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 | 19.54 |
| SRR5949850 | polyp and skeleton · 28C, 24hr | polyp and skeleton | not recorded | 28C, 24hr | SRP115860 | 8.17 |
| SRR12578064 | polyp and skeleton · 31C, 24hr | polyp and skeleton | not recorded | 31C, 24hr | SRP115860 | 10.77 |
| 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 | 26 | ENSBQFP00000011158 | 0.916291449896532 |
| Negatively correlated | 4 | ENSBQFP00000005940 | -0.650291204842883 |
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. Partner counts were matched on ENSBQFP00000044638, the spelling this network uses.
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. | ready | open → |
| 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 → |
