Genomic Location: chr9Alt:11079940...11083563
NR annotation: CAB4004345.1, Retrovirus-related Pol poly from transposon TNT 1-94, partial [Paramuricea clavata]
Species Acropora digitifera · all data for this species · gene families
| CDS |
| g19784.t1 |
| Transcript |
| chr9Alt.g19784.t1 |
| Protein |
| chr9Alt.g19784.t1 |
| UniProt accession | Description |
|---|---|
| P10978 | Retrovirus-related Pol polyprotein from transposon TNT 1-94 OS=Nicotiana tabacum OX=4097 PE=2 SV=1 |
| P04146 | Copia protein OS=Drosophila melanogaster OX=7227 GN=GIP PE=1 SV=3 |
| Q9ZT94 | Retrovirus-related Pol polyprotein from transposon RE2 OS=Arabidopsis thaliana OX=3702 GN=RE2 PE=4 SV=1 |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF07727 all species → | RVT_2 | Reverse transcriptase (RNA-dependent DNA polymerase) | Family | Interproscan |
| PF14223 all species → | Retrotran_gag_2 | gag-polypeptide of LTR copia-type | Family | Interproscan |
| PF00098 all species → | zf-CCHC | Zinc knuckle | Domain | Interproscan |
| PF13976 all species → | gag_pre-integrs | GAG-pre-integrase domain | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR013103 all species → | Domain | Reverse transcriptase, RNA-dependent DNA polymerase | Interproscan |
| IPR043502 all species → | Homologous_superfamily | DNA/RNA polymerase superfamily | Interproscan |
| IPR001878 all species → | Domain | Zinc finger, CCHC-type | Interproscan |
| IPR036397 all species → | Homologous_superfamily | Ribonuclease H superfamily | Interproscan |
| IPR012337 all species → | Homologous_superfamily | Ribonuclease H-like superfamily | Interproscan |
| IPR036875 all species → | Homologous_superfamily | Zinc finger, CCHC-type superfamily | Interproscan |
| IPR025724 all species → | Domain | GAG-pre-integrase domain | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR42648 all species → | TRANSPOSASE, PUTATIVE-RELATED | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0003676 all species → | Molecular Function | nucleic acid binding | Interproscan |
| GO:0008270 all species → | Molecular Function | zinc ion binding | Interproscan |
g19784.t1.Transcript abundance of g19784.t1 across 39 RNA-seq samples of Acropora digitifera. 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 |
|---|---|---|---|---|---|
| Coral branch | 39 | 21 | 1.32 | 6.46 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR23047208 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 6.46 |
| SRR23047210 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 5.59 |
| SRR23047213 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 4.53 |
| SRR23047223 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 3.70 |
| SRR23047216 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 3.70 |
| SRR23047242 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 3.64 |
| SRR23047239 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 3.57 |
| SRR23047229 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 3.52 |
| SRR23047233 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 3.33 |
| SRR23047226 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 3.31 |
| SRR23047232 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 2.49 |
| SRR23047219 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 2.41 |
| SRR23047211 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 1.83 |
| SRR23047209 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 1.47 |
| SRR23047236 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.56 |
| SRR23047206 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.36 |
| SRR23047244 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.29 |
| SRR23047230 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.22 |
| SRR23047207 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.19 |
| SRR23047241 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.15 |
| SRR23047212 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.07 |
| SRR23047214 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047215 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047217 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047218 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047220 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047221 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047222 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047224 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047225 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047227 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047228 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047231 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047234 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047235 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047237 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047238 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047240 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047243 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (ADIGI_TPM,
StringTie quantification over 39 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 Acropora digitifera 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 | 45 | g12885.t1 | 0.982260734838245 |
| Negatively correlated | 14 | g30671.t1 | -0.809225017303462 |
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 Acropora digitifera, 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.
| Assay | Sample | Peaks | Region |
|---|---|---|---|
| DNase-seq (DHS) | WholeAnimal | 2 | Distal Intergenic 2 |
Browse the full epigenomic landscape of this species: DNase-seq (DHS).
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 → |
