Genomic Location: sc0000117_pilon:531305...562817
NR annotation: XP_029213858.1, DNA (cytosine-5)-methyltransferase 3A-like [Acropora millepora]
Species Acropora gemmifera · all data for this species · gene families
| CDS |
| agem_s0117.g20.t1 |
| Transcript |
| agem_s0117.g20.t1 |
| Protein |
| agem_s0117.g20.t1 |
| UniProt accession | Description |
|---|---|
| Q4W5Z4 | DNA (cytosine-5)-methyltransferase 3A OS=Gallus gallus OX=9031 GN=DNMT3A PE=2 SV=1 |
| Q1LZ53 | DNA (cytosine-5)-methyltransferase 3A OS=Rattus norvegicus OX=10116 GN=Dnmt3a PE=1 SV=1 |
| Q9Y6K1 | DNA (cytosine-5)-methyltransferase 3A OS=Homo sapiens OX=9606 GN=DNMT3A PE=1 SV=4 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0004463 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF00145 all species → | DNA_methylase | C-5 cytosine-specific DNA methylase | Domain | Interproscan |
| PF21255 all species → | ADDz_Dnmt3b | DNMT3, ADD PHD zinc finger | Domain | Interproscan |
| PF00855 all species → | PWWP | PWWP domain | Domain | Interproscan |
| PF17980 all species → | ADD_DNMT3 | Cysteine rich ADD domain in DNMT3 | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR001525 all species → | Family | C-5 cytosine methyltransferase | Interproscan |
| IPR049554 all species → | Domain | DNMT3, ADD domain, PHD zinc finger | Interproscan |
| IPR025766 all species → | Domain | ADD domain | Interproscan |
| IPR018117 all species → | Active_site | DNA methylase, C-5 cytosine-specific, active site | Interproscan |
| IPR000313 all species → | Domain | PWWP domain | Interproscan |
| IPR011011 all species → | Homologous_superfamily | Zinc finger, FYVE/PHD-type | Interproscan |
| IPR040552 all species → | Domain | DNMT3, cysteine rich ADD domain, GATA1-like zinc finger | Interproscan |
| IPR029063 all species → | Homologous_superfamily | S-adenosyl-L-methionine-dependent methyltransferase superfamily | Interproscan |
| IPR013083 all species → | Homologous_superfamily | Zinc finger, RING/FYVE/PHD-type | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR23068 all species → | DNA CYTOSINE-5- -METHYLTRANSFERASE 3-RELATED | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0008168 all species → | Molecular Function | methyltransferase activity | Interproscan |
| GO:0005634 all species → | Cellular Component | nucleus | Interproscan |
agem_s0117.g20.t1.Transcript abundance of agem_s0117.g20.t1 across 48 RNA-seq samples of Acropora gemmifera. 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 |
|---|---|---|---|---|---|
| branch tip | 48 | 4 | 3.64 | 49.29 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR3169422 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 49.29 |
| SRR3223317 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 44.95 |
| SRR2169558 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 43.47 |
| SRR3223319 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 37.26 |
| SRR3169421 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169423 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169425 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169426 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169518 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169527 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169528 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169529 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169530 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169531 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169532 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169533 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169534 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169535 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169536 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169537 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169538 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169539 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169540 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169541 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182410 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182448 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182557 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182684 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182685 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182686 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182775 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182776 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182777 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182778 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182779 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182780 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182781 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182784 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182785 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182786 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182787 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182788 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182789 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182790 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182791 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182792 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182793 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182794 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (AGEMM_TPM,
StringTie quantification over 48 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 gemmifera 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 | 13 | agem_s0059.g127.t1 | 0.999602193527314 |
| Negatively correlated | 5 | agem_s0028.g73.t1 | -0.620360200308589 |
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 gemmifera, 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 → |
