Genomic Location: sc0000322_pilon:198689...222535
NR annotation: XP_044169806.1, pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3-like isoform X1 [Acropora millepora]
Species Acropora muricata · all data for this species · gene families
| CDS |
| amur_s0322.g12.t1 |
| Transcript |
| amur_s0322.g12.t1 |
| Protein |
| amur_s0322.g12.t1 |
| UniProt accession | Description |
|---|---|
| Q5RJT2 | pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3 OS=Rattus norvegicus OX=10116 GN=Ftsj3 PE=1 SV=1 |
| Q9DBE9 | pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3 OS=Mus musculus OX=10090 GN=Ftsj3 PE=1 SV=1 |
| Q5RAS1 | pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3 OS=Pongo abelii OX=9601 GN=FTSJ3 PE=2 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0003939 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF01728 all species → | FtsJ | FtsJ-like methyltransferase | Family | Interproscan |
| PF07780 all species → | Spb1_C | Spb1 C-terminal domain | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR029063 all species → | Homologous_superfamily | S-adenosyl-L-methionine-dependent methyltransferase superfamily | Interproscan |
| IPR050082 all species → | Family | Ribosomal RNA large subunit methyltransferase RlmE | Interproscan |
| IPR002877 all species → | Domain | Ribosomal RNA methyltransferase, FtsJ domain | Interproscan |
| IPR012920 all species → | Domain | Ribosomal RNA methyltransferase, SPB1-like, C-terminal | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR10920 all species → | RIBOSOMAL RNA METHYLTRANSFERASE | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0000463 all species → | Biological Process | maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) | Interproscan |
| GO:0000466 all species → | Biological Process | maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) | Interproscan |
| GO:0001510 all species → | Biological Process | RNA methylation | Interproscan |
| GO:0005730 all species → | Cellular Component | nucleolus | Interproscan |
| GO:0008173 all species → | Molecular Function | RNA methyltransferase activity | Interproscan |
| GO:0008650 all species → | Molecular Function | rRNA (uridine-2'-O-)-methyltransferase activity | Interproscan |
| GO:0016435 all species → | Molecular Function | rRNA (guanine) methyltransferase activity | Interproscan |
| GO:0030687 all species → | Cellular Component | preribosome, large subunit precursor | Interproscan |
| GO:0031167 all species → | Biological Process | rRNA methylation | Interproscan |
| GO:0008168 all species → | Molecular Function | methyltransferase activity | Interproscan |
| GO:0032259 all species → | Biological Process | methylation | Interproscan |
| GO:0005634 all species → | Cellular Component | nucleus | Interproscan |
| GO:0006364 all species → | Biological Process | rRNA processing | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K14857 | SPB1, FTSJ3; AdoMet-dependent rRNA methyltransferase SPB1 | EC:2.1.1.- | Ribosome biogenesis | ko03009 | deepkoala |
Transcript abundance of amur_s0322.g12.t1 across 82 RNA-seq samples of Acropora muricata. 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 |
|---|---|---|---|---|---|
| Polyps | 79 | 69 | 97.27 | 4,527.17 | |
| Severed branch | 3 | 0 | 0.00 | 0.00 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR12927881 | Polyps | Polyps | E2 day0 | not recorded | SRP199550 | 4,527.17 |
| SRR27868201 | Polyps | Polyps | regeneration day15 | not recorded | SRP199550 | 143.82 |
| SRR12959206 | Polyps | Polyps | E2 day0 | not recorded | SRP199550 | 92.75 |
| SRR27868199 | Polyps | Polyps | regeneration day18 | not recorded | SRP199550 | 83.92 |
| SRR27868186 | Polyps | Polyps | regeneration day30 | not recorded | SRP199550 | 81.70 |
| SRR27868182 | Polyps | Polyps | regeneration day33 | not recorded | SRP199550 | 68.38 |
| SRR12959207 | Polyps | Polyps | E2 day15 | not recorded | SRP199550 | 66.08 |
| SRR27940227 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 58.42 |
| SRR27868194 | Polyps | Polyps | regeneration day21 | not recorded | SRP199550 | 57.84 |
| SRR27868184 | Polyps | Polyps | regeneration day30 | not recorded | SRP199550 | 55.67 |
| SRR27868159 | Polyps | Polyps | regeneration day6 | not recorded | SRP199550 | 53.52 |
| SRR27868206 | Polyps | Polyps | regeneration day12 | not recorded | SRP199550 | 52.12 |
| SRR27868190 | Polyps | Polyps | regeneration day27 | not recorded | SRP199550 | 52.10 |
| SRR12786900 | Polyps | Polyps | OA 2 day0 | not recorded | SRP199550 | 52.04 |
| SRR27940222 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 51.49 |
| SRR27868188 | Polyps | Polyps | regeneration day27 | not recorded | SRP199550 | 49.48 |
| SRR12959217 | Polyps | Polyps | E2 day0 | not recorded | SRP199550 | 49.22 |
| SRR27868203 | Polyps | Polyps | regeneration day15 | not recorded | SRP199550 | 49.18 |
| SRR27868195 | Polyps | Polyps | regeneration day21 | not recorded | SRP199550 | 47.71 |
| SRR27868181 | Polyps | Polyps | regeneration day33 | not recorded | SRP199550 | 47.49 |
| SRR27868196 | Polyps | Polyps | regeneration day21 | not recorded | SRP199550 | 47.40 |
| SRR12786899 | Polyps | Polyps | OA 2 day0 | not recorded | SRP199550 | 47.39 |
| SRR12904784 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 47.30 |
| SRR27940224 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 47.15 |
| SRR12786901 | Polyps | Polyps | OA 2 day0 | not recorded | SRP199550 | 46.72 |
| SRR27868158 | Polyps | Polyps | regeneration day6 | not recorded | SRP199550 | 45.98 |
| SRR27868205 | Polyps | Polyps | regeneration day12 | not recorded | SRP199550 | 45.89 |
| SRR27868189 | Polyps | Polyps | regeneration day27 | not recorded | SRP199550 | 45.73 |
| SRR12959205 | Polyps | Polyps | E2 day15 | not recorded | SRP199550 | 45.58 |
| SRR12959204 | Polyps | Polyps | E2 day15 | not recorded | SRP199550 | 45.46 |
| SRR27868208 | Polyps | Polyps | regeneration day9 | not recorded | SRP199550 | 45.15 |
| SRR12959195 | Polyps | Polyps | E2 day0 | not recorded | SRP199550 | 44.01 |
| SRR27868179 | Polyps | Polyps | regeneration day36 | not recorded | SRP199550 | 43.99 |
| SRR27868200 | Polyps | Polyps | regeneration day18 | not recorded | SRP199550 | 43.90 |
| SRR12710859 | Polyps | Polyps | OA 2 day9 | not recorded | SRP199550 | 43.27 |
| SRR27868174 | Polyps | Polyps | regeneration day39 | not recorded | SRP199550 | 43.20 |
| SRR12710860 | Polyps | Polyps | OA 2 day9 | not recorded | SRP199550 | 43.19 |
| SRR27868207 | Polyps | Polyps | regeneration day9 | not recorded | SRP199550 | 43.13 |
| SRR12710861 | Polyps | Polyps | OA 2 day9 | not recorded | SRP199550 | 43.06 |
| SRR12710849 | Polyps | Polyps | OA 2 day3 | not recorded | SRP199550 | 42.38 |
| SRR27940226 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 41.99 |
| SRR12710851 | Polyps | Polyps | OA 2 day3 | not recorded | SRP199550 | 41.35 |
| SRR27868197 | Polyps | Polyps | regeneration day18 | not recorded | SRP199550 | 40.95 |
| SRR27868176 | Polyps | Polyps | regeneration day3 | not recorded | SRP199550 | 40.64 |
| SRR27868204 | Polyps | Polyps | regeneration day12 | not recorded | SRP199550 | 40.44 |
| SRR27868180 | Polyps | Polyps | regeneration day36 | not recorded | SRP199550 | 39.90 |
| SRR12959191 | Polyps | polyps | E2 day21 | not recorded | SRP199550 | 39.72 |
| SRR27868202 | Polyps | Polyps | regeneration day15 | not recorded | SRP199550 | 39.56 |
| SRR27868209 | Polyps | Polyps | regeneration day0 | not recorded | SRP199550 | 38.99 |
| SRR12959220 | Polyps | Polyps | E2 day9 | not recorded | SRP199550 | 38.91 |
| SRR12959219 | Polyps | Polyps | E2 day9 | not recorded | SRP199550 | 38.59 |
| SRR12904785 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 38.45 |
| SRR12959193 | Polyps | Polyps | E2 day21 | not recorded | SRP199550 | 37.87 |
| SRR12710850 | Polyps | Polyps | OA 2 day3 | not recorded | SRP199550 | 37.84 |
| SRR27868198 | Polyps | Polyps | regeneration day0 | not recorded | SRP199550 | 36.50 |
| SRR27868210 | Polyps | Polyps | regeneration day0 | not recorded | SRP199550 | 36.22 |
| SRR27940228 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 36.21 |
| SRR12904786 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 36.11 |
| SRR12959233 | Polyps | Polyps | E2 day3 | not recorded | SRP199550 | 36.06 |
| SRR27868178 | Polyps | Polyps | regeneration day36 | not recorded | SRP199550 | 35.76 |
| SRR12959192 | Polyps | Polyps | E2 day21 | not recorded | SRP199550 | 35.75 |
| SRR27868192 | Polyps | Polyps | regeneration day24 | not recorded | SRP199550 | 35.70 |
| SRR27868165 | Polyps | Polyps | regeneration day3 | not recorded | SRP199550 | 34.68 |
| SRR12959231 | Polyps | Polyps | E2 day3 | not recorded | SRP199550 | 32.57 |
| SRR12959218 | Polyps | Polyps | E2 day9 | not recorded | SRP199550 | 32.13 |
| SRR27868177 | Polyps | Polyps | regeneration day39 | not recorded | SRP199550 | 30.89 |
| SRR27868160 | Polyps | Polyps | regeneration day6 | not recorded | SRP199550 | 27.25 |
| SRR27868193 | Polyps | Polyps | regeneration day24 | not recorded | SRP199550 | 22.96 |
| SRR27868187 | Polyps | Polyps | regeneration day3 | not recorded | SRP199550 | 20.74 |
| SRR12807382 | Polyps | Polyps | OA2 day0 | not recorded | SRP199550 | 0.00 |
| SRR12959232 | Polyps | Polyps | E2 day3 | not recorded | SRP199550 | 0.00 |
| SRR27868175 | Polyps | Polyps | regeneration day39 | not recorded | SRP199550 | 0.00 |
| SRR27868183 | Polyps | Polyps | regeneration day33 | not recorded | SRP199550 | 0.00 |
| SRR27868185 | Polyps | Polyps | regeneration day30 | not recorded | SRP199550 | 0.00 |
| SRR27868191 | Polyps | Polyps | regeneration day24 | not recorded | SRP199550 | 0.00 |
| SRR27940225 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 0.00 |
| SRR27940229 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 0.00 |
| SRR9613488 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 0.00 |
| SRR9613516 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 0.00 |
| SRR12995717 | Severed branch | Severed branch | regeneration day0 | not recorded | SRP199550 | 0.00 |
| SRR12996627 | Severed branch | Severed branch | regeneration day0 | not recorded | SRP199550 | 0.00 |
| SRR12996628 | Severed branch | Severed branch | regeneration High gene expression | not recorded | SRP199550 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (AMURI_TPM,
StringTie quantification over 82 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 muricata 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 | 16 | amur_s0318.g21.t1 | 0.99926542936612 |
| Negatively correlated | 4 | amur_s5480.g1.t1 | -0.285692669482583 |
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 muricata, 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.
| Dataset | Tissue / stage | Cells | Cell types | This gene | Marker of |
|---|---|---|---|---|---|
| AMURI_regen | Polyps · regeneration | 8,721 | 28 | unmapped | – |
A gene is in viewer when the dataset ships a per-cell expression vector for it; marker only means it is in the dataset’s ranked marker table but no vector was exported, so the atlas cannot draw it; not in this dataset means the dataset’s own gene-ID table does not list it, so no expression claim can be made for that dataset. unmapped is deliberately weaker still: the dataset has no gene-ID table on CnidoSite yet, so nothing is claimed in either direction. Where markers are listed, the numbers are log2 fold change and the percentage of cells of that type in which the gene was detected.
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 → |