Genomic Location: QPEY01000524.1:1716557...1717867
NR annotation: WP_010926715.1, 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD [Bordetella bronchiseptica]
Species Hydra viridissima · all data for this species · gene families
| CDS |
| BRAKERKRET00000023313 |
| Transcript |
| BRAKERKRET00000023313 |
| Protein |
| BRAKERKREP00000023313.1 |
| UniProt accession | Description |
|---|---|
| Q7WI42 | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD OS=Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50) OX=257310 GN=rlmD PE=3 SV=1 |
| Q7W676 | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD OS=Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253) OX=257311 GN=rlmD PE=3 SV=2 |
| Q7VXM6 | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD OS=Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251) OX=257313 GN=rlmD PE=3 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0033481 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF01938 all species → | TRAM | TRAM domain | Domain | Interproscan |
| PF05958 all species → | tRNA_U5-meth_tr | tRNA (Uracil-5-)-methyltransferase | Family | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR012340 all species → | Homologous_superfamily | Nucleic acid-binding, OB-fold | Interproscan |
| IPR002792 all species → | Domain | TRAM domain | Interproscan |
| IPR010280 all species → | Family | (Uracil-5)-methyltransferase family | Interproscan |
| IPR029063 all species → | Homologous_superfamily | S-adenosyl-L-methionine-dependent methyltransferase superfamily | Interproscan |
| IPR030391 all species → | Conserved_site | RNA methyltransferase TrmA, conserved site | Interproscan |
| IPR030390 all species → | Active_site | RNA methyltransferase TrmA, active site | Interproscan |
| IPR001566 all species → | Family | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR11061 all species → | RNA M5U METHYLTRANSFERASE | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0006396 all species → | Biological Process | RNA processing | Interproscan |
| GO:0008173 all species → | Molecular Function | RNA methyltransferase activity | Interproscan |
| GO:0003723 all species → | Molecular Function | RNA binding | Interproscan |
| GO:0070041 all species → | Molecular Function | rRNA (uridine-C5-)-methyltransferase activity | Interproscan |
| GO:0070475 all species → | Biological Process | rRNA base methylation | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K03215 | rumA; 23S rRNA (uracil1939-C5)-methyltransferase | EC:2.1.1.190 | Ribosome biogenesis | ko03009 | deepkoala |
Transcript abundance of BRAKERKREP00000023313.1 across 29 RNA-seq samples of Hydra viridissima. 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 body | 18 | 0 | 0.00 | 0.00 | |
| Whole | 6 | 0 | 0.00 | 0.00 | |
| aposymbioic hydra M9 strain · aposymbioic hydra rep1 | 1 | 0 | 0.00 | 0.00 | |
| aposymbioic hydra M9 strain · aposymbioic hydra rep2 | 1 | 0 | 0.00 | 0.00 | |
| symbioic hydra M9 strain · symbioic hydra rep1 | 1 | 0 | 0.00 | 0.00 | |
| symbioic hydra M9 strain · symbioic hydra rep2 | 1 | 0 | 0.00 | 0.00 | |
| unannotated | 1 | 0 | 0.00 | 0.00 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR21134050 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134051 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134052 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134053 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134054 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134055 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134056 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134057 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134058 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134059 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134060 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134061 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134062 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134063 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134064 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134065 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134066 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134067 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR10058802 | Whole | Whole | not recorded | not recorded | SRP220397 | 0.00 |
| SRR10058803 | Whole | Whole | not recorded | not recorded | SRP220397 | 0.00 |
| SRR10058804 | Whole | Whole | not recorded | not recorded | SRP220397 | 0.00 |
| SRR10058805 | Whole | Whole | not recorded | not recorded | SRP220397 | 0.00 |
| SRR10058806 | Whole | Whole | not recorded | not recorded | SRP220397 | 0.00 |
| SRR10058807 | Whole | Whole | not recorded | not recorded | SRP220397 | 0.00 |
| DRR048593 | aposymbioic hydra M9 strain · aposymbioic hydra rep1 | not recorded | not recorded | aposymbioic hydra rep1 | DRP003902 | 0.00 |
| DRR048594 | aposymbioic hydra M9 strain · aposymbioic hydra rep2 | not recorded | not recorded | aposymbioic hydra rep2 | DRP003902 | 0.00 |
| DRR048595 | symbioic hydra M9 strain · symbioic hydra rep1 | not recorded | not recorded | symbioic hydra rep1 | DRP003902 | 0.00 |
| DRR048596 | symbioic hydra M9 strain · symbioic hydra rep2 | not recorded | not recorded | symbioic hydra rep2 | DRP003902 | 0.00 |
| ERR13389755 | unannotated | not recorded | not recorded | not recorded | ERP162636 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (HVIRI_TPM,
StringTie quantification over 29 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 Hydra viridissima 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 Hydra viridissima 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 Hydra viridissima, 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 → |
