Genomic Location: HOLI00001:3986151...3987470
NR annotation: WP_042125742.1, tRNA pseudouridine(55) synthase TruB [Pseudomonas japonica]
Species Hydra oligactis · all data for this species · gene families
| CDS |
| HOLI00001.g52119.t1 |
| Transcript |
| HOLI00001.g52119.t1 |
| Protein |
| HOLI00001.G52119 |
| UniProt accession | Description |
|---|---|
| A5W985 | tRNA pseudouridine synthase B OS=Pseudomonas putida (strain ATCC 700007 / DSM 6899 / JCM 31910 / BCRC 17059 / LMG 24140 / F1) OX=351746 GN=truB PE=3 SV=1 |
| B0KHX6 | tRNA pseudouridine synthase B OS=Pseudomonas putida (strain GB-1) OX=76869 GN=truB PE=3 SV=1 |
| Q1IF41 | tRNA pseudouridine synthase B OS=Pseudomonas entomophila (strain L48) OX=384676 GN=truB PE=3 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0004107 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF09157 all species → | TruB-C_2 | Pseudouridine synthase II TruB, C-terminal | Domain | Interproscan |
| PF02033 all species → | RBFA | Ribosome-binding factor A | Family | Interproscan |
| PF01509 all species → | TruB_N | TruB family pseudouridylate synthase (N terminal domain) | Family | Interproscan |
| PF16198 all species → | TruB_C_2 | tRNA pseudouridylate synthase B C-terminal domain | Family | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR014780 all species → | Family | tRNA pseudouridine synthase II, TruB | Interproscan |
| IPR015240 all species → | Domain | tRNA pseudouridine synthase II, TruB, subfamily 1, C-terminal | Interproscan |
| IPR000238 all species → | Family | Ribosome-binding factor A | Interproscan |
| IPR002501 all species → | Domain | Pseudouridine synthase II, N-terminal | Interproscan |
| IPR036974 all species → | Homologous_superfamily | PUA domain superfamily | Interproscan |
| IPR032819 all species → | Domain | tRNA pseudouridylate synthase B, C-terminal | Interproscan |
| IPR020103 all species → | Homologous_superfamily | Pseudouridine synthase, catalytic domain superfamily | Interproscan |
| IPR023799 all species → | Homologous_superfamily | Ribosome-binding factor A domain superfamily | Interproscan |
| IPR015947 all species → | Homologous_superfamily | PUA-like superfamily | Interproscan |
| IPR020053 all species → | Conserved_site | Ribosome-binding factor A, conserved site | Interproscan |
| IPR015946 all species → | Homologous_superfamily | K homology domain-like, alpha/beta | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR13767 all species → | TRNA-PSEUDOURIDINE SYNTHASE | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0001522 all species → | Biological Process | pseudouridine synthesis | Interproscan |
| GO:0003723 all species → | Molecular Function | RNA binding | Interproscan |
| GO:0009451 all species → | Biological Process | RNA modification | Interproscan |
| GO:0009982 all species → | Molecular Function | pseudouridine synthase activity | Interproscan |
| GO:0006364 all species → | Biological Process | rRNA processing | Interproscan |
| GO:0006396 all species → | Biological Process | RNA processing | Interproscan |
| GO:0005739 all species → | Cellular Component | mitochondrion | Interproscan |
| GO:0006400 all species → | Biological Process | tRNA modification | Interproscan |
| GO:1990481 all species → | Biological Process | mRNA pseudouridine synthesis | Interproscan |
HOLI00001.G52119.Genes whose expression across the transcriptome samples of Hydra oligactis 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.
No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.
Whether this gene can be visualised in the single-cell atlases of Hydra oligactis, 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 → |
