Genomic Location: not available for this species
NR annotation: WP_170414338.1, valine--tRNA ligase [Ruegeria arenilitoris]
Species Cassiopea xamachana · all data for this species · gene families
| UniProt accession | Description |
|---|---|
| Q5LP30 | Valine--tRNA ligase OS=Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3) OX=246200 GN=valS PE=3 SV=1 |
| B9KMT9 | Valine--tRNA ligase OS=Cereibacter sphaeroides (strain KD131 / KCTC 12085) OX=557760 GN=valS PE=3 SV=1 |
| Q3J4Z5 | Valine--tRNA ligase OS=Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.) OX=272943 GN=valS PE=3 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0002928 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF08264 all species → | Anticodon_1 | Anticodon-binding domain of tRNA ligase | Domain | Interproscan |
| PF00133 all species → | tRNA-synt_1 | tRNA synthetases class I (I, L, M and V) | Domain | Interproscan |
| PF10458 all species → | Val_tRNA-synt_C | Valyl tRNA synthetase tRNA binding arm | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR010978 all species → | Homologous_superfamily | Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm | Interproscan |
| IPR009008 all species → | Homologous_superfamily | Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain | Interproscan |
| IPR013155 all species → | Domain | Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding | Interproscan |
| IPR002303 all species → | Family | Valine-tRNA ligase | Interproscan |
| IPR037118 all species → | Homologous_superfamily | Valyl-tRNA synthetase, tRNA-binding arm superfamily | Interproscan |
| IPR014729 all species → | Homologous_superfamily | Rossmann-like alpha/beta/alpha sandwich fold | Interproscan |
| IPR009080 all species → | Homologous_superfamily | Aminoacyl-tRNA synthetase, class Ia, anticodon-binding | Interproscan |
| IPR002300 all species → | Domain | Aminoacyl-tRNA synthetase, class Ia | Interproscan |
| IPR019499 all species → | Domain | Valyl-tRNA synthetase, tRNA-binding arm | Interproscan |
| IPR033705 all species → | Domain | Valyl tRNA synthetase, anticodon-binding domain | Interproscan |
| IPR001412 all species → | Conserved_site | Aminoacyl-tRNA synthetase, class I, conserved site | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR11946 all species → | VALYL-TRNA SYNTHETASES | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0000166 all species → | Molecular Function | nucleotide binding | Interproscan |
| GO:0002161 all species → | Molecular Function | aminoacyl-tRNA editing activity | Interproscan |
| GO:0006418 all species → | Biological Process | tRNA aminoacylation for protein translation | Interproscan |
| GO:0004812 all species → | Molecular Function | aminoacyl-tRNA ligase activity | Interproscan |
| GO:0004832 all species → | Molecular Function | valine-tRNA ligase activity | Interproscan |
| GO:0005524 all species → | Molecular Function | ATP binding | Interproscan |
| GO:0005829 all species → | Cellular Component | cytosol | Interproscan |
| GO:0006438 all species → | Biological Process | valyl-tRNA aminoacylation | Interproscan |
| GO:0005737 all species → | Cellular Component | cytoplasm | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K01873 | VARS, valS; valyl-tRNA synthetase | EC:6.1.1.9 | Transfer RNA biogenesis | ko03016 | deepkoala |
Genes whose expression across the transcriptome samples of Cassiopea xamachana 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 Cassiopea xamachana, 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. | sequence table not available | – |
| 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. | sequence table not available | – |
| 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 → |
