Genomic Location: Contig136:177119...178711
NR annotation: MBE5819395.1, phenylalanine--tRNA ligase subunit beta [Clostridiales bacterium]
Species Hemicorallium imperiale · all data for this species · gene families
evm.model.Contig136.69 in HIMPE (the gene ID may belong to a different isoform naming scheme). Try the gene search.| UniProt accession | Description |
|---|---|
| Q4L5E4 | Phenylalanine--tRNA ligase beta subunit OS=Staphylococcus haemolyticus (strain JCSC1435) OX=279808 GN=pheT PE=1 SV=1 |
| Q5HQ35 | Phenylalanine--tRNA ligase beta subunit OS=Staphylococcus epidermidis (strain ATCC 35984 / DSM 28319 / BCRC 17069 / CCUG 31568 / BM 3577 / RP62A) OX=176279 GN=pheT PE=3 SV=1 |
| Q8CSY8 | Phenylalanine--tRNA ligase beta subunit OS=Staphylococcus epidermidis (strain ATCC 12228 / FDA PCI 1200) OX=176280 GN=pheT PE=3 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0015731 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF03483 all species → | B3_4 | B3/4 domain | Domain | Interproscan |
| PF17759 all species → | tRNA_synthFbeta | Phenylalanyl tRNA synthetase beta chain CLM domain | Domain | Interproscan |
| PF03147 all species → | FDX-ACB | Ferredoxin-fold anticodon binding domain | Domain | Interproscan |
| PF03484 all species → | B5 | tRNA synthetase B5 domain | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR005146 all species → | Domain | B3/B4 tRNA-binding domain | Interproscan |
| IPR045864 all species → | Homologous_superfamily | Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) | Interproscan |
| IPR005121 all species → | Domain | Ferrodoxin-fold anticodon-binding domain | Interproscan |
| IPR036690 all species → | Homologous_superfamily | Ferrodoxin-fold anticodon-binding domain superfamily | Interproscan |
| IPR041616 all species → | Domain | Phenylalanyl tRNA synthetase beta chain, core domain | Interproscan |
| IPR005147 all species → | Domain | tRNA synthetase, B5-domain | Interproscan |
| IPR020825 all species → | Homologous_superfamily | Phenylalanyl-tRNA synthetase-like, B3/B4 | Interproscan |
| IPR045060 all species → | Family | Phenylalanine-tRNA ligase, class IIc, beta subunit | Interproscan |
| IPR009061 all species → | Homologous_superfamily | Putative DNA-binding domain superfamily | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR10947 all species → | PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN AND LEUCINE-RICH REPEAT-CONTAINING PROTEIN 47 | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0003723 all species → | Molecular Function | RNA binding | Interproscan |
| GO:0004826 all species → | Molecular Function | phenylalanine-tRNA ligase activity | Interproscan |
| GO:0000287 all species → | Molecular Function | magnesium ion binding | Interproscan |
| GO:0005524 all species → | Molecular Function | ATP binding | Interproscan |
| GO:0006432 all species → | Biological Process | phenylalanyl-tRNA aminoacylation | Interproscan |
| GO:0009328 all species → | Cellular Component | phenylalanine-tRNA ligase complex | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K01890 | FARSB, pheT; phenylalanyl-tRNA synthetase beta chain | EC:6.1.1.20 | Transfer RNA biogenesis | ko03016 | deepkoala |
Genes whose expression across the transcriptome samples of Hemicorallium imperiale 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 Hemicorallium imperiale, 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. | not in the sequence table | 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. | not in the sequence table | 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 → |
