Genomic Location: chr8:564123...566969
NR annotation: XP_031550365.1, uncharacterized protein LOC116287807 [Actinia tenebrosa]
Species Anthopleura xanthogrammica · all data for this species · gene families
| CDS |
| ENSOJPT00000005812 |
| Transcript |
| ENSOJPT00000005812 |
| Protein |
| ENSOJPP00000004993.1 |
| UniProt accession | Description |
|---|---|
| P46850 | RNA-splicing ligase RtcB OS=Escherichia coli (strain K12) OX=83333 GN=rtcB PE=1 SV=3 |
| P0DX92 | RNA-splicing ligase RtcB1 OS=Escherichia coli (strain ATCC 25922 / DSM 1103 / LMG 8223 / NCIMB 12210 / NCTC 12241 / WDCM 00013 / Seattle 1946) OX=1322345 GN=rtcB1 PE=1 SV=1 |
| Q6LXF9 | tRNA-splicing ligase RtcB OS=Methanococcus maripaludis (strain DSM 14266 / JCM 13030 / NBRC 101832 / S2 / LL) OX=267377 GN=rtcB PE=3 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0008938 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF01139 all species → | RtcB | tRNA-splicing ligase RtcB | Family | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR036025 all species → | Homologous_superfamily | tRNA-splicing ligase RtcB-like superfamily | Interproscan |
| IPR001233 all species → | Family | RNA-splicing ligase, RtcB | Interproscan |
| IPR052915 all species → | Family | RNA-splicing ligase RtcB-like | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR43749 all species → | RNA-SPLICING LIGASE RTCB | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0006396 all species → | Biological Process | RNA processing | Interproscan |
| GO:0008452 all species → | Molecular Function | RNA ligase activity | Interproscan |
| GO:0003909 all species → | Molecular Function | DNA ligase activity | Interproscan |
| GO:0006281 all species → | Biological Process | DNA repair | Interproscan |
| GO:0030145 all species → | Molecular Function | manganese ion binding | Interproscan |
| GO:0042245 all species → | Biological Process | RNA repair | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K14415 | RTCB, rtcB; tRNA-splicing ligase RtcB (3'-phosphate/5'-hydroxy nucleic acid ligase) | EC:6.5.1.8 | Transfer RNA biogenesis | ko03016 | deepkoala |
Genes whose expression across the transcriptome samples of Anthopleura xanthogrammica 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 Anthopleura xanthogrammica, 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 → |
