Genomic Location: scaffold_2:34370042...34370467
NR annotation: no NCBI-NR hit recorded
Species Tripedalia maipoensis · all data for this species · gene families
| CDS |
| g5606.t1 |
| Transcript |
| g5606.t1 |
| Protein |
| g5606.t1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0009860 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF01423 all species → | LSM | LSM domain | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR052840 all species → | Family | U7 snRNA-associated Sm-like | Interproscan |
| IPR001163 all species → | Domain | Sm domain, eukaryotic/archaea-type | Interproscan |
| IPR010920 all species → | Homologous_superfamily | LSM domain superfamily | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR21196 all species → | U7 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM10 | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0006398 all species → | Biological Process | mRNA 3'-end processing by stem-loop binding and cleavage | Interproscan |
| GO:0016604 all species → | Cellular Component | nuclear body | Interproscan |
| GO:0071208 all species → | Molecular Function | histone pre-mRNA DCP binding | Interproscan |
| GO:0071209 all species → | Molecular Function | U7 snRNA binding | Interproscan |
| GO:0071254 all species → | Cellular Component | cytoplasmic U snRNP body | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K25591 | LSM10; U7 snRNA-associated Sm-like protein LSm10 | - | Messenger RNA biogenesis | ko03019 | deepkoala |
Genes whose expression across the transcriptome samples of Tripedalia maipoensis 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 Tripedalia maipoensis, 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 → |
