Genomic Location: NW_027103704.1:747636...781954
NR annotation: XP_047133417.1, nuclear valosin-containing protein-like [Hydra vulgaris]
Species Clytia hemisphaerica · all data for this species · gene families
| CDS |
| XP_066916911.1 |
| Protein |
| XP_066916911.1 |
| UniProt accession | Description |
|---|---|
| Q9DBY8 | Nuclear valosin-containing protein-like OS=Mus musculus OX=10090 GN=Nvl PE=1 SV=1 |
| O15381 | Nuclear valosin-containing protein-like OS=Homo sapiens OX=9606 GN=NVL PE=1 SV=1 |
| O14325 | Uncharacterized AAA domain-containing protein C16E9.10c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=SPBC16E9.10c PE=1 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0000716 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF16725 all species → | Nucleolin_bd | Nucleolin binding domain | Domain | Interproscan |
| PF17862 all species → | AAA_lid_3 | AAA+ lid domain | Domain | Interproscan |
| PF00004 all species → | AAA | ATPase family associated with various cellular activities (AAA) | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR027417 all species → | Homologous_superfamily | P-loop containing nucleoside triphosphate hydrolase | Interproscan |
| IPR003593 all species → | Domain | AAA+ ATPase domain | Interproscan |
| IPR003960 all species → | Conserved_site | ATPase, AAA-type, conserved site | Interproscan |
| IPR031996 all species → | Domain | NVL2, nucleolin binding domain | Interproscan |
| IPR041569 all species → | Domain | AAA ATPase, AAA+ lid domain | Interproscan |
| IPR038100 all species → | Homologous_superfamily | NVL2, N-terminal domain superfamily | Interproscan |
| IPR050168 all species → | Family | AAA ATPase domain-containing protein | Interproscan |
| IPR003959 all species → | Domain | ATPase, AAA-type, core | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR23077 all species → | AAA-FAMILY ATPASE | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0016887 all species → | Molecular Function | ATP hydrolysis activity | Interproscan |
| GO:0005524 all species → | Molecular Function | ATP binding | Interproscan |
| GO:0003723 all species → | Molecular Function | RNA binding | Interproscan |
| GO:0005634 all species → | Cellular Component | nucleus | Interproscan |
| GO:0042254 all species → | Biological Process | ribosome biogenesis | Interproscan |
| GO:0051973 all species → | Biological Process | obsolete positive regulation of telomerase activity | Interproscan |
| GO:1990275 all species → | Molecular Function | preribosome binding | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K14571 | RIX7, NVL; ribosome biogenesis ATPase | - | Ribosome biogenesis | ko03009 | deepkoala |
Transcript abundance of XP_066916911.1 across 40 RNA-seq samples of Clytia hemisphaerica. This gene has no row in the species' RNA-seq expression matrix, so every value below is shown as zero — the matrix simply does not cover this transcript. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.
| Condition | Samples | TPM > 0 | Mean TPM | Max TPM | Mean, relative to max |
|---|---|---|---|---|---|
| Mature medusa | 5 | 0 | 0.00 | 0.00 | |
| medusa · Experiment Condition A1 | 4 | 0 | 0.00 | 0.00 | |
| medusa · Experiment Condition A2 | 4 | 0 | 0.00 | 0.00 | |
| medusa · Experiment Condition A3 | 4 | 0 | 0.00 | 0.00 | |
| Early gastrula | 2 | 0 | 0.00 | 0.00 | |
| Planula 24hpf | 2 | 0 | 0.00 | 0.00 | |
| Planula 48hpf | 2 | 0 | 0.00 | 0.00 | |
| Planula 72hpf | 2 | 0 | 0.00 | 0.00 | |
| Primary polyp | 2 | 0 | 0.00 | 0.00 | |
| Gastrozooid | 2 | 0 | 0.00 | 0.00 | |
| Gonozooid | 2 | 0 | 0.00 | 0.00 | |
| Stolon | 2 | 0 | 0.00 | 0.00 | |
| Baby medusa | 2 | 0 | 0.00 | 0.00 | |
| medusa · Experiment Condition B1 | 2 | 0 | 0.00 | 0.00 | |
| medusa · Experiment Condition B2 | 2 | 0 | 0.00 | 0.00 | |
| Mixed | 1 | 0 | 0.00 | 0.00 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| ERR2816248 | Mature medusa | not recorded | Mature medusa | not recorded | ERP110164 | 0.00 |
| ERR2816249 | Mature medusa | not recorded | Mature medusa | not recorded | ERP110164 | 0.00 |
| ERR2816250 | Mature medusa | not recorded | Mature medusa | not recorded | ERP110164 | 0.00 |
| ERR2816251 | Mature medusa | not recorded | Mature medusa | not recorded | ERP110164 | 0.00 |
| ERR2862245 | Mature medusa | not recorded | Mature medusa | not recorded | ERP110164 | 0.00 |
| ERR3299475 | medusa · Experiment Condition A1 | not recorded | medusa | Experiment Condition A1 | ERP115020 | 0.00 |
| ERR3299476 | medusa · Experiment Condition A1 | not recorded | medusa | Experiment Condition A1 | ERP115020 | 0.00 |
| ERR3299477 | medusa · Experiment Condition A1 | not recorded | medusa | Experiment Condition A1 | ERP115020 | 0.00 |
| ERR3299478 | medusa · Experiment Condition A1 | not recorded | medusa | Experiment Condition A1 | ERP115020 | 0.00 |
| ERR3299479 | medusa · Experiment Condition A2 | not recorded | medusa | Experiment Condition A2 | ERP115020 | 0.00 |
| ERR3299480 | medusa · Experiment Condition A2 | not recorded | medusa | Experiment Condition A2 | ERP115020 | 0.00 |
| ERR3299481 | medusa · Experiment Condition A2 | not recorded | medusa | Experiment Condition A2 | ERP115020 | 0.00 |
| ERR3299482 | medusa · Experiment Condition A2 | not recorded | medusa | Experiment Condition A2 | ERP115020 | 0.00 |
| ERR3299483 | medusa · Experiment Condition A3 | not recorded | medusa | Experiment Condition A3 | ERP115020 | 0.00 |
| ERR3299484 | medusa · Experiment Condition A3 | not recorded | medusa | Experiment Condition A3 | ERP115020 | 0.00 |
| ERR3299485 | medusa · Experiment Condition A3 | not recorded | medusa | Experiment Condition A3 | ERP115020 | 0.00 |
| ERR3299486 | medusa · Experiment Condition A3 | not recorded | medusa | Experiment Condition A3 | ERP115020 | 0.00 |
| ERR2816230 | Early gastrula | not recorded | Early gastrula | not recorded | ERP110164 | 0.00 |
| ERR2816231 | Early gastrula | not recorded | Early gastrula | not recorded | ERP110164 | 0.00 |
| ERR2816232 | Planula 24hpf | not recorded | Planula 24hpf | not recorded | ERP110164 | 0.00 |
| ERR2816233 | Planula 24hpf | not recorded | Planula 24hpf | not recorded | ERP110164 | 0.00 |
| ERR2816234 | Planula 48hpf | not recorded | Planula 48hpf | not recorded | ERP110164 | 0.00 |
| ERR2816235 | Planula 48hpf | not recorded | Planula 48hpf | not recorded | ERP110164 | 0.00 |
| ERR2816236 | Planula 72hpf | not recorded | Planula 72hpf | not recorded | ERP110164 | 0.00 |
| ERR2816237 | Planula 72hpf | not recorded | Planula 72hpf | not recorded | ERP110164 | 0.00 |
| ERR2816238 | Primary polyp | not recorded | Primary polyp | not recorded | ERP110164 | 0.00 |
| ERR2816239 | Primary polyp | not recorded | Primary polyp | not recorded | ERP110164 | 0.00 |
| ERR2816240 | Gastrozooid | not recorded | Gastrozooid | not recorded | ERP110164 | 0.00 |
| ERR2816241 | Gastrozooid | not recorded | Gastrozooid | not recorded | ERP110164 | 0.00 |
| ERR2816242 | Gonozooid | not recorded | Gonozooid | not recorded | ERP110164 | 0.00 |
| ERR2816243 | Gonozooid | not recorded | Gonozooid | not recorded | ERP110164 | 0.00 |
| ERR2816244 | Stolon | not recorded | Stolon | not recorded | ERP110164 | 0.00 |
| ERR2816245 | Stolon | not recorded | Stolon | not recorded | ERP110164 | 0.00 |
| ERR2816246 | Baby medusa | not recorded | Baby medusa | not recorded | ERP110164 | 0.00 |
| ERR2816247 | Baby medusa | not recorded | Baby medusa | not recorded | ERP110164 | 0.00 |
| ERR3299471 | medusa · Experiment Condition B1 | not recorded | medusa | Experiment Condition B1 | ERP115020 | 0.00 |
| ERR3299472 | medusa · Experiment Condition B1 | not recorded | medusa | Experiment Condition B1 | ERP115020 | 0.00 |
| ERR3299473 | medusa · Experiment Condition B2 | not recorded | medusa | Experiment Condition B2 | ERP115020 | 0.00 |
| ERR3299474 | medusa · Experiment Condition B2 | not recorded | medusa | Experiment Condition B2 | ERP115020 | 0.00 |
| ERR2862244 | Mixed | not recorded | Mixed | not recorded | ERP110164 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (CHEMI_TPM,
StringTie quantification over 40 runs), joined to SRA sample
metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped
by the descriptor carried in the expression matrix itself.
Genes whose expression across the transcriptome samples of Clytia hemisphaerica 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.
| Direction | Partners | Most correlated partner | PCC |
|---|---|---|---|
| Positively correlated | 0 | not in this network | - |
| Negatively correlated | 0 | not in this network | - |
This gene has no edge at all in the Clytia hemisphaerica network, in either direction — it is not one of the genes the network was built from (the network covers genes with enough expression variation across the transcriptome samples). The counts above are a property of the network, not a failed lookup.
Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.
Whether this gene can be visualised in the single-cell atlases of Clytia hemisphaerica, 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 → |
