Genomic Location: NC_088930.1:6795663...6841947
NR annotation: XP_047135994.1, 116 kDa U5 small nuclear ribonucleoprotein component [Hydra vulgaris]
Species Hydra vulgaris · all data for this species · gene families
| CDS |
| LOC100209856 |
| Transcript |
| rna-XM_065809940.1 |
| Protein |
| XP_065666012.1 |
| UniProt accession | Description |
|---|---|
| Q5F3X4 | 116 kDa U5 small nuclear ribonucleoprotein component OS=Gallus gallus OX=9031 GN=EFTUD2 PE=2 SV=1 |
| Q15029 | 116 kDa U5 small nuclear ribonucleoprotein component OS=Homo sapiens OX=9606 GN=EFTUD2 PE=1 SV=1 |
| A4FUD3 | 116 kDa U5 small nuclear ribonucleoprotein component OS=Bos taurus OX=9913 GN=EFTUD2 PE=2 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0001678 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF03764 all species → | EFG_IV | Elongation factor G, domain IV | Domain | Interproscan |
| PF00009 all species → | GTP_EFTU | Elongation factor Tu GTP binding domain | Domain | Interproscan |
| PF00679 all species → | EFG_C | Elongation factor G C-terminus | Domain | Interproscan |
| PF14492 all species → | EFG_III | Elongation Factor G, domain III | Domain | Interproscan |
| PF16004 all species → | EFTUD2 | 116 kDa U5 small nuclear ribonucleoprotein component N-terminus | Family | Interproscan |
| PF03144 all species → | GTP_EFTU_D2 | Elongation factor Tu domain 2 | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR005517 all species → | Domain | Translation elongation factor EFG/EF2, domain IV | Interproscan |
| IPR000795 all species → | Domain | Translational (tr)-type GTP-binding domain | Interproscan |
| IPR044121 all species → | Domain | Snu114, GTP-binding domain | Interproscan |
| IPR000640 all species → | Domain | Elongation factor EFG, domain V-like | Interproscan |
| IPR014721 all species → | Homologous_superfamily | Small ribosomal subunit protein uS5 domain 2-type fold, subgroup | Interproscan |
| IPR027417 all species → | Homologous_superfamily | P-loop containing nucleoside triphosphate hydrolase | Interproscan |
| IPR035655 all species → | Domain | 116kDa U5 small nuclear ribonucleoprotein component, C-terminal | Interproscan |
| IPR035647 all species → | Homologous_superfamily | EF-G domain III/V-like | Interproscan |
| IPR009000 all species → | Homologous_superfamily | Translation protein, beta-barrel domain superfamily | Interproscan |
| IPR020568 all species → | Homologous_superfamily | Ribosomal protein uS5 domain 2-type superfamily | Interproscan |
| IPR041095 all species → | Domain | Elongation Factor G, domain II | Interproscan |
| IPR031950 all species → | Domain | 116kDa U5 small nuclear ribonucleoprotein component, N-terminal | Interproscan |
| IPR031157 all species → | Conserved_site | Tr-type G domain, conserved site | Interproscan |
| IPR004161 all species → | Domain | Translation elongation factor EFTu-like, domain 2 | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR42908 all species → | TRANSLATION ELONGATION FACTOR-RELATED | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0005525 all species → | Molecular Function | GTP binding | Interproscan |
| GO:0003924 all species → | Molecular Function | GTPase activity | Interproscan |
| GO:0000398 all species → | Biological Process | mRNA splicing, via spliceosome | Interproscan |
| GO:0005829 all species → | Cellular Component | cytosol | Interproscan |
| GO:0030623 all species → | Molecular Function | U5 snRNA binding | Interproscan |
| GO:0046540 all species → | Cellular Component | U4/U6 x U5 tri-snRNP complex | Interproscan |
| GO:0071007 all species → | Cellular Component | U2-type catalytic step 2 spliceosome | Interproscan |
| GO:1990904 all species → | Cellular Component | ribonucleoprotein complex | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K12852 | EFTUD2; 116 kDa U5 small nuclear ribonucleoprotein component | - | Spliceosome | ko03041 | deepkoala |
Transcript abundance of XP_065666012.1 across 60 RNA-seq samples of Hydra vulgaris. 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 |
|---|---|---|---|---|---|
| Regenerating head · dmso treatment | 18 | 0 | 0.00 | 0.00 | |
| Regenerating head · 25uM U0126 treatment | 15 | 0 | 0.00 | 0.00 | |
| Regenerating foot · dmso treatment | 9 | 0 | 0.00 | 0.00 | |
| Regenerating foot · 25uM U0126 treatment | 8 | 0 | 0.00 | 0.00 | |
| Regenerating head · u0126 treatment | 3 | 0 | 0.00 | 0.00 | |
| Whole animal · 25uM U0126 treatment | 3 | 0 | 0.00 | 0.00 | |
| Whole animal · dmso treatment | 3 | 0 | 0.00 | 0.00 | |
| Regenerating foot · u0126 treatment | 1 | 0 | 0.00 | 0.00 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR36435271 | Regenerating head · dmso treatment | Regenerating head | 12hpa | dmso treatment | SRP654941 | 0.00 |
| SRR36435272 | Regenerating head · dmso treatment | Regenerating head | 12hpa | dmso treatment | SRP654941 | 0.00 |
| SRR36435273 | Regenerating head · dmso treatment | Regenerating head | 12hpa | dmso treatment | SRP654941 | 0.00 |
| SRR36435277 | Regenerating head · dmso treatment | Regenerating head | 8hpa | dmso treatment | SRP654941 | 0.00 |
| SRR36435279 | Regenerating head · dmso treatment | Regenerating head | 8hpa | dmso treatment | SRP654941 | 0.00 |
| SRR36435280 | Regenerating head · dmso treatment | Regenerating head | 8hpa | dmso treatment | SRP654941 | 0.00 |
| SRR36435284 | Regenerating head · dmso treatment | Regenerating head | 0hpa | dmso treatment | SRP654941 | 0.00 |
| SRR36435285 | Regenerating head · dmso treatment | Regenerating head | 0hpa | dmso treatment | SRP654941 | 0.00 |
| SRR36435286 | Regenerating head · dmso treatment | Regenerating head | 0hpa | dmso treatment | SRP654941 | 0.00 |
| SRR36435304 | Regenerating head · dmso treatment | Regenerating head | 1.5hpa | dmso treatment | SRP654941 | 0.00 |
| SRR36435305 | Regenerating head · dmso treatment | Regenerating head | 1.5hpa | dmso treatment | SRP654941 | 0.00 |
| SRR36435306 | Regenerating head · dmso treatment | Regenerating head | 1.5hpa | dmso treatment | SRP654941 | 0.00 |
| SRR36435307 | Regenerating head · dmso treatment | Regenerating head | 3hpa | dmso treatment | SRP654941 | 0.00 |
| SRR36435308 | Regenerating head · dmso treatment | Regenerating head | 3hpa | dmso treatment | SRP654941 | 0.00 |
| SRR36435309 | Regenerating head · dmso treatment | Regenerating head | 3hpa | dmso treatment | SRP654941 | 0.00 |
| SRR36435310 | Regenerating head · dmso treatment | Regenerating head | 0hpa | dmso treatment | SRP654941 | 0.00 |
| SRR36435312 | Regenerating head · dmso treatment | Regenerating head | 0hpa | dmso treatment | SRP654941 | 0.00 |
| SRR36435313 | Regenerating head · dmso treatment | Regenerating head | 0hpa | dmso treatment | SRP654941 | 0.00 |
| SRR36435274 | Regenerating head · 25uM U0126 treatment | Regenerating head | 8hpa | 25uM U0126 treatment | SRP654941 | 0.00 |
| SRR36435275 | Regenerating head · 25uM U0126 treatment | Regenerating head | 8hpa | 25uM U0126 treatment | SRP654941 | 0.00 |
| SRR36435276 | Regenerating head · 25uM U0126 treatment | Regenerating head | 8hpa | 25uM U0126 treatment | SRP654941 | 0.00 |
| SRR36435281 | Regenerating head · 25uM U0126 treatment | Regenerating head | 0hpa | 25uM U0126 treatment | SRP654941 | 0.00 |
| SRR36435282 | Regenerating head · 25uM U0126 treatment | Regenerating head | 0hpa | 25uM U0126 treatment | SRP654941 | 0.00 |
| SRR36435283 | Regenerating head · 25uM U0126 treatment | Regenerating head | 0hpa | 25uM U0126 treatment | SRP654941 | 0.00 |
| SRR36435294 | Regenerating head · 25uM U0126 treatment | Regenerating head | 1.5hpa | 25uM U0126 treatment | SRP654941 | 0.00 |
| SRR36435295 | Regenerating head · 25uM U0126 treatment | Regenerating head | 1.5hpa | 25uM U0126 treatment | SRP654941 | 0.00 |
| SRR36435296 | Regenerating head · 25uM U0126 treatment | Regenerating head | 1.5hpa | 25uM U0126 treatment | SRP654941 | 0.00 |
| SRR36435297 | Regenerating head · 25uM U0126 treatment | Regenerating head | 3hpa | 25uM U0126 treatment | SRP654941 | 0.00 |
| SRR36435298 | Regenerating head · 25uM U0126 treatment | Regenerating head | 3hpa | 25uM U0126 treatment | SRP654941 | 0.00 |
| SRR36435299 | Regenerating head · 25uM U0126 treatment | Regenerating head | 3hpa | 25uM U0126 treatment | SRP654941 | 0.00 |
| SRR36435301 | Regenerating head · 25uM U0126 treatment | Regenerating head | 0hpa | 25uM U0126 treatment | SRP654941 | 0.00 |
| SRR36435302 | Regenerating head · 25uM U0126 treatment | Regenerating head | 0hpa | 25uM U0126 treatment | SRP654941 | 0.00 |
| SRR36435303 | Regenerating head · 25uM U0126 treatment | Regenerating head | 0hpa | 25uM U0126 treatment | SRP654941 | 0.00 |
| SRR36435265 | Regenerating foot · dmso treatment | Regenerating foot | 1.5hpa | dmso treatment | SRP654941 | 0.00 |
| SRR36435266 | Regenerating foot · dmso treatment | Regenerating foot | 1.5hpa | dmso treatment | SRP654941 | 0.00 |
| SRR36435267 | Regenerating foot · dmso treatment | Regenerating foot | 1.5hpa | dmso treatment | SRP654941 | 0.00 |
| SRR36435278 | Regenerating foot · dmso treatment | Regenerating foot | 3hpa | dmso treatment | SRP654941 | 0.00 |
| SRR36435289 | Regenerating foot · dmso treatment | Regenerating foot | 3hpa | dmso treatment | SRP654941 | 0.00 |
| SRR36435300 | Regenerating foot · dmso treatment | Regenerating foot | 3hpa | dmso treatment | SRP654941 | 0.00 |
| SRR36435311 | Regenerating foot · dmso treatment | Regenerating foot | 0hpa | dmso treatment | SRP654941 | 0.00 |
| SRR36435322 | Regenerating foot · dmso treatment | Regenerating foot | 0hpa | dmso treatment | SRP654941 | 0.00 |
| SRR36435323 | Regenerating foot · dmso treatment | Regenerating foot | 0hpa | dmso treatment | SRP654941 | 0.00 |
| SRR36435314 | Regenerating foot · 25uM U0126 treatment | Regenerating foot | 1.5hpa | 25uM U0126 treatment | SRP654941 | 0.00 |
| SRR36435315 | Regenerating foot · 25uM U0126 treatment | Regenerating foot | 1.5hpa | 25uM U0126 treatment | SRP654941 | 0.00 |
| SRR36435316 | Regenerating foot · 25uM U0126 treatment | Regenerating foot | 1.5hpa | 25uM U0126 treatment | SRP654941 | 0.00 |
| SRR36435317 | Regenerating foot · 25uM U0126 treatment | Regenerating foot | 3hpa | 25uM U0126 treatment | SRP654941 | 0.00 |
| SRR36435318 | Regenerating foot · 25uM U0126 treatment | Regenerating foot | 3hpa | 25uM U0126 treatment | SRP654941 | 0.00 |
| SRR36435319 | Regenerating foot · 25uM U0126 treatment | Regenerating foot | 3hpa | 25uM U0126 treatment | SRP654941 | 0.00 |
| SRR36435320 | Regenerating foot · 25uM U0126 treatment | Regenerating foot | 0hpa | 25uM U0126 treatment | SRP654941 | 0.00 |
| SRR36435321 | Regenerating foot · 25uM U0126 treatment | Regenerating foot | 0hpa | 25uM U0126 treatment | SRP654941 | 0.00 |
| SRR36435268 | Regenerating head · u0126 treatment | Regenerating head | 12hpa | u0126 treatment | SRP654941 | 0.00 |
| SRR36435269 | Regenerating head · u0126 treatment | Regenerating head | 12hpa | u0126 treatment | SRP654941 | 0.00 |
| SRR36435270 | Regenerating head · u0126 treatment | Regenerating head | 12hpa | u0126 treatment | SRP654941 | 0.00 |
| SRR36435287 | Whole animal · 25uM U0126 treatment | Whole animal | 12h | 25uM U0126 treatment | SRP654941 | 0.00 |
| SRR36435288 | Whole animal · 25uM U0126 treatment | Whole animal | 12h | 25uM U0126 treatment | SRP654941 | 0.00 |
| SRR36435290 | Whole animal · 25uM U0126 treatment | Whole animal | 12h | 25uM U0126 treatment | SRP654941 | 0.00 |
| SRR36435291 | Whole animal · dmso treatment | Whole animal | 12h | dmso treatment | SRP654941 | 0.00 |
| SRR36435292 | Whole animal · dmso treatment | Whole animal | 12h | dmso treatment | SRP654941 | 0.00 |
| SRR36435293 | Whole animal · dmso treatment | Whole animal | 12h | dmso treatment | SRP654941 | 0.00 |
| SRR36435264 | Regenerating foot · u0126 treatment | Regenerating foot | 0hpa | u0126 treatment | SRP654941 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (HVULG_TPM,
StringTie quantification over 60 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 Hydra vulgaris 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 Hydra vulgaris 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 Hydra vulgaris, 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.
| Dataset | Tissue / stage | Cells | Cell types | This gene | Marker of |
|---|---|---|---|---|---|
| HVULG_siebert_atlas | Whole animals · Adult (whole animal) | 25,438 | 42 | not in this dataset | – |
A gene is in viewer when the dataset ships a per-cell expression vector for it; marker only means it is in the dataset’s ranked marker table but no vector was exported, so the atlas cannot draw it; not in this dataset means the dataset’s own gene-ID table does not list it, so no expression claim can be made for that dataset. unmapped is deliberately weaker still: the dataset has no gene-ID table on CnidoSite yet, so nothing is claimed in either direction. Where markers are listed, the numbers are log2 fold change and the percentage of cells of that type in which the gene was detected.
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.
| Assay | Sample | Peaks | Region |
|---|
No called peak overlaps this gene in 1 available assay. Either the gene is not near an accessible or marked region in those samples, or it is not represented in the peak caller’s annotation.
Browse the full epigenomic landscape of this species: ChIP-seq.
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 → |
