Genomic Location: QPEY01000214.1:75127...76918
NR annotation: XP_002161913.1, tubulin beta chain [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families
| CDS |
| BRAKERKRET00000020649 |
| Transcript |
| BRAKERKRET00000020649 |
| Protein |
| BRAKERKREP00000020649.1 |
| UniProt accession | Description |
|---|---|
| Q3MHM5 | Tubulin beta-4B chain OS=Bos taurus OX=9913 GN=TUBB4B PE=1 SV=1 |
| P68371 | Tubulin beta-4B chain OS=Homo sapiens OX=9606 GN=TUBB4B PE=1 SV=1 |
| P68372 | Tubulin beta-4B chain OS=Mus musculus OX=10090 GN=Tubb4b PE=1 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0000525 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF00091 all species → | Tubulin | Tubulin/FtsZ family, GTPase domain | Domain | Interproscan |
| PF03953 all species → | Tubulin_C | Tubulin C-terminal domain | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR003008 all species → | Domain | Tubulin/FtsZ, GTPase domain | Interproscan |
| IPR037103 all species → | Homologous_superfamily | Tubulin/FtsZ-like, C-terminal domain | Interproscan |
| IPR036525 all species → | Homologous_superfamily | Tubulin/FtsZ, GTPase domain superfamily | Interproscan |
| IPR000217 all species → | Family | Tubulin | Interproscan |
| IPR018316 all species → | Domain | Tubulin/FtsZ, 2-layer sandwich domain | Interproscan |
| IPR013838 all species → | Binding_site | Beta tubulin, autoregulation binding site | Interproscan |
| IPR023123 all species → | Homologous_superfamily | Tubulin, C-terminal | Interproscan |
| IPR017975 all species → | Conserved_site | Tubulin, conserved site | Interproscan |
| IPR008280 all species → | Homologous_superfamily | Tubulin/FtsZ, C-terminal | Interproscan |
| IPR002453 all species → | Family | Beta tubulin | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR11588 all species → | TUBULIN | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0005525 all species → | Molecular Function | GTP binding | Interproscan |
| GO:0005874 all species → | Cellular Component | microtubule | Interproscan |
| GO:0007017 all species → | Biological Process | microtubule-based process | Interproscan |
| GO:0000226 all species → | Biological Process | microtubule cytoskeleton organization | Interproscan |
| GO:0000278 all species → | Biological Process | mitotic cell cycle | Interproscan |
| GO:0005200 all species → | Molecular Function | structural constituent of cytoskeleton | Interproscan |
| GO:0005737 all species → | Cellular Component | cytoplasm | Interproscan |
| GO:0003924 all species → | Molecular Function | GTPase activity | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K07375 | TUBB; tubulin beta | - | Exosome | ko04147 | deepkoala |
Transcript abundance of BRAKERKREP00000020649.1 across 29 RNA-seq samples of Hydra viridissima. 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 |
|---|---|---|---|---|---|
| whole body | 18 | 0 | 0.00 | 0.00 | |
| Whole | 6 | 0 | 0.00 | 0.00 | |
| aposymbioic hydra M9 strain · aposymbioic hydra rep1 | 1 | 0 | 0.00 | 0.00 | |
| aposymbioic hydra M9 strain · aposymbioic hydra rep2 | 1 | 0 | 0.00 | 0.00 | |
| symbioic hydra M9 strain · symbioic hydra rep1 | 1 | 0 | 0.00 | 0.00 | |
| symbioic hydra M9 strain · symbioic hydra rep2 | 1 | 0 | 0.00 | 0.00 | |
| unannotated | 1 | 0 | 0.00 | 0.00 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR21134050 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134051 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134052 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134053 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134054 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134055 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134056 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134057 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134058 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134059 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134060 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134061 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134062 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134063 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134064 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134065 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134066 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134067 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR10058802 | Whole | Whole | not recorded | not recorded | SRP220397 | 0.00 |
| SRR10058803 | Whole | Whole | not recorded | not recorded | SRP220397 | 0.00 |
| SRR10058804 | Whole | Whole | not recorded | not recorded | SRP220397 | 0.00 |
| SRR10058805 | Whole | Whole | not recorded | not recorded | SRP220397 | 0.00 |
| SRR10058806 | Whole | Whole | not recorded | not recorded | SRP220397 | 0.00 |
| SRR10058807 | Whole | Whole | not recorded | not recorded | SRP220397 | 0.00 |
| DRR048593 | aposymbioic hydra M9 strain · aposymbioic hydra rep1 | not recorded | not recorded | aposymbioic hydra rep1 | DRP003902 | 0.00 |
| DRR048594 | aposymbioic hydra M9 strain · aposymbioic hydra rep2 | not recorded | not recorded | aposymbioic hydra rep2 | DRP003902 | 0.00 |
| DRR048595 | symbioic hydra M9 strain · symbioic hydra rep1 | not recorded | not recorded | symbioic hydra rep1 | DRP003902 | 0.00 |
| DRR048596 | symbioic hydra M9 strain · symbioic hydra rep2 | not recorded | not recorded | symbioic hydra rep2 | DRP003902 | 0.00 |
| ERR13389755 | unannotated | not recorded | not recorded | not recorded | ERP162636 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (HVIRI_TPM,
StringTie quantification over 29 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 viridissima 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 viridissima 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 viridissima, 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 → |
