Genomic Location: QPEY01000524.1:1426583...1427791
NR annotation: WP_012248888.1, transcription termination factor Rho [Bordetella petrii]
Species Hydra viridissima · all data for this species · gene families
| CDS |
| BRAKERKRET00000023818 |
| Transcript |
| BRAKERKRET00000023818 |
| Protein |
| BRAKERKREP00000023818.1 |
| UniProt accession | Description |
|---|---|
| Q7NXP1 | Transcription termination factor Rho OS=Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / CCUG 213 / NBRC 12614 / NCIMB 9131 / NCTC 9757 / MK) OX=243365 GN=rho PE=3 SV=1 |
| Q06447 | Transcription termination factor Rho OS=Neisseria gonorrhoeae OX=485 GN=rho PE=3 SV=1 |
| Q9HTV1 | Transcription termination factor Rho OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=rho PE=3 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0012246 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF00006 all species → | ATP-synt_ab | ATP synthase alpha/beta family, nucleotide-binding domain | Domain | Interproscan |
| PF07498 all species → | Rho_N | Rho termination factor, N-terminal domain | Domain | Interproscan |
| PF07497 all species → | Rho_RNA_bind | Rho termination factor, RNA-binding domain | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR011113 all species → | Domain | Rho termination factor, RNA-binding domain | Interproscan |
| IPR012340 all species → | Homologous_superfamily | Nucleic acid-binding, OB-fold | Interproscan |
| IPR011129 all species → | Domain | Cold shock domain | Interproscan |
| IPR000194 all species → | Domain | ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain | Interproscan |
| IPR011112 all species → | Domain | Rho termination factor, N-terminal | Interproscan |
| IPR036269 all species → | Homologous_superfamily | Rho termination factor, N-terminal domain superfamily | Interproscan |
| IPR004665 all species → | Family | Transcription termination factor Rho | Interproscan |
| IPR041703 all species → | Domain | Transcription termination factor Rho, ATP binding domain | Interproscan |
| IPR027417 all species → | Homologous_superfamily | P-loop containing nucleoside triphosphate hydrolase | Interproscan |
| IPR003593 all species → | Domain | AAA+ ATPase domain | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR46425 all species → | TRANSCRIPTION TERMINATION FACTOR RHO | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0003723 all species → | Molecular Function | RNA binding | Interproscan |
| GO:0006353 all species → | Biological Process | DNA-templated transcription termination | Interproscan |
| GO:0003676 all species → | Molecular Function | nucleic acid binding | Interproscan |
| GO:0005524 all species → | Molecular Function | ATP binding | Interproscan |
| GO:0008186 all species → | Molecular Function | ATP-dependent activity, acting on RNA | Interproscan |
| GO:0016887 all species → | Molecular Function | ATP hydrolysis activity | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K03628 | rho; transcription termination factor Rho | - | Messenger RNA biogenesis | ko03019 | deepkoala |
Transcript abundance of BRAKERKREP00000023818.1 across 29 RNA-seq samples of Hydra viridissima. 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 | 11 | 1.96 | 12.46 | |
| Whole | 6 | 6 | 2.66 | 3.89 | |
| aposymbioic hydra M9 strain · aposymbioic hydra rep1 | 1 | 1 | 3.94 | 3.94 | |
| aposymbioic hydra M9 strain · aposymbioic hydra rep2 | 1 | 1 | 5.31 | 5.31 | |
| symbioic hydra M9 strain · symbioic hydra rep1 | 1 | 1 | 4.90 | 4.90 | |
| symbioic hydra M9 strain · symbioic hydra rep2 | 1 | 1 | 7.77 | 7.77 | |
| unannotated | 1 | 0 | 0.00 | 0.00 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR21134060 | whole body | whole body | not recorded | not recorded | SRP392977 | 12.46 |
| SRR21134051 | whole body | whole body | not recorded | not recorded | SRP392977 | 9.03 |
| SRR21134061 | whole body | whole body | not recorded | not recorded | SRP392977 | 4.13 |
| SRR21134050 | whole body | whole body | not recorded | not recorded | SRP392977 | 2.93 |
| SRR21134064 | whole body | whole body | not recorded | not recorded | SRP392977 | 2.28 |
| SRR21134052 | whole body | whole body | not recorded | not recorded | SRP392977 | 2.17 |
| SRR21134056 | whole body | whole body | not recorded | not recorded | SRP392977 | 1.39 |
| SRR21134066 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.44 |
| SRR21134057 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.29 |
| SRR21134054 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.08 |
| SRR21134055 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.04 |
| SRR21134053 | 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 |
| SRR21134062 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134063 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134065 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134067 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR10058806 | Whole | Whole | not recorded | not recorded | SRP220397 | 3.89 |
| SRR10058807 | Whole | Whole | not recorded | not recorded | SRP220397 | 3.68 |
| SRR10058803 | Whole | Whole | not recorded | not recorded | SRP220397 | 3.13 |
| SRR10058802 | Whole | Whole | not recorded | not recorded | SRP220397 | 2.46 |
| SRR10058805 | Whole | Whole | not recorded | not recorded | SRP220397 | 1.77 |
| SRR10058804 | Whole | Whole | not recorded | not recorded | SRP220397 | 1.04 |
| DRR048593 | aposymbioic hydra M9 strain · aposymbioic hydra rep1 | not recorded | not recorded | aposymbioic hydra rep1 | DRP003902 | 3.94 |
| DRR048594 | aposymbioic hydra M9 strain · aposymbioic hydra rep2 | not recorded | not recorded | aposymbioic hydra rep2 | DRP003902 | 5.31 |
| DRR048595 | symbioic hydra M9 strain · symbioic hydra rep1 | not recorded | not recorded | symbioic hydra rep1 | DRP003902 | 4.90 |
| DRR048596 | symbioic hydra M9 strain · symbioic hydra rep2 | not recorded | not recorded | symbioic hydra rep2 | DRP003902 | 7.77 |
| 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 | 3 | BRAKERKREP00000024112.1 | -0.562700179529987 |
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. | ready | open → |
| 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 → |
