Genomic Location: QPEY01000524.1:1628645...1631039
NR annotation: WP_088590420.1, PBP1A family penicillin-binding protein [Achromobacter marplatensis]
Species Hydra viridissima · all data for this species · gene families
| CDS |
| BRAKERKRET00000022875 |
| Transcript |
| BRAKERKRET00000022875 |
| Protein |
| BRAKERKREP00000022875.1 |
| UniProt accession | Description |
|---|---|
| O87579 | Penicillin-binding protein 1A OS=Neisseria lactamica OX=486 GN=mrcA PE=3 SV=1 |
| P0A0Z5 | Penicillin-binding protein 1A OS=Neisseria meningitidis serogroup A / serotype 4A (strain DSM 15465 / Z2491) OX=122587 GN=mrcA PE=3 SV=1 |
| P0A0Z6 | Penicillin-binding protein 1A OS=Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58) OX=122586 GN=mrcA PE=3 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0017737 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF17092 all species → | PCB_OB | Penicillin-binding protein OB-like domain | Family | Interproscan |
| PF00905 all species → | Transpeptidase | Penicillin binding protein transpeptidase domain | Domain | Interproscan |
| PF00912 all species → | Transgly | Transglycosylase | Family | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR012338 all species → | Homologous_superfamily | Beta-lactamase/transpeptidase-like | Interproscan |
| IPR036950 all species → | Homologous_superfamily | Penicillin binding protein transglycosylase domain | Interproscan |
| IPR031376 all species → | Domain | Penicillin-binding protein, OB-like domain | Interproscan |
| IPR001460 all species → | Domain | Penicillin-binding protein, transpeptidase | Interproscan |
| IPR023346 all species → | Homologous_superfamily | Lysozyme-like domain superfamily | Interproscan |
| IPR001264 all species → | Domain | Glycosyl transferase, family 51 | Interproscan |
| IPR050396 all species → | Family | Glycosyltransferase 51/Transpeptidase | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR32282 all species → | BINDING PROTEIN TRANSPEPTIDASE, PUTATIVE-RELATED | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0008658 all species → | Molecular Function | penicillin binding | Interproscan |
| GO:0008955 all species → | Molecular Function | peptidoglycan glycosyltransferase activity | Interproscan |
| GO:0009252 all species → | Biological Process | peptidoglycan biosynthetic process | Interproscan |
| GO:0046677 all species → | Biological Process | response to antibiotic | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K05366 | mrcA; penicillin-binding protein 1A | EC:2.4.99.28 EC:3.4.16.4 | Peptidoglycan biosynthesis and degradation proteins | ko01011 | deepkoala |
Transcript abundance of BRAKERKREP00000022875.1 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 → |
