Genomic Location: QPEY01000524.1:1519679...1521514
NR annotation: WP_076520334.1, penicillin-binding protein 1C [Achromobacter sp. MFA1 R4]
Species Hydra viridissima · all data for this species · gene families
| CDS |
| BRAKERKRET00000023453 |
| Transcript |
| BRAKERKRET00000023453 |
| Protein |
| BRAKERKREP00000023453.1 |
| UniProt accession | Description |
|---|---|
| P76577 | Penicillin-binding protein 1C OS=Escherichia coli (strain K12) OX=83333 GN=pbpC PE=1 SV=1 |
| P45345 | Penicillin-binding protein 1B OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) OX=71421 GN=mrcB PE=3 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0050290 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF00912 all species → | Transgly | Transglycosylase | Family | Interproscan |
| PF00905 all species → | Transpeptidase | Penicillin binding protein transpeptidase domain | Domain | Interproscan |
| PF06832 all species → | BiPBP_C | Penicillin-Binding Protein C-terminus Family | Family | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR012338 all species → | Homologous_superfamily | Beta-lactamase/transpeptidase-like | Interproscan |
| IPR001264 all species → | Domain | Glycosyl transferase, family 51 | Interproscan |
| IPR001460 all species → | Domain | Penicillin-binding protein, transpeptidase | Interproscan |
| IPR050396 all species → | Family | Glycosyltransferase 51/Transpeptidase | Interproscan |
| IPR009647 all species → | Domain | Penicillin-binding, C-terminal | Interproscan |
| IPR011815 all species → | Family | Penicillin-binding protein 1C | Interproscan |
| IPR036950 all species → | Homologous_superfamily | Penicillin binding protein transglycosylase domain | Interproscan |
| IPR023346 all species → | Homologous_superfamily | Lysozyme-like domain superfamily | 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 |
|---|---|---|---|---|---|
| K05367 | pbpC; penicillin-binding protein 1C | EC:2.4.99.28 | Peptidoglycan biosynthesis and degradation proteins | ko01011 | deepkoala |
Transcript abundance of BRAKERKREP00000023453.1 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 | 8 | 1.88 | 27.76 | |
| Whole | 6 | 5 | 0.04 | 0.17 | |
| aposymbioic hydra M9 strain · aposymbioic hydra rep1 | 1 | 1 | 0.02 | 0.02 | |
| aposymbioic hydra M9 strain · aposymbioic hydra rep2 | 1 | 1 | 0.01 | 0.01 | |
| symbioic hydra M9 strain · symbioic hydra rep1 | 1 | 1 | 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 |
|---|---|---|---|---|---|---|
| SRR21134052 | whole body | whole body | not recorded | not recorded | SRP392977 | 27.76 |
| SRR21134057 | whole body | whole body | not recorded | not recorded | SRP392977 | 2.19 |
| SRR21134066 | whole body | whole body | not recorded | not recorded | SRP392977 | 1.86 |
| SRR21134055 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.83 |
| SRR21134056 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.69 |
| SRR21134054 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.25 |
| SRR21134064 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.21 |
| SRR21134060 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.06 |
| SRR21134050 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134051 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| 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 |
| 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 |
| SRR21134065 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134067 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR10058804 | Whole | Whole | not recorded | not recorded | SRP220397 | 0.17 |
| SRR10058805 | Whole | Whole | not recorded | not recorded | SRP220397 | 0.03 |
| SRR10058803 | Whole | Whole | not recorded | not recorded | SRP220397 | 0.03 |
| SRR10058806 | Whole | Whole | not recorded | not recorded | SRP220397 | 0.02 |
| SRR10058807 | Whole | Whole | not recorded | not recorded | SRP220397 | 0.01 |
| SRR10058802 | 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 | 0.02 |
| DRR048594 | aposymbioic hydra M9 strain · aposymbioic hydra rep2 | not recorded | not recorded | aposymbioic hydra rep2 | DRP003902 | 0.01 |
| 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 | 16 | 20353_g | 0.999940635317045 |
| Negatively correlated | 3 | g25494 | -0.278687022018014 |
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 → |
