Genomic Location: HiC_scaffold_2:1005025...1005744
NR annotation: MBQ4874518.1, pyridoxine 5'-phosphate synthase [Rickettsiaceae bacterium H1]
Species Hydractinia symbiolongicarpus · all data for this species · gene families
| CDS |
| HSymV2.0_g02.02491_t1 |
| Transcript |
| HSymV2.0_g02.02491_t1 |
| Protein |
| HSymV2.0_g02.02491_t1 |
| UniProt accession | Description |
|---|---|
| Q21XM2 | Pyridoxine 5'-phosphate synthase OS=Albidiferax ferrireducens (strain ATCC BAA-621 / DSM 15236 / T118) OX=338969 GN=pdxJ PE=3 SV=1 |
| Q11PM4 | Pyridoxine 5'-phosphate synthase OS=Cytophaga hutchinsonii (strain ATCC 33406 / DSM 1761 / CIP 103989 / NBRC 15051 / NCIMB 9469 / D465) OX=269798 GN=pdxJ PE=3 SV=1 |
| Q5L912 | Pyridoxine 5'-phosphate synthase OS=Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2) OX=272559 GN=pdxJ PE=3 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0015805 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF03740 all species → | PdxJ | Pyridoxal phosphate biosynthesis protein PdxJ | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR036130 all species → | Homologous_superfamily | Pyridoxine 5'-phosphate synthase | Interproscan |
| IPR013785 all species → | Homologous_superfamily | Aldolase-type TIM barrel | Interproscan |
| IPR004569 all species → | Family | Pyridoxal phosphate (active vitamin B6) biosynthesis PdxJ | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR30456 all species → | PYRIDOXINE 5'-PHOSPHATE SYNTHASE | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0005737 all species → | Cellular Component | cytoplasm | Interproscan |
| GO:0008615 all species → | Biological Process | pyridoxine biosynthetic process | Interproscan |
| GO:0033856 all species → | Molecular Function | pyridoxine 5'-phosphate synthase activity | Interproscan |
| GO:0005829 all species → | Cellular Component | cytosol | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K03474 | pdxJ; pyridoxine 5-phosphate synthase | EC:2.6.99.2 | Vitamin B6 metabolism | ko00750 | deepkoala |
Transcript abundance of HSymV2.0_g02.02491_t1 across 44 RNA-seq samples of Hydractinia symbiolongicarpus. 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 embryo | 36 | 0 | 0.00 | 0.00 | |
| Whole embryo · Triptolide 20 uM | 4 | 0 | 0.00 | 0.00 | |
| Whole embryo · DMSO 0.5% | 4 | 0 | 0.00 | 0.00 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR24482133 | Whole embryo | Whole embryo | 6 hpf | not recorded | SRP436676 | 0.00 |
| SRR24482134 | Whole embryo | Whole embryo | 5 hpf | not recorded | SRP436676 | 0.00 |
| SRR24482135 | Whole embryo | Whole embryo | 4 hpf | not recorded | SRP436676 | 0.00 |
| SRR24482136 | Whole embryo | Whole embryo | 4 hpf | not recorded | SRP436676 | 0.00 |
| SRR24482137 | Whole embryo | Whole embryo | 3 hpf | not recorded | SRP436676 | 0.00 |
| SRR24482138 | Whole embryo | Whole embryo | 3 hpf | not recorded | SRP436676 | 0.00 |
| SRR24482139 | Whole embryo | Whole embryo | 2 hpf | not recorded | SRP436676 | 0.00 |
| SRR24482140 | Whole embryo | Whole embryo | 2 hpf | not recorded | SRP436676 | 0.00 |
| SRR24482141 | Whole embryo | Whole embryo | 1 hpf | not recorded | SRP436676 | 0.00 |
| SRR24482142 | Whole embryo | Whole embryo | 30 mpf | not recorded | SRP436676 | 0.00 |
| SRR24482143 | Whole embryo | Whole embryo | Unfertilized egg | not recorded | SRP436676 | 0.00 |
| SRR24482144 | Whole embryo | Whole embryo | Unfertilized egg | not recorded | SRP436676 | 0.00 |
| SRR24482145 | Whole embryo | Whole embryo | Unfertilized egg | not recorded | SRP436676 | 0.00 |
| SRR24482153 | Whole embryo | Whole embryo | 7 hpf | not recorded | SRP436676 | 0.00 |
| SRR24482155 | Whole embryo | Whole embryo | 72 hpf | not recorded | SRP436676 | 0.00 |
| SRR24482156 | Whole embryo | Whole embryo | 72 hpf | not recorded | SRP436676 | 0.00 |
| SRR24482157 | Whole embryo | Whole embryo | 48 hpf | not recorded | SRP436676 | 0.00 |
| SRR24482158 | Whole embryo | Whole embryo | 48 hpf | not recorded | SRP436676 | 0.00 |
| SRR24482159 | Whole embryo | Whole embryo | 24 hpf | not recorded | SRP436676 | 0.00 |
| SRR24482160 | Whole embryo | Whole embryo | 24 hpf | not recorded | SRP436676 | 0.00 |
| SRR24482161 | Whole embryo | Whole embryo | 7 hpf | not recorded | SRP436676 | 0.00 |
| SRR24482162 | Whole embryo | Whole embryo | 7 hpf | not recorded | SRP436676 | 0.00 |
| SRR24482163 | Whole embryo | Whole embryo | 6 hpf | not recorded | SRP436676 | 0.00 |
| SRR24482165 | Whole embryo | Whole embryo | 4 hpf | not recorded | SRP436676 | 0.00 |
| SRR24482166 | Whole embryo | Whole embryo | 4 hpf | not recorded | SRP436676 | 0.00 |
| SRR24482167 | Whole embryo | Whole embryo | 3 hpf | not recorded | SRP436676 | 0.00 |
| SRR24482168 | Whole embryo | Whole embryo | 3 hpf | not recorded | SRP436676 | 0.00 |
| SRR24482169 | Whole embryo | Whole embryo | 2 hpf | not recorded | SRP436676 | 0.00 |
| SRR24482170 | Whole embryo | Whole embryo | 2 hpf | not recorded | SRP436676 | 0.00 |
| SRR24482171 | Whole embryo | Whole embryo | 1 hpf | not recorded | SRP436676 | 0.00 |
| SRR24482172 | Whole embryo | Whole embryo | 30 mpf | not recorded | SRP436676 | 0.00 |
| SRR24482173 | Whole embryo | Whole embryo | Unfertilized egg | not recorded | SRP436676 | 0.00 |
| SRR24482174 | Whole embryo | Whole embryo | Unfertilized egg | not recorded | SRP436676 | 0.00 |
| SRR24482175 | Whole embryo | Whole embryo | Unfertilized egg | not recorded | SRP436676 | 0.00 |
| SRR24482176 | Whole embryo | Whole embryo | 1 hpf | not recorded | SRP436676 | 0.00 |
| SRR24482177 | Whole embryo | Whole embryo | 1 hpf | not recorded | SRP436676 | 0.00 |
| SRR24482146 | Whole embryo · Triptolide 20 uM | Whole embryo | 7 hpf | Triptolide 20 uM | SRP436676 | 0.00 |
| SRR24482147 | Whole embryo · Triptolide 20 uM | Whole embryo | 7 hpf | Triptolide 20 uM | SRP436676 | 0.00 |
| SRR24482149 | Whole embryo · Triptolide 20 uM | Whole embryo | 7 hpf | Triptolide 20 uM | SRP436676 | 0.00 |
| SRR24482150 | Whole embryo · Triptolide 20 uM | Whole embryo | 7 hpf | Triptolide 20 uM | SRP436676 | 0.00 |
| SRR24482148 | Whole embryo · DMSO 0.5% | Whole embryo | 7 hpf | DMSO 0.5% | SRP436676 | 0.00 |
| SRR24482151 | Whole embryo · DMSO 0.5% | Whole embryo | 7 hpf | DMSO 0.5% | SRP436676 | 0.00 |
| SRR24482152 | Whole embryo · DMSO 0.5% | Whole embryo | 7 hpf | DMSO 0.5% | SRP436676 | 0.00 |
| SRR24482154 | Whole embryo · DMSO 0.5% | Whole embryo | 7 hpf | DMSO 0.5% | SRP436676 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (HSYMB_TPM,
StringTie quantification over 44 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 Hydractinia symbiolongicarpus 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 Hydractinia symbiolongicarpus 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 Hydractinia symbiolongicarpus, 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 → |
