Genomic Location: HiC_scaffold_2:66087...67268
NR annotation: WP_037548027.1, phosphoglycerate dehydrogenase [Spirochaeta lutea]
Species Hydractinia symbiolongicarpus · all data for this species · gene families
| CDS |
| HSymV2.0_g02.02058_t1 |
| Transcript |
| HSymV2.0_g02.02058_t1 |
| Protein |
| HSymV2.0_g02.02058_t1 |
| UniProt accession | Description |
|---|---|
| Q58424 | D-3-phosphoglycerate dehydrogenase OS=Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) OX=243232 GN=serA PE=3 SV=1 |
| O27051 | D-3-phosphoglycerate dehydrogenase OS=Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) OX=187420 GN=serA PE=3 SV=1 |
| P73821 | D-3-phosphoglycerate dehydrogenase OS=Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa) OX=1111708 GN=serA PE=3 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0003461 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF02826 all species → | 2-Hacid_dh_C | D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain | Domain | Interproscan |
| PF00389 all species → | 2-Hacid_dh | D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR045865 all species → | Homologous_superfamily | ACT-like domain | Interproscan |
| IPR006140 all species → | Domain | D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain | Interproscan |
| IPR006139 all species → | Domain | D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain | Interproscan |
| IPR050857 all species → | Family | D-isomer specific 2-hydroxyacid dehydrogenases | Interproscan |
| IPR036291 all species → | Homologous_superfamily | NAD(P)-binding domain superfamily | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR42789 all species → | D-ISOMER SPECIFIC 2-HYDROXYACID DEHYDROGENASE FAMILY PROTEIN (AFU_ORTHOLOGUE AFUA_6G10090) | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0051287 all species → | Molecular Function | NAD binding | Interproscan |
| GO:0016616 all species → | Molecular Function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K00058 | serA, PHGDH; D-3-phosphoglycerate dehydrogenase / 2-oxoglutarate reductase | EC:1.1.1.95 EC:1.1.1.399 | Exosome | ko04147 | deepkoala |
Transcript abundance of HSymV2.0_g02.02058_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 → |
