Genomic Location: QPEY01000009.1:358814...367585
NR annotation: XP_012556392.1, protein transport protein Sec24D [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families
| CDS |
| BRAKERKRET00000003149 |
| Transcript |
| BRAKERKRET00000003149 |
| Protein |
| BRAKERKREP00000003149.1 |
| UniProt accession | Description |
|---|---|
| P53992 | Protein transport protein Sec24C OS=Homo sapiens OX=9606 GN=SEC24C PE=1 SV=3 |
| O94855 | Protein transport protein Sec24D OS=Homo sapiens OX=9606 GN=SEC24D PE=1 SV=2 |
| Q9M291 | Protein transport protein SEC24 B OS=Arabidopsis thaliana OX=3702 GN=SEC24B PE=2 SV=3 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0001507 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF04811 all species → | Sec23_trunk | Sec23/Sec24 trunk domain | Domain | Interproscan |
| PF00626 all species → | Gelsolin | Gelsolin repeat | Domain | Interproscan |
| PF04810 all species → | zf-Sec23_Sec24 | Sec23/Sec24 zinc finger | Domain | Interproscan |
| PF08033 all species → | Sec23_BS | Sec23/Sec24 beta-sandwich domain | Domain | Interproscan |
| PF04815 all species → | Sec23_helical | Sec23/Sec24 helical domain | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR036175 all species → | Homologous_superfamily | Sec23/Sec24 helical domain superfamily | Interproscan |
| IPR041742 all species → | Domain | Sec24-like, trunk domain | Interproscan |
| IPR029006 all species → | Homologous_superfamily | ADF-H/Gelsolin-like domain superfamily | Interproscan |
| IPR036465 all species → | Homologous_superfamily | von Willebrand factor A-like domain superfamily | Interproscan |
| IPR006896 all species → | Domain | Sec23/Sec24, trunk domain | Interproscan |
| IPR007123 all species → | Domain | Gelsolin-like domain | Interproscan |
| IPR036180 all species → | Homologous_superfamily | Gelsolin-like domain superfamily | Interproscan |
| IPR006895 all species → | Domain | Zinc finger, Sec23/Sec24-type | Interproscan |
| IPR012990 all species → | Domain | Sec23/Sec24 beta-sandwich | Interproscan |
| IPR006900 all species → | Domain | Sec23/Sec24, helical domain | Interproscan |
| IPR036174 all species → | Homologous_superfamily | Zinc finger, Sec23/Sec24-type superfamily | Interproscan |
| IPR050550 all species → | Family | SEC23/SEC24 family, SEC24 subfamily | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR13803 all species → | SEC24-RELATED PROTEIN | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0006886 all species → | Biological Process | intracellular protein transport | Interproscan |
| GO:0006888 all species → | Biological Process | endoplasmic reticulum to Golgi vesicle-mediated transport | Interproscan |
| GO:0030127 all species → | Cellular Component | COPII vesicle coat | Interproscan |
| GO:0008270 all species → | Molecular Function | zinc ion binding | Interproscan |
| GO:0000149 all species → | Molecular Function | SNARE binding | Interproscan |
| GO:0070971 all species → | Cellular Component | endoplasmic reticulum exit site | Interproscan |
| GO:0090110 all species → | Biological Process | COPII-coated vesicle cargo loading | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K14007 | SEC24; protein transport protein SEC24 | - | Membrane trafficking | ko04131 | deepkoala |
Transcript abundance of BRAKERKREP00000003149.1 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 | 2 | 1.53 | 14.03 | |
| Whole | 6 | 5 | 12.20 | 16.94 | |
| aposymbioic hydra M9 strain · aposymbioic hydra rep1 | 1 | 1 | 10.41 | 10.41 | |
| aposymbioic hydra M9 strain · aposymbioic hydra rep2 | 1 | 1 | 8.33 | 8.33 | |
| symbioic hydra M9 strain · symbioic hydra rep1 | 1 | 1 | 3.23 | 3.23 | |
| 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 |
|---|---|---|---|---|---|---|
| SRR21134060 | whole body | whole body | not recorded | not recorded | SRP392977 | 14.03 |
| SRR21134064 | whole body | whole body | not recorded | not recorded | SRP392977 | 13.59 |
| 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 |
| 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 |
| SRR21134066 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134067 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR10058803 | Whole | Whole | not recorded | not recorded | SRP220397 | 16.94 |
| SRR10058807 | Whole | Whole | not recorded | not recorded | SRP220397 | 15.24 |
| SRR10058806 | Whole | Whole | not recorded | not recorded | SRP220397 | 13.94 |
| SRR10058805 | Whole | Whole | not recorded | not recorded | SRP220397 | 13.71 |
| SRR10058804 | Whole | Whole | not recorded | not recorded | SRP220397 | 13.38 |
| 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 | 10.41 |
| DRR048594 | aposymbioic hydra M9 strain · aposymbioic hydra rep2 | not recorded | not recorded | aposymbioic hydra rep2 | DRP003902 | 8.33 |
| DRR048595 | symbioic hydra M9 strain · symbioic hydra rep1 | not recorded | not recorded | symbioic hydra rep1 | DRP003902 | 3.23 |
| 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 | 22 | g9988 | 0.996860497810379 |
| Negatively correlated | 3 | BRAKERKREP00000024112.1 | -0.675923044175149 |
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 → |
