Genomic Location: QPEY01000155.1:90976...147963
NR annotation: XP_047135671.1, vacuolar protein sorting-associated protein 13A [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families
| CDS |
| BRAKERKRET00000018944 |
| Transcript |
| BRAKERKRET00000018944 |
| Protein |
| BRAKERKREP00000018944.1 |
| UniProt accession | Description |
|---|---|
| Q8BX70 | Intermembrane lipid transfer protein VPS13C OS=Mus musculus OX=10090 GN=Vps13c PE=1 SV=2 |
| Q709C8 | Intermembrane lipid transfer protein VPS13C OS=Homo sapiens OX=9606 GN=VPS13C PE=1 SV=1 |
| Q9BGZ0 | Intermembrane lipid transfer protein VPS13A OS=Macaca fascicularis OX=9541 GN=VPS13A PE=2 SV=2 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0000767 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF09333 all species → | ATG2-VPS13_C | ATG2/VPS13, C terminal domain | Domain | Interproscan |
| PF21679 all species → | VPS13_C | Intermembrane lipid transfer protein VPS13, C-terminal | Domain | Interproscan |
| PF06650 all species → | VPS13_VAB | Vacuolar-sorting associated protein 13, adaptor binding domain | Domain | Interproscan |
| PF16909 all species → | VPS13_DH-like | Vacuolar-sorting-associated 13 protein, DH-like domain | Family | Interproscan |
| PF16910 all species → | VPS13_mid_rpt | VPS13, central RBG modules | Repeat | Interproscan |
| PF16908 all species → | VPS13_ext_chorein | Vacuolar sorting-associated protein 13, extended-chorein | Repeat | Interproscan |
| PF12624 all species → | Chorein_N | VPS13-like, N-terminal | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR002999 all species → | Domain | Tudor domain | Interproscan |
| IPR015412 all species → | Domain | Atg2/VPS13, C-terminal | Interproscan |
| IPR049424 all species → | Domain | Intermembrane lipid transfer protein VPS13, C-terminal | Interproscan |
| IPR026847 all species → | Family | Vacuolar protein sorting-associated protein 13 | Interproscan |
| IPR009543 all species → | Domain | Vacuolar protein sorting-associated protein 13, VPS13 adaptor binding domain | Interproscan |
| IPR031645 all species → | Domain | Vacuolar protein sorting-associated protein 13, DH-like domain | Interproscan |
| IPR031642 all species → | Domain | VPS13, middle RBG modules | Interproscan |
| IPR031646 all species → | Domain | Vacuolar protein sorting-associated protein 13, extended chorein | Interproscan |
| IPR026854 all species → | Domain | Vacuolar protein sorting-associated protein 13-like, N-terminal domain | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR16166 all species → | VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN VPS13 | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0006623 all species → | Biological Process | protein targeting to vacuole | Interproscan |
| GO:0019898 all species → | Cellular Component | extrinsic component of membrane | Interproscan |
| GO:0045053 all species → | Biological Process | protein retention in Golgi apparatus | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K19525 | VPS13A_C; vacuolar protein sorting-associated protein 13A/C | - | Membrane trafficking | ko04131 | deepkoala |
Transcript abundance of BRAKERKREP00000018944.1 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 | 9 | 2.59 | 18.43 | |
| Whole | 6 | 6 | 8.02 | 11.28 | |
| aposymbioic hydra M9 strain · aposymbioic hydra rep1 | 1 | 1 | 6.09 | 6.09 | |
| aposymbioic hydra M9 strain · aposymbioic hydra rep2 | 1 | 1 | 8.06 | 8.06 | |
| symbioic hydra M9 strain · symbioic hydra rep1 | 1 | 1 | 6.10 | 6.10 | |
| symbioic hydra M9 strain · symbioic hydra rep2 | 1 | 1 | 1.26 | 1.26 | |
| 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 | 18.43 |
| SRR21134064 | whole body | whole body | not recorded | not recorded | SRP392977 | 8.12 |
| SRR21134052 | whole body | whole body | not recorded | not recorded | SRP392977 | 7.07 |
| SRR21134056 | whole body | whole body | not recorded | not recorded | SRP392977 | 3.94 |
| SRR21134066 | whole body | whole body | not recorded | not recorded | SRP392977 | 3.53 |
| SRR21134055 | whole body | whole body | not recorded | not recorded | SRP392977 | 2.31 |
| SRR21134054 | whole body | whole body | not recorded | not recorded | SRP392977 | 1.59 |
| SRR21134057 | whole body | whole body | not recorded | not recorded | SRP392977 | 1.04 |
| SRR21134059 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.57 |
| 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 |
| 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 |
| SRR10058806 | Whole | Whole | not recorded | not recorded | SRP220397 | 11.28 |
| SRR10058805 | Whole | Whole | not recorded | not recorded | SRP220397 | 10.19 |
| SRR10058803 | Whole | Whole | not recorded | not recorded | SRP220397 | 8.16 |
| SRR10058807 | Whole | Whole | not recorded | not recorded | SRP220397 | 7.71 |
| SRR10058804 | Whole | Whole | not recorded | not recorded | SRP220397 | 7.38 |
| SRR10058802 | Whole | Whole | not recorded | not recorded | SRP220397 | 3.39 |
| DRR048593 | aposymbioic hydra M9 strain · aposymbioic hydra rep1 | not recorded | not recorded | aposymbioic hydra rep1 | DRP003902 | 6.09 |
| DRR048594 | aposymbioic hydra M9 strain · aposymbioic hydra rep2 | not recorded | not recorded | aposymbioic hydra rep2 | DRP003902 | 8.06 |
| DRR048595 | symbioic hydra M9 strain · symbioic hydra rep1 | not recorded | not recorded | symbioic hydra rep1 | DRP003902 | 6.10 |
| DRR048596 | symbioic hydra M9 strain · symbioic hydra rep2 | not recorded | not recorded | symbioic hydra rep2 | DRP003902 | 1.26 |
| 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 | 5 | BRAKERKREP00000016563.1 | 0.954457842602024 |
| Negatively correlated | 3 | BRAKERKREP00000024112.1 | -0.705052440299447 |
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 → |
