Genomic Location: HiC_scaffold_3:33741338...33763392
NR annotation: XP_047131119.1, uncharacterized protein LOC100214647 [Hydra vulgaris]
Species Hydractinia symbiolongicarpus · all data for this species · gene families
| CDS |
| HSymV2.0_g03.05995_t1 |
| Transcript |
| HSymV2.0_g03.05995_t1 |
| Protein |
| HSymV2.0_g03.05995_t1 |
| UniProt accession | Description |
|---|---|
| P27393 | Collagen alpha-2(IV) chain OS=Ascaris suum OX=6253 PE=2 SV=1 |
| Q7SIB3 | Collagen alpha-2(IV) chain (Fragment) OS=Bos taurus OX=9913 GN=COL4A2 PE=1 SV=1 |
| P17140 | Collagen alpha-2(IV) chain OS=Caenorhabditis elegans OX=6239 GN=let-2 PE=1 SV=2 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0001701 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF00092 all species → | VWA | von Willebrand factor type A domain | Domain | Interproscan |
| PF01413 all species → | C4 | C-terminal tandem repeated domain in type 4 procollagen | Domain | Interproscan |
| PF00095 all species → | WAP | WAP-type (Whey Acidic Protein) 'four-disulfide core' | Domain | Interproscan |
| PF01391 all species → | Collagen | Collagen triple helix repeat (20 copies) | Repeat | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR036465 all species → | Homologous_superfamily | von Willebrand factor A-like domain superfamily | Interproscan |
| IPR002035 all species → | Domain | von Willebrand factor, type A | Interproscan |
| IPR001442 all species → | Domain | Collagen IV, non-collagenous | Interproscan |
| IPR008197 all species → | Domain | WAP-type 'four-disulfide core' domain | Interproscan |
| IPR016187 all species → | Homologous_superfamily | C-type lectin fold | Interproscan |
| IPR008160 all species → | Repeat | Collagen triple helix repeat | Interproscan |
| IPR036954 all species → | Homologous_superfamily | Collagen IV, non-collagenous domain superfamily | Interproscan |
| IPR050525 all species → | Family | Extracellular Matrix Assembly and Organization | Interproscan |
| IPR036645 all species → | Homologous_superfamily | Elafin-like superfamily | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR24020 all species → | COLLAGEN ALPHA | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0005201 all species → | Molecular Function | extracellular matrix structural constituent | Interproscan |
| GO:0005581 all species → | Cellular Component | collagen trimer | Interproscan |
| GO:0005576 all species → | Cellular Component | extracellular region | Interproscan |
| GO:0030414 all species → | Molecular Function | peptidase inhibitor activity | Interproscan |
HSymV2.0_g03.05995_t1.Transcript abundance of HSymV2.0_g03.05995_t1 across 44 RNA-seq samples of Hydractinia symbiolongicarpus. 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 | 8 | 5.55 | 56.86 | |
| Whole embryo · Triptolide 20 uM | 4 | 0 | 0.00 | 0.00 | |
| Whole embryo · DMSO 0.5% | 4 | 1 | 0.06 | 0.23 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR24482160 | Whole embryo | Whole embryo | 24 hpf | not recorded | SRP436676 | 56.86 |
| SRR24482159 | Whole embryo | Whole embryo | 24 hpf | not recorded | SRP436676 | 40.02 |
| SRR24482157 | Whole embryo | Whole embryo | 48 hpf | not recorded | SRP436676 | 35.86 |
| SRR24482158 | Whole embryo | Whole embryo | 48 hpf | not recorded | SRP436676 | 31.07 |
| SRR24482155 | Whole embryo | Whole embryo | 72 hpf | not recorded | SRP436676 | 21.29 |
| SRR24482156 | Whole embryo | Whole embryo | 72 hpf | not recorded | SRP436676 | 14.62 |
| SRR24482161 | Whole embryo | Whole embryo | 7 hpf | not recorded | SRP436676 | 0.12 |
| SRR24482169 | Whole embryo | Whole embryo | 2 hpf | not recorded | SRP436676 | 0.11 |
| 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 |
| 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 |
| 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 | 0.23 |
| 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 | 40 | HSymV2.0_g09.16991_t1 | 0.999185894681241 |
| Negatively correlated | 3 | HSymV2.0_g07.12046_t1 | -0.880909929175088 |
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. | 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 → |
