Genomic Location: HiC_scaffold_14:9803456...9821865
NR annotation: XP_047123570.1, protocadherin Fat 4 isoform X2 [Hydra vulgaris]
Species Hydractinia symbiolongicarpus · all data for this species · gene families
| CDS |
| HSymV2.0_g14.24261_t1 |
| Transcript |
| HSymV2.0_g14.24261_t1 |
| Protein |
| HSymV2.0_g14.24261_t1 |
| UniProt accession | Description |
|---|---|
| Q2PZL6 | Protocadherin Fat 4 OS=Mus musculus OX=10090 GN=Fat4 PE=1 SV=2 |
| Q6V0I7 | Protocadherin Fat 4 OS=Homo sapiens OX=9606 GN=FAT4 PE=1 SV=2 |
| Q99PF4 | Cadherin-23 OS=Mus musculus OX=10090 GN=Cdh23 PE=1 SV=2 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0000196 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF00017 all species → | SH2 | SH2 domain | Domain | Interproscan |
| PF01085 all species → | HH_signal | Hedgehog amino-terminal signalling domain | Domain | Interproscan |
| PF00008 all species → | EGF | EGF-like domain | Domain | Interproscan |
| PF13927 all species → | Ig_3 | Immunoglobulin domain | Domain | Interproscan |
| PF00028 all species → | Cadherin | Cadherin domain | Domain | Interproscan |
| PF00092 all species → | VWA | von Willebrand factor type A domain | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR020894 all species → | Conserved_site | Cadherin conserved site | Interproscan |
| IPR000980 all species → | Domain | SH2 domain | Interproscan |
| IPR009045 all species → | Homologous_superfamily | Hedgehog signalling/DD-peptidase zinc-binding domain superfamily | Interproscan |
| IPR015919 all species → | Homologous_superfamily | Cadherin-like superfamily | Interproscan |
| IPR007110 all species → | Domain | Immunoglobulin-like domain | Interproscan |
| IPR036179 all species → | Homologous_superfamily | Immunoglobulin-like domain superfamily | Interproscan |
| IPR013783 all species → | Homologous_superfamily | Immunoglobulin-like fold | Interproscan |
| IPR002126 all species → | Domain | Cadherin-like | Interproscan |
| IPR001881 all species → | Domain | EGF-like calcium-binding domain | Interproscan |
| IPR000320 all species → | Domain | Hedgehog, N-terminal signalling domain | Interproscan |
| IPR002035 all species → | Domain | von Willebrand factor, type A | Interproscan |
| IPR000742 all species → | Domain | EGF-like domain | Interproscan |
| IPR000152 all species → | PTM | EGF-type aspartate/asparagine hydroxylation site | Interproscan |
| IPR001657 all species → | Family | Hedgehog protein | Interproscan |
| IPR003599 all species → | Domain | Immunoglobulin subtype | Interproscan |
| IPR003598 all species → | Domain | Immunoglobulin subtype 2 | Interproscan |
| IPR036465 all species → | Homologous_superfamily | von Willebrand factor A-like domain superfamily | Interproscan |
| IPR018097 all species → | Conserved_site | EGF-like calcium-binding, conserved site | Interproscan |
| IPR036860 all species → | Homologous_superfamily | SH2 domain superfamily | Interproscan |
| IPR050174 all species → | Family | Protocadherin/Cadherin-related Cell Adhesion | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR24028 all species → | CADHERIN-87A | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0005886 all species → | Cellular Component | plasma membrane | Interproscan |
| GO:0007155 all species → | Biological Process | cell adhesion | Interproscan |
| GO:0005509 all species → | Molecular Function | calcium ion binding | Interproscan |
| GO:0016020 all species → | Cellular Component | membrane | Interproscan |
| GO:0007156 all species → | Biological Process | homophilic cell adhesion via plasma membrane adhesion molecules | Interproscan |
| GO:0007267 all species → | Biological Process | cell-cell signaling | Interproscan |
| GO:0007275 all species → | Biological Process | multicellular organism development | Interproscan |
| GO:0005887 all species → | Cellular Component | plasma membrane | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K16669 | FAT4; protocadherin Fat 4 | - | Cell adhesion molecules | ko04515 | deepkoala |
Transcript abundance of HSymV2.0_g14.24261_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 | 36 | 10.36 | 21.50 | |
| Whole embryo · Triptolide 20 uM | 4 | 3 | 7.71 | 14.86 | |
| Whole embryo · DMSO 0.5% | 4 | 4 | 4.46 | 8.01 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR24482143 | Whole embryo | Whole embryo | Unfertilized egg | not recorded | SRP436676 | 21.50 |
| SRR24482145 | Whole embryo | Whole embryo | Unfertilized egg | not recorded | SRP436676 | 17.79 |
| SRR24482141 | Whole embryo | Whole embryo | 1 hpf | not recorded | SRP436676 | 17.72 |
| SRR24482142 | Whole embryo | Whole embryo | 30 mpf | not recorded | SRP436676 | 17.67 |
| SRR24482139 | Whole embryo | Whole embryo | 2 hpf | not recorded | SRP436676 | 17.56 |
| SRR24482140 | Whole embryo | Whole embryo | 2 hpf | not recorded | SRP436676 | 17.45 |
| SRR24482135 | Whole embryo | Whole embryo | 4 hpf | not recorded | SRP436676 | 17.29 |
| SRR24482138 | Whole embryo | Whole embryo | 3 hpf | not recorded | SRP436676 | 17.27 |
| SRR24482144 | Whole embryo | Whole embryo | Unfertilized egg | not recorded | SRP436676 | 16.70 |
| SRR24482137 | Whole embryo | Whole embryo | 3 hpf | not recorded | SRP436676 | 16.04 |
| SRR24482134 | Whole embryo | Whole embryo | 5 hpf | not recorded | SRP436676 | 15.86 |
| SRR24482177 | Whole embryo | Whole embryo | 1 hpf | not recorded | SRP436676 | 15.84 |
| SRR24482136 | Whole embryo | Whole embryo | 4 hpf | not recorded | SRP436676 | 15.00 |
| SRR24482157 | Whole embryo | Whole embryo | 48 hpf | not recorded | SRP436676 | 12.82 |
| SRR24482173 | Whole embryo | Whole embryo | Unfertilized egg | not recorded | SRP436676 | 12.39 |
| SRR24482174 | Whole embryo | Whole embryo | Unfertilized egg | not recorded | SRP436676 | 12.37 |
| SRR24482133 | Whole embryo | Whole embryo | 6 hpf | not recorded | SRP436676 | 12.05 |
| SRR24482156 | Whole embryo | Whole embryo | 72 hpf | not recorded | SRP436676 | 11.59 |
| SRR24482175 | Whole embryo | Whole embryo | Unfertilized egg | not recorded | SRP436676 | 10.12 |
| SRR24482160 | Whole embryo | Whole embryo | 24 hpf | not recorded | SRP436676 | 10.04 |
| SRR24482172 | Whole embryo | Whole embryo | 30 mpf | not recorded | SRP436676 | 9.97 |
| SRR24482159 | Whole embryo | Whole embryo | 24 hpf | not recorded | SRP436676 | 7.74 |
| SRR24482176 | Whole embryo | Whole embryo | 1 hpf | not recorded | SRP436676 | 6.99 |
| SRR24482158 | Whole embryo | Whole embryo | 48 hpf | not recorded | SRP436676 | 6.79 |
| SRR24482153 | Whole embryo | Whole embryo | 7 hpf | not recorded | SRP436676 | 6.36 |
| SRR24482171 | Whole embryo | Whole embryo | 1 hpf | not recorded | SRP436676 | 5.77 |
| SRR24482169 | Whole embryo | Whole embryo | 2 hpf | not recorded | SRP436676 | 3.58 |
| SRR24482170 | Whole embryo | Whole embryo | 2 hpf | not recorded | SRP436676 | 3.38 |
| SRR24482167 | Whole embryo | Whole embryo | 3 hpf | not recorded | SRP436676 | 3.25 |
| SRR24482155 | Whole embryo | Whole embryo | 72 hpf | not recorded | SRP436676 | 2.64 |
| SRR24482165 | Whole embryo | Whole embryo | 4 hpf | not recorded | SRP436676 | 2.54 |
| SRR24482168 | Whole embryo | Whole embryo | 3 hpf | not recorded | SRP436676 | 2.42 |
| SRR24482163 | Whole embryo | Whole embryo | 6 hpf | not recorded | SRP436676 | 2.09 |
| SRR24482166 | Whole embryo | Whole embryo | 4 hpf | not recorded | SRP436676 | 1.94 |
| SRR24482162 | Whole embryo | Whole embryo | 7 hpf | not recorded | SRP436676 | 1.32 |
| SRR24482161 | Whole embryo | Whole embryo | 7 hpf | not recorded | SRP436676 | 1.06 |
| SRR24482150 | Whole embryo · Triptolide 20 uM | Whole embryo | 7 hpf | Triptolide 20 uM | SRP436676 | 14.86 |
| SRR24482149 | Whole embryo · Triptolide 20 uM | Whole embryo | 7 hpf | Triptolide 20 uM | SRP436676 | 14.80 |
| SRR24482147 | Whole embryo · Triptolide 20 uM | Whole embryo | 7 hpf | Triptolide 20 uM | SRP436676 | 1.17 |
| SRR24482146 | Whole embryo · Triptolide 20 uM | Whole embryo | 7 hpf | Triptolide 20 uM | SRP436676 | 0.00 |
| SRR24482151 | Whole embryo · DMSO 0.5% | Whole embryo | 7 hpf | DMSO 0.5% | SRP436676 | 8.01 |
| SRR24482152 | Whole embryo · DMSO 0.5% | Whole embryo | 7 hpf | DMSO 0.5% | SRP436676 | 7.97 |
| SRR24482154 | Whole embryo · DMSO 0.5% | Whole embryo | 7 hpf | DMSO 0.5% | SRP436676 | 1.13 |
| SRR24482148 | Whole embryo · DMSO 0.5% | Whole embryo | 7 hpf | DMSO 0.5% | SRP436676 | 0.75 |
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 | 14 | HSymV2.0_g02.03750_t1 | 0.956956466362372 |
| Negatively correlated | 30 | HSymV2.0_g03.04812_t1 | -0.851861894321874 |
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 → |
