Genomic Location: not available for this species
NR annotation: CAB3981958.1, collagen alpha-1(IV) chain [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families
CAB3981958.1 in PCLAV (the gene ID may belong to a different isoform naming scheme). Try the gene search.| UniProt accession | Description |
|---|---|
| P27393 | Collagen alpha-2(IV) chain OS=Ascaris suum OX=6253 PE=2 SV=1 |
| P29400 | Collagen alpha-5(IV) chain OS=Homo sapiens OX=9606 GN=COL4A5 PE=1 SV=2 |
| Q28247 | Collagen alpha-5(IV) chain OS=Canis lupus familiaris OX=9615 GN=COL4A5 PE=2 SV=2 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0001701 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF01413 all species → | C4 | C-terminal tandem repeated domain in type 4 procollagen | Domain | Interproscan |
| PF01391 all species → | Collagen | Collagen triple helix repeat (20 copies) | Repeat | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR050149 all species → | Family | Collagen superfamily | Interproscan |
| IPR036954 all species → | Homologous_superfamily | Collagen IV, non-collagenous domain superfamily | Interproscan |
| IPR016187 all species → | Homologous_superfamily | C-type lectin fold | Interproscan |
| IPR001442 all species → | Domain | Collagen IV, non-collagenous | Interproscan |
| IPR008160 all species → | Repeat | Collagen triple helix repeat | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR24023 all species → | COLLAGEN ALPHA | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0005615 all species → | Cellular Component | extracellular space | Interproscan |
| GO:0030020 all species → | Molecular Function | extracellular matrix structural constituent conferring tensile strength | Interproscan |
| GO:0030198 all species → | Biological Process | extracellular matrix organization | Interproscan |
| GO:0031012 all species → | Cellular Component | extracellular matrix | Interproscan |
| GO:0062023 all species → | Cellular Component | collagen-containing extracellular matrix | Interproscan |
| GO:0005201 all species → | Molecular Function | extracellular matrix structural constituent | Interproscan |
| GO:0005581 all species → | Cellular Component | collagen trimer | Interproscan |
CAB3981958.1.Transcript abundance of CAB3981958.1 across 21 RNA-seq samples of Paramuricea clavata. 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 |
|---|---|---|---|---|---|
| apical branchlet · Control at T25 | 6 | 0 | 0.00 | 0.00 | |
| apical branchlet · Temperature treatment at T0 | 6 | 0 | 0.00 | 0.00 | |
| apical branchlet · Temperature treatment at T25 | 5 | 0 | 0.00 | 0.00 | |
| apical branchlet · Control at T0 | 4 | 0 | 0.00 | 0.00 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR19977433 | apical branchlet · Control at T25 | apical branchlet | not recorded | Control at T25 | SRP384900 | 0.00 |
| SRR19977439 | apical branchlet · Control at T25 | apical branchlet | not recorded | Control at T25 | SRP384900 | 0.00 |
| SRR19977440 | apical branchlet · Control at T25 | apical branchlet | not recorded | Control at T25 | SRP384900 | 0.00 |
| SRR19977441 | apical branchlet · Control at T25 | apical branchlet | not recorded | Control at T25 | SRP384900 | 0.00 |
| SRR19977444 | apical branchlet · Control at T25 | apical branchlet | not recorded | Control at T25 | SRP384900 | 0.00 |
| SRR19977455 | apical branchlet · Control at T25 | apical branchlet | not recorded | Control at T25 | SRP384900 | 0.00 |
| SRR19977426 | apical branchlet · Temperature treatment at T0 | apical branchlet | not recorded | Temperature treatment at T0 | SRP384900 | 0.00 |
| SRR19977427 | apical branchlet · Temperature treatment at T0 | apical branchlet | not recorded | Temperature treatment at T0 | SRP384900 | 0.00 |
| SRR19977428 | apical branchlet · Temperature treatment at T0 | apical branchlet | not recorded | Temperature treatment at T0 | SRP384900 | 0.00 |
| SRR19977436 | apical branchlet · Temperature treatment at T0 | apical branchlet | not recorded | Temperature treatment at T0 | SRP384900 | 0.00 |
| SRR19977437 | apical branchlet · Temperature treatment at T0 | apical branchlet | not recorded | Temperature treatment at T0 | SRP384900 | 0.00 |
| SRR19977438 | apical branchlet · Temperature treatment at T0 | apical branchlet | not recorded | Temperature treatment at T0 | SRP384900 | 0.00 |
| SRR19977425 | apical branchlet · Temperature treatment at T25 | apical branchlet | not recorded | Temperature treatment at T25 | SRP384900 | 0.00 |
| SRR19977432 | apical branchlet · Temperature treatment at T25 | apical branchlet | not recorded | Temperature treatment at T25 | SRP384900 | 0.00 |
| SRR19977434 | apical branchlet · Temperature treatment at T25 | apical branchlet | not recorded | Temperature treatment at T25 | SRP384900 | 0.00 |
| SRR19977435 | apical branchlet · Temperature treatment at T25 | apical branchlet | not recorded | Temperature treatment at T25 | SRP384900 | 0.00 |
| SRR19977463 | apical branchlet · Temperature treatment at T25 | apical branchlet | not recorded | Temperature treatment at T25 | SRP384900 | 0.00 |
| SRR19977442 | apical branchlet · Control at T0 | apical branchlet | not recorded | Control at T0 | SRP384900 | 0.00 |
| SRR19977443 | apical branchlet · Control at T0 | apical branchlet | not recorded | Control at T0 | SRP384900 | 0.00 |
| SRR19977445 | apical branchlet · Control at T0 | apical branchlet | not recorded | Control at T0 | SRP384900 | 0.00 |
| SRR19977446 | apical branchlet · Control at T0 | apical branchlet | not recorded | Control at T0 | SRP384900 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (PCLAV_TPM,
StringTie quantification over 21 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 Paramuricea clavata 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 Paramuricea clavata 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 Paramuricea clavata, 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. | not in the sequence table | 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. | not in the sequence table | 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 → |
