Genomic Location: not available for this species
NR annotation: CAB3977840.1, Breast cancer type 2 susceptibility [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families
CAB3977840.1 in PCLAV (the gene ID may belong to a different isoform naming scheme). Try the gene search.| UniProt accession | Description |
|---|---|
| P51587 | Breast cancer type 2 susceptibility protein OS=Homo sapiens OX=9606 GN=BRCA2 PE=1 SV=4 |
| P97929 | Breast cancer type 2 susceptibility protein homolog OS=Mus musculus OX=10090 GN=Brca2 PE=1 SV=2 |
| O35923 | Breast cancer type 2 susceptibility protein homolog OS=Rattus norvegicus OX=10116 GN=Brca2 PE=1 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0002608 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF09169 all species → | BRCA-2_helical | BRCA2, helical | Domain | Interproscan |
| PF09121 all species → | Tower | Tower | Domain | Interproscan |
| PF09104 all species → | BRCA-2_OB3 | BRCA2, oligonucleotide/oligosaccharide-binding, domain 3 | Domain | Interproscan |
| PF21318 all species → | BRCA2DBD_OB2 | BRCA2, OB2 | Domain | Interproscan |
| PF00634 all species → | BRCA2 | BRCA2 repeat | Family | Interproscan |
| PF09103 all species → | BRCA-2_OB1 | BRCA2, oligonucleotide/oligosaccharide-binding, domain 1 | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR002093 all species → | Repeat | BRCA2 repeat | Interproscan |
| IPR015252 all species → | Domain | Breast cancer type 2 susceptibility protein, helical domain | Interproscan |
| IPR012340 all species → | Homologous_superfamily | Nucleic acid-binding, OB-fold | Interproscan |
| IPR015205 all species → | Domain | Tower domain | Interproscan |
| IPR015188 all species → | Domain | BRCA2, OB3 | Interproscan |
| IPR015187 all species → | Domain | BRCA2, OB1 | Interproscan |
| IPR036315 all species → | Homologous_superfamily | BRCA2 helical domain superfamily | Interproscan |
| IPR015525 all species → | Family | Breast cancer type 2 susceptibility protein | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR11289 all species → | BREAST CANCER TYPE 2 SUSCEPTIBILITY PROTEIN BRCA2 | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0000724 all species → | Biological Process | double-strand break repair via homologous recombination | Interproscan |
| GO:0005634 all species → | Cellular Component | nucleus | Interproscan |
| GO:0006281 all species → | Biological Process | DNA repair | Interproscan |
| GO:0006355 all species → | Biological Process | regulation of DNA-templated transcription | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K08775 | BRCA2, FANCD1; breast cancer 2 susceptibility protein | - | DNA repair and recombination proteins | ko03400 | deepkoala |
Transcript abundance of CAB3977840.1 across 21 RNA-seq samples of Paramuricea clavata. 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 | 5 | 0.76 | 1.86 | |
| apical branchlet · Temperature treatment at T0 | 6 | 6 | 0.94 | 2.46 | |
| apical branchlet · Temperature treatment at T25 | 5 | 5 | 2.32 | 7.22 | |
| apical branchlet · Control at T0 | 4 | 3 | 1.00 | 2.41 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR19977439 | apical branchlet · Control at T25 | apical branchlet | not recorded | Control at T25 | SRP384900 | 1.86 |
| SRR19977455 | apical branchlet · Control at T25 | apical branchlet | not recorded | Control at T25 | SRP384900 | 1.21 |
| SRR19977440 | apical branchlet · Control at T25 | apical branchlet | not recorded | Control at T25 | SRP384900 | 0.55 |
| SRR19977444 | apical branchlet · Control at T25 | apical branchlet | not recorded | Control at T25 | SRP384900 | 0.53 |
| SRR19977441 | apical branchlet · Control at T25 | apical branchlet | not recorded | Control at T25 | SRP384900 | 0.41 |
| SRR19977433 | apical branchlet · Control at T25 | apical branchlet | not recorded | Control at T25 | SRP384900 | 0.00 |
| SRR19977436 | apical branchlet · Temperature treatment at T0 | apical branchlet | not recorded | Temperature treatment at T0 | SRP384900 | 2.46 |
| SRR19977428 | apical branchlet · Temperature treatment at T0 | apical branchlet | not recorded | Temperature treatment at T0 | SRP384900 | 1.53 |
| SRR19977437 | apical branchlet · Temperature treatment at T0 | apical branchlet | not recorded | Temperature treatment at T0 | SRP384900 | 0.63 |
| SRR19977438 | apical branchlet · Temperature treatment at T0 | apical branchlet | not recorded | Temperature treatment at T0 | SRP384900 | 0.45 |
| SRR19977426 | apical branchlet · Temperature treatment at T0 | apical branchlet | not recorded | Temperature treatment at T0 | SRP384900 | 0.38 |
| SRR19977427 | apical branchlet · Temperature treatment at T0 | apical branchlet | not recorded | Temperature treatment at T0 | SRP384900 | 0.16 |
| SRR19977463 | apical branchlet · Temperature treatment at T25 | apical branchlet | not recorded | Temperature treatment at T25 | SRP384900 | 7.22 |
| SRR19977432 | apical branchlet · Temperature treatment at T25 | apical branchlet | not recorded | Temperature treatment at T25 | SRP384900 | 1.69 |
| SRR19977434 | apical branchlet · Temperature treatment at T25 | apical branchlet | not recorded | Temperature treatment at T25 | SRP384900 | 1.61 |
| SRR19977435 | apical branchlet · Temperature treatment at T25 | apical branchlet | not recorded | Temperature treatment at T25 | SRP384900 | 0.66 |
| SRR19977425 | apical branchlet · Temperature treatment at T25 | apical branchlet | not recorded | Temperature treatment at T25 | SRP384900 | 0.43 |
| SRR19977445 | apical branchlet · Control at T0 | apical branchlet | not recorded | Control at T0 | SRP384900 | 2.41 |
| SRR19977442 | apical branchlet · Control at T0 | apical branchlet | not recorded | Control at T0 | SRP384900 | 1.23 |
| SRR19977443 | apical branchlet · Control at T0 | apical branchlet | not recorded | Control at T0 | SRP384900 | 0.38 |
| 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 | 6 | CAB4033912.1 | 0.903829038700359 |
| Negatively correlated | 18 | CAB3993085.1 | -0.531364954889579 |
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. | 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 → |
