Genomic Location: not available for this species
NR annotation: CAB4003139.1, homeobox Hox-A5-like [Paramuricea clavata]
Species Paramuricea clavata · all data for this species · gene families
CAB4003139.1 in PCLAV (the gene ID may belong to a different isoform naming scheme). Try the gene search.| UniProt accession | Description |
|---|---|
| P15860 | Homeobox protein H90 (Fragment) OS=Apis mellifera OX=7460 PE=3 SV=1 |
| Q28600 | Homeobox protein Hox-A7 (Fragment) OS=Ovis aries OX=9940 GN=HOXA7 PE=2 SV=1 |
| P14839 | Homeobox protein Hox-B6 (Fragment) OS=Gallus gallus OX=9031 GN=HOXB6 PE=3 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0000051 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF00046 all species → | Homeodomain | Homeodomain | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR020479 all species → | Domain | Homeobox domain, metazoa | Interproscan |
| IPR001356 all species → | Domain | Homeobox domain | Interproscan |
| IPR009057 all species → | Homologous_superfamily | Homeobox-like domain superfamily | Interproscan |
| IPR046333 all species → | Family | Homeobox protein Hox-A10/abdominal-B-like | Interproscan |
| IPR017970 all species → | Conserved_site | Homeobox, conserved site | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR45874 all species → | HOMEOBOX PROTEIN ABDOMINAL-B | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0003677 all species → | Molecular Function | DNA binding | Interproscan |
| GO:0000978 all species → | Molecular Function | RNA polymerase II cis-regulatory region sequence-specific DNA binding | Interproscan |
| GO:0000981 all species → | Molecular Function | DNA-binding transcription factor activity, RNA polymerase II-specific | Interproscan |
| GO:0005634 all species → | Cellular Component | nucleus | Interproscan |
| GO:0006357 all species → | Biological Process | regulation of transcription by RNA polymerase II | Interproscan |
| GO:0006355 all species → | Biological Process | regulation of DNA-templated transcription | Interproscan |
CAB4003139.1.Transcript abundance of CAB4003139.1 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 | 4 | 10.18 | 19.41 | |
| apical branchlet · Temperature treatment at T0 | 6 | 3 | 6.66 | 19.60 | |
| apical branchlet · Temperature treatment at T25 | 5 | 1 | 1.15 | 5.73 | |
| apical branchlet · Control at T0 | 4 | 1 | 3.80 | 15.19 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR19977455 | apical branchlet · Control at T25 | apical branchlet | not recorded | Control at T25 | SRP384900 | 19.41 |
| SRR19977441 | apical branchlet · Control at T25 | apical branchlet | not recorded | Control at T25 | SRP384900 | 17.40 |
| SRR19977444 | apical branchlet · Control at T25 | apical branchlet | not recorded | Control at T25 | SRP384900 | 15.71 |
| SRR19977440 | apical branchlet · Control at T25 | apical branchlet | not recorded | Control at T25 | SRP384900 | 8.58 |
| 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 |
| SRR19977428 | apical branchlet · Temperature treatment at T0 | apical branchlet | not recorded | Temperature treatment at T0 | SRP384900 | 19.60 |
| SRR19977427 | apical branchlet · Temperature treatment at T0 | apical branchlet | not recorded | Temperature treatment at T0 | SRP384900 | 15.65 |
| SRR19977438 | apical branchlet · Temperature treatment at T0 | apical branchlet | not recorded | Temperature treatment at T0 | SRP384900 | 4.71 |
| SRR19977426 | 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 |
| SRR19977435 | apical branchlet · Temperature treatment at T25 | apical branchlet | not recorded | Temperature treatment at T25 | SRP384900 | 5.73 |
| 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 |
| SRR19977463 | apical branchlet · Temperature treatment at T25 | apical branchlet | not recorded | Temperature treatment at T25 | SRP384900 | 0.00 |
| SRR19977443 | apical branchlet · Control at T0 | apical branchlet | not recorded | Control at T0 | SRP384900 | 15.19 |
| SRR19977442 | 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 | 26 | CAB3979462.1 | 0.969074303991185 |
| Negatively correlated | 3 | CAB3979839.1 | -0.720824564030091 |
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 → |
