Genomic Location: sc0000211_pilon:473405...504981
NR annotation: XP_044177134.1, LOW QUALITY PROTEIN: sister chromatid cohesion protein PDS5 homolog B-like [Acropora millepora]
Species Acropora selago · all data for this species · gene families
| CDS |
| asel_s0211.g39.t1 |
| Transcript |
| asel_s0211.g39.t1 |
| Protein |
| asel_s0211.g39.t1 |
| UniProt accession | Description |
|---|---|
| Q498H0 | Sister chromatid cohesion protein PDS5 homolog B-A OS=Xenopus laevis OX=8355 GN=pds5b-a PE=1 SV=1 |
| Q5F3U9 | Sister chromatid cohesion protein PDS5 homolog B OS=Gallus gallus OX=9031 GN=PDS5B PE=2 SV=3 |
| Q4VA53 | Sister chromatid cohesion protein PDS5 homolog B OS=Mus musculus OX=10090 GN=Pds5b PE=1 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0003692 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF20168 all species → | PDS5 | Sister chromatid cohesion protein PDS5 protein | Repeat | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR016024 all species → | Homologous_superfamily | Armadillo-type fold | Interproscan |
| IPR011989 all species → | Homologous_superfamily | Armadillo-like helical | Interproscan |
| IPR039776 all species → | Family | Sister chromatid cohesion protein Pds5 | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR12663 all species → | ANDROGEN INDUCED INHIBITOR OF PROLIFERATION AS3 / PDS5-RELATED | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0000785 all species → | Cellular Component | chromatin | Interproscan |
| GO:0005634 all species → | Cellular Component | nucleus | Interproscan |
| GO:0006281 all species → | Biological Process | DNA repair | Interproscan |
| GO:0007064 all species → | Biological Process | mitotic sister chromatid cohesion | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K11267 | PDS5; sister chromatid cohesion protein PDS5 | - | Chromosome and associated proteins | ko03036 | deepkoala |
Transcript abundance of asel_s0211.g39.t1 across 24 RNA-seq samples of Acropora selago. 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 |
|---|---|---|---|---|---|
| coral larvae | 24 | 21 | 3.28 | 6.31 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR14308024 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 6.31 |
| SRR14308011 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 5.85 |
| SRR14308007 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 4.92 |
| SRR14308012 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 4.55 |
| SRR14308027 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 4.24 |
| SRR14308013 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 3.98 |
| SRR14308015 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 3.97 |
| SRR14308022 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 3.93 |
| SRR14308004 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 3.86 |
| SRR14308014 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 3.80 |
| SRR14308019 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 3.70 |
| SRR14308010 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 3.57 |
| SRR14308006 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 3.36 |
| SRR14308021 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 3.27 |
| SRR14308017 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 3.27 |
| SRR14308008 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 2.97 |
| SRR14308016 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 2.89 |
| SRR14308026 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 2.81 |
| SRR14308025 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 2.53 |
| SRR14308023 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 2.47 |
| SRR14308020 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 2.38 |
| SRR14308005 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 0.00 |
| SRR14308009 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 0.00 |
| SRR14308018 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (ASELA_TPM,
StringTie quantification over 24 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 Acropora selago 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 | 29 | asel_s0209.g19.t1 | 0.943012562042104 |
| Negatively correlated | 4 | asel_s2176.g1.t1 | -0.804362616117406 |
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 Acropora selago, 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.
| Sample | Methylation profile |
|---|---|
| Coral_Fragment_Parent | open |
| Larval_Pool_Offspring | open |
The DNA Methylation page locates this gene by scanning the bisulphite table, which holds one row per cytosine. For the largest datasets that scan takes a while to return; it does not mean the link is broken.
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 → |
