Genomic Location: sc0000002_pilon:3335794...3341161
NR annotation: XP_029193043.1, replication protein A 32 kDa subunit-A-like isoform X1 [Acropora millepora]
Species Acropora gemmifera · all data for this species · gene families
| CDS |
| agem_s0002.g248.t1 |
| Transcript |
| agem_s0002.g248.t1 |
| Protein |
| agem_s0002.g248.t1 |
| UniProt accession | Description |
|---|---|
| A1L2H9 | Replication protein A 32 kDa subunit-B OS=Xenopus laevis OX=8355 GN=rpa2-b PE=2 SV=1 |
| Q6DFS2 | Replication protein A 32 kDa subunit OS=Xenopus tropicalis OX=8364 GN=rpa2 PE=2 SV=1 |
| Q6IP18 | Replication protein A 32 kDa subunit-A OS=Xenopus laevis OX=8355 GN=rpa2-a PE=1 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0006367 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF08784 all species → | RPA_C | Replication protein A C terminal | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR036388 all species → | Homologous_superfamily | Winged helix-like DNA-binding domain superfamily | Interproscan |
| IPR036390 all species → | Homologous_superfamily | Winged helix DNA-binding domain superfamily | Interproscan |
| IPR012340 all species → | Homologous_superfamily | Nucleic acid-binding, OB-fold | Interproscan |
| IPR040260 all species → | Family | Replication factor A protein-like | Interproscan |
| IPR014892 all species → | Domain | Replication protein A, C-terminal | Interproscan |
| IPR014646 all species → | Family | Replication factor A protein 2 | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR13989 all species → | REPLICATION PROTEIN A-RELATED | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0000724 all species → | Biological Process | double-strand break repair via homologous recombination | Interproscan |
| GO:0000781 all species → | Cellular Component | chromosome, telomeric region | Interproscan |
| GO:0003697 all species → | Molecular Function | single-stranded DNA binding | Interproscan |
| GO:0005662 all species → | Cellular Component | DNA replication factor A complex | Interproscan |
| GO:0006260 all species → | Biological Process | DNA replication | Interproscan |
| GO:0006289 all species → | Biological Process | nucleotide-excision repair | Interproscan |
| GO:0035861 all species → | Cellular Component | site of double-strand break | Interproscan |
| GO:0003677 all species → | Molecular Function | DNA binding | Interproscan |
| GO:0005634 all species → | Cellular Component | nucleus | Interproscan |
| GO:0006281 all species → | Biological Process | DNA repair | Interproscan |
| GO:0006310 all species → | Biological Process | DNA recombination | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K10739 | RFA2, RPA2; replication factor A2 | - | DNA repair and recombination proteins | ko03400 | deepkoala |
Transcript abundance of agem_s0002.g248.t1 across 48 RNA-seq samples of Acropora gemmifera. 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 |
|---|---|---|---|---|---|
| branch tip | 48 | 14 | 109.25 | 835.63 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR3169540 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 835.63 |
| SRR3169533 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 513.43 |
| SRR3169527 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 503.09 |
| SRR3169425 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 459.85 |
| SRR3169426 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 434.19 |
| SRR3169532 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 395.88 |
| SRR3169534 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 364.42 |
| SRR3169528 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 347.42 |
| SRR3182789 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 322.59 |
| SRR3169422 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 319.99 |
| SRR3169530 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 318.01 |
| SRR3169518 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 301.36 |
| SRR3223317 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 72.06 |
| SRR3223319 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 56.25 |
| SRR2169558 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169421 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169423 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169529 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169531 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169535 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169536 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169537 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169538 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169539 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169541 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182410 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182448 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182557 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182684 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182685 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182686 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182775 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182776 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182777 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182778 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182779 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182780 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182781 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182784 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182785 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182786 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182787 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182788 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182790 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182791 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182792 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182793 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182794 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (AGEMM_TPM,
StringTie quantification over 48 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 gemmifera 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 | 7 | agem_s0134.g27.t1 | -0.447395769947727 |
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 gemmifera, 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 → |
