Genomic Location: sc0000013_pilon:2210390...2225274
NR annotation: XP_044169062.1, cleavage and polyadenylation specificity factor subunit 2-like [Acropora millepora]
Species Acropora gemmifera · all data for this species · gene families
| CDS |
| agem_s0013.g138.t1 |
| Transcript |
| agem_s0013.g138.t1 |
| Protein |
| agem_s0013.g138.t1 |
| UniProt accession | Description |
|---|---|
| Q10568 | Cleavage and polyadenylation specificity factor subunit 2 OS=Bos taurus OX=9913 GN=CPSF2 PE=1 SV=1 |
| Q9P2I0 | Cleavage and polyadenylation specificity factor subunit 2 OS=Homo sapiens OX=9606 GN=CPSF2 PE=1 SV=2 |
| O35218 | Cleavage and polyadenylation specificity factor subunit 2 OS=Mus musculus OX=10090 GN=Cpsf2 PE=1 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0004930 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF10996 all species → | Beta-Casp | Beta-Casp domain | Domain | Interproscan |
| PF07521 all species → | RMMBL | Zn-dependent metallo-hydrolase RNA specificity domain | Motif | Interproscan |
| PF13299 all species → | CPSF100_C | Cleavage and polyadenylation factor 2 C-terminal | Family | Interproscan |
| PF16661 all species → | Lactamase_B_6 | Metallo-beta-lactamase superfamily domain | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR027075 all species → | Family | Cleavage and polyadenylation specificity factor subunit 2 | Interproscan |
| IPR022712 all species → | Domain | Beta-Casp domain | Interproscan |
| IPR036866 all species → | Homologous_superfamily | Ribonuclease Z/Hydroxyacylglutathione hydrolase-like | Interproscan |
| IPR011108 all species → | Domain | Zn-dependent metallo-hydrolase, RNA specificity domain | Interproscan |
| IPR025069 all species → | Domain | Cleavage and polyadenylation specificity factor 2, C-terminal | Interproscan |
| IPR035639 all species → | Domain | CPSF2, metallo-hydrolase domain | Interproscan |
| IPR001279 all species → | Domain | Metallo-beta-lactamase | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR45922 all species → | CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 2 | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0003723 all species → | Molecular Function | RNA binding | Interproscan |
| GO:0005847 all species → | Cellular Component | mRNA cleavage and polyadenylation specificity factor complex | Interproscan |
| GO:0006378 all species → | Biological Process | obsolete mRNA polyadenylation | Interproscan |
| GO:0006398 all species → | Biological Process | mRNA 3'-end processing by stem-loop binding and cleavage | Interproscan |
| GO:0098789 all species → | Biological Process | obsolete pre-mRNA cleavage required for polyadenylation | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K14402 | CPSF2, CFT2; cleavage and polyadenylation specificity factor subunit 2 | - | Messenger RNA biogenesis | ko03019 | deepkoala |
Transcript abundance of agem_s0013.g138.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 | 2 | 0.97 | 24.76 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR3223317 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 24.76 |
| SRR3223319 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 21.81 |
| SRR2169558 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169421 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169422 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169423 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169425 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169426 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169518 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169527 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169528 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169529 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169530 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169531 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169532 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169533 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169534 | 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 |
| SRR3169540 | 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 |
| SRR3182789 | 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 | 10 | agem_s0017.g79.t1 | 0.999999998839232 |
| Negatively correlated | 3 | agem_s0028.g73.t1 | -0.501876976576865 |
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 → |
