Genomic Location: sc0000014_pilon:2026834...2041468
NR annotation: XP_044179195.1, rab5 GDP/GTP exchange factor-like isoform X1 [Acropora millepora]
Species Acropora gemmifera · all data for this species · gene families
| CDS |
| agem_s0014.g118.t1 |
| Transcript |
| agem_s0014.g118.t1 |
| Protein |
| agem_s0014.g118.t1 |
| UniProt accession | Description |
|---|---|
| Q9JM13 | Rab5 GDP/GTP exchange factor OS=Mus musculus OX=10090 GN=Rabgef1 PE=1 SV=1 |
| Q9UJ41 | Rab5 GDP/GTP exchange factor OS=Homo sapiens OX=9606 GN=RABGEF1 PE=1 SV=3 |
| O18973 | Rab5 GDP/GTP exchange factor OS=Bos taurus OX=9913 GN=RABGEF1 PE=1 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0004081 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF02204 all species → | VPS9 | Vacuolar sorting protein 9 (VPS9) domain | Family | Interproscan |
| PF01754 all species → | zf-A20 | A20-like zinc finger | Family | Interproscan |
| PF18151 all species → | DUF5601 | Domain of unknown function (DUF5601) | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR002653 all species → | Domain | Zinc finger, A20-type | Interproscan |
| IPR003123 all species → | Domain | VPS9 domain | Interproscan |
| IPR045046 all species → | Family | Vacuolar protein sorting-associated protein 9-like | Interproscan |
| IPR037191 all species → | Homologous_superfamily | VPS9 domain superfamily | Interproscan |
| IPR041545 all species → | Domain | RABX5, catalytic core helical domain | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR23101 all species → | RAB GDP/GTP EXCHANGE FACTOR | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0003677 all species → | Molecular Function | DNA binding | Interproscan |
| GO:0008270 all species → | Molecular Function | zinc ion binding | Interproscan |
| GO:0005085 all species → | Molecular Function | guanyl-nucleotide exchange factor activity | Interproscan |
| GO:0005829 all species → | Cellular Component | cytosol | Interproscan |
| GO:0016192 all species → | Biological Process | vesicle-mediated transport | Interproscan |
| GO:0030139 all species → | Cellular Component | endocytic vesicle | Interproscan |
| GO:0031267 all species → | Molecular Function | small GTPase binding | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K20131 | RABGEF1; Rab5 GDP/GTP exchange factor | - | Membrane trafficking | ko04131 | deepkoala |
Transcript abundance of agem_s0014.g118.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 | 3 | 2.95 | 60.60 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR2169558 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 60.60 |
| SRR3223317 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 45.51 |
| SRR3223319 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 35.33 |
| 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 | 9 | agem_s0050.g82.t1 | 0.999998827871235 |
| Negatively correlated | 3 | agem_s0028.g73.t1 | -0.604263287990511 |
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 → |
