Genomic Location: chr3:5851814...5866228
NR annotation: XP_002161072.1, guanine nucleotide exchange factor for Rab-3A-like [Hydra vulgaris]
Species Aurelia coerulea · all data for this species · gene families
| CDS |
| evm.model.ptg000006l.317 |
| Transcript |
| evm.model.ptg000006l.317 |
| Protein |
| evm.model.ptg000006l.317 |
| UniProt accession | Description |
|---|---|
| Q62739 | Rab-3A-interacting protein OS=Rattus norvegicus OX=10116 GN=Rab3ip PE=1 SV=2 |
| Q8TBN0 | Guanine nucleotide exchange factor for Rab-3A OS=Homo sapiens OX=9606 GN=RAB3IL1 PE=1 SV=1 |
| Q96QF0 | Rab-3A-interacting protein OS=Homo sapiens OX=9606 GN=RAB3IP PE=1 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0006191 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF06428 all species → | Sec2p | GDP/GTP exchange factor Sec2p | Coiled-coil | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR040351 all species → | Family | Guanine nucleotide exchange factor RAB3IL/RAB3IP/Sec2 | Interproscan |
| IPR009449 all species → | Domain | GDP/GTP exchange factor Sec2, N-terminal | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR14430 all species → | RABIN3-RELATED | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0005085 all species → | Molecular Function | guanyl-nucleotide exchange factor activity | Interproscan |
| GO:0006887 all species → | Biological Process | exocytosis | Interproscan |
| GO:0070319 all species → | Cellular Component | Golgi to plasma membrane transport vesicle | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K16779 | RAB3IP, RABIN8; Rab-3A-interacting protein | - | Chromosome and associated proteins | ko03036 | deepkoala |
Transcript abundance of evm.model.ptg000006l.317 across 30 RNA-seq samples of Aurelia coerulea. 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.
Every sample in this dataset carries its own condition — the source metadata gives each run a distinct treatment label — so this table is effectively a sample list. The per-sample chart below is the informative view here.
| Condition | Samples | TPM > 0 | Mean TPM | Max TPM | Mean, relative to max |
|---|---|---|---|---|---|
| whole organism · T_A1ES | 1 | 1 | 1.16 | 1.16 | |
| whole organism · T_C3E | 1 | 1 | 3.04 | 3.04 | |
| whole organism · T_C2P | 1 | 1 | 1.36 | 1.36 | |
| whole organism · T_A2ES | 1 | 1 | 3.81 | 3.81 | |
| whole organism · T_A3ES | 1 | 1 | 4.10 | 4.10 | |
| whole organism · T_C1AS | 1 | 1 | 1.85 | 1.85 | |
| whole organism · T_C2AS | 1 | 1 | 2.61 | 2.61 | |
| whole organism · T_C3AS | 1 | 1 | 2.11 | 2.11 | |
| whole organism · T_A1AS | 1 | 1 | 6.98 | 6.98 | |
| whole organism · T_A2AS | 1 | 1 | 3.91 | 3.91 | |
| whole organism · T_A3AS | 1 | 1 | 5.22 | 5.22 | |
| whole organism · T_C1E | 1 | 1 | 4.08 | 4.08 | |
| whole organism · T_C2E | 1 | 1 | 2.75 | 2.75 | |
| whole organism · T_C3P | 1 | 1 | 0.93 | 0.93 | |
| whole organism · T_AE1 | 1 | 1 | 6.66 | 6.66 | |
| whole organism · T_C3ES | 1 | 1 | 1.90 | 1.90 | |
| whole organism · T_AE2 | 1 | 1 | 7.35 | 7.35 | |
| whole organism · T_AE3 | 1 | 1 | 9.63 | 9.63 | |
| whole organism · T_AES1 | 1 | 1 | 11.15 | 11.15 | |
| whole organism · T_AES2 | 1 | 1 | 11.51 | 11.51 | |
| whole organism · T_AES3 | 1 | 1 | 5.97 | 5.97 | |
| whole organism · T_AAS1 | 1 | 1 | 6.88 | 6.88 | |
| whole organism · T_AAS2 | 1 | 1 | 4.72 | 4.72 | |
| whole organism · T_AAS3 | 1 | 1 | 3.13 | 3.13 | |
| whole organism · T_A1P | 1 | 1 | 1.01 | 1.01 | |
| whole organism · T_A2P | 1 | 1 | 1.17 | 1.17 | |
| whole organism · T_A3P | 1 | 1 | 0.34 | 0.34 | |
| whole organism · T_C1ES | 1 | 1 | 3.70 | 3.70 | |
| whole organism · T_C2ES | 1 | 1 | 2.31 | 2.31 | |
| whole organism · T_C1P | 1 | 1 | 0.52 | 0.52 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR25982246 | whole organism · T_A1ES | whole organism | not recorded | T_A1ES | SRP459341 | 1.16 |
| SRR25982262 | whole organism · T_C3E | whole organism | not recorded | T_C3E | SRP459341 | 3.04 |
| SRR25982274 | whole organism · T_C2P | whole organism | not recorded | T_C2P | SRP459341 | 1.36 |
| SRR25982273 | whole organism · T_A2ES | whole organism | not recorded | T_A2ES | SRP459341 | 3.81 |
| SRR25982272 | whole organism · T_A3ES | whole organism | not recorded | T_A3ES | SRP459341 | 4.10 |
| SRR25982271 | whole organism · T_C1AS | whole organism | not recorded | T_C1AS | SRP459341 | 1.85 |
| SRR25982270 | whole organism · T_C2AS | whole organism | not recorded | T_C2AS | SRP459341 | 2.61 |
| SRR25982269 | whole organism · T_C3AS | whole organism | not recorded | T_C3AS | SRP459341 | 2.11 |
| SRR25982268 | whole organism · T_A1AS | whole organism | not recorded | T_A1AS | SRP459341 | 6.98 |
| SRR25982267 | whole organism · T_A2AS | whole organism | not recorded | T_A2AS | SRP459341 | 3.91 |
| SRR25982266 | whole organism · T_A3AS | whole organism | not recorded | T_A3AS | SRP459341 | 5.22 |
| SRR25982265 | whole organism · T_C1E | whole organism | not recorded | T_C1E | SRP459341 | 4.08 |
| SRR25982264 | whole organism · T_C2E | whole organism | not recorded | T_C2E | SRP459341 | 2.75 |
| SRR25982263 | whole organism · T_C3P | whole organism | not recorded | T_C3P | SRP459341 | 0.93 |
| SRR25982261 | whole organism · T_AE1 | whole organism | not recorded | T_AE1 | SRP459341 | 6.66 |
| SRR25982247 | whole organism · T_C3ES | whole organism | not recorded | T_C3ES | SRP459341 | 1.90 |
| SRR25982260 | whole organism · T_AE2 | whole organism | not recorded | T_AE2 | SRP459341 | 7.35 |
| SRR25982259 | whole organism · T_AE3 | whole organism | not recorded | T_AE3 | SRP459341 | 9.63 |
| SRR25982258 | whole organism · T_AES1 | whole organism | not recorded | T_AES1 | SRP459341 | 11.15 |
| SRR25982257 | whole organism · T_AES2 | whole organism | not recorded | T_AES2 | SRP459341 | 11.51 |
| SRR25982256 | whole organism · T_AES3 | whole organism | not recorded | T_AES3 | SRP459341 | 5.97 |
| SRR25982255 | whole organism · T_AAS1 | whole organism | not recorded | T_AAS1 | SRP459341 | 6.88 |
| SRR25982254 | whole organism · T_AAS2 | whole organism | not recorded | T_AAS2 | SRP459341 | 4.72 |
| SRR25982253 | whole organism · T_AAS3 | whole organism | not recorded | T_AAS3 | SRP459341 | 3.13 |
| SRR25982252 | whole organism · T_A1P | whole organism | not recorded | T_A1P | SRP459341 | 1.01 |
| SRR25982251 | whole organism · T_A2P | whole organism | not recorded | T_A2P | SRP459341 | 1.17 |
| SRR25982250 | whole organism · T_A3P | whole organism | not recorded | T_A3P | SRP459341 | 0.34 |
| SRR25982249 | whole organism · T_C1ES | whole organism | not recorded | T_C1ES | SRP459341 | 3.70 |
| SRR25982248 | whole organism · T_C2ES | whole organism | not recorded | T_C2ES | SRP459341 | 2.31 |
| SRR25982275 | whole organism · T_C1P | whole organism | not recorded | T_C1P | SRP459341 | 0.52 |
Source: CnidoSite RNA-seq expression matrices (ACOER_TPM,
StringTie quantification over 30 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 Aurelia coerulea 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 | 11 | evm.model.ptg000010l.108 | 0.956955495731254 |
| Negatively correlated | 4 | evm.model.ptg000031l.354 | -0.817622508363001 |
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 Aurelia coerulea, 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 → |
