Genomic Location: NC_133888.1:2339371...2362359
NR annotation: XP_044164007.1, ras guanyl-releasing protein 3-like isoform X1 [Acropora millepora]
Species Acropora palmata · all data for this species · gene families
| CDS |
| XP_074629085.1 |
| Protein |
| XP_074629085.1 |
| UniProt accession | Description |
|---|---|
| Q8IV61 | Ras guanyl-releasing protein 3 OS=Homo sapiens OX=9606 GN=RASGRP3 PE=1 SV=1 |
| A4IJ06 | RAS guanyl-releasing protein 1 OS=Xenopus tropicalis OX=8364 GN=rasgrp1 PE=2 SV=1 |
| Q6NTL4 | RAS guanyl-releasing protein 1 OS=Xenopus laevis OX=8355 GN=rasgrp1 PE=2 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0002655 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF00617 all species → | RasGEF | RasGEF domain | Family | Interproscan |
| PF00618 all species → | RasGEF_N | RasGEF N-terminal motif | Domain | Interproscan |
| PF00130 all species → | C1_1 | Phorbol esters/diacylglycerol binding domain (C1 domain) | Domain | Interproscan |
| PF13499 all species → | EF-hand_7 | EF-hand domain pair | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR008937 all species → | Family | Ras-like guanine nucleotide exchange factor | Interproscan |
| IPR020454 all species → | Domain | Diacylglycerol/phorbol-ester binding | Interproscan |
| IPR002219 all species → | Domain | Protein kinase C-like, phorbol ester/diacylglycerol-binding domain | Interproscan |
| IPR001895 all species → | Domain | Ras guanine-nucleotide exchange factors catalytic domain | Interproscan |
| IPR002048 all species → | Domain | EF-hand domain | Interproscan |
| IPR000651 all species → | Domain | Ras-like guanine nucleotide exchange factor, N-terminal | Interproscan |
| IPR018247 all species → | Binding_site | EF-Hand 1, calcium-binding site | Interproscan |
| IPR011992 all species → | Homologous_superfamily | EF-hand domain pair | Interproscan |
| IPR023578 all species → | Homologous_superfamily | Ras guanine nucleotide exchange factor domain superfamily | Interproscan |
| IPR046349 all species → | Homologous_superfamily | C1-like domain superfamily | Interproscan |
| IPR036964 all species → | Homologous_superfamily | Ras guanine-nucleotide exchange factor, catalytic domain superfamily | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR23113 all species → | GUANINE NUCLEOTIDE EXCHANGE FACTOR | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0005085 all species → | Molecular Function | guanyl-nucleotide exchange factor activity | Interproscan |
| GO:0005886 all species → | Cellular Component | plasma membrane | Interproscan |
| GO:0007264 all species → | Biological Process | small GTPase-mediated signal transduction | Interproscan |
| GO:0007265 all species → | Biological Process | Ras protein signal transduction | Interproscan |
| GO:0043547 all species → | Biological Process | positive regulation of GTPase activity | Interproscan |
| GO:0005509 all species → | Molecular Function | calcium ion binding | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K12362 | RASGRP3; RAS guanyl-releasing protein 3 | - | Domain-containing proteins not elsewhere classified | ko04990 | deepkoala |
Transcript abundance of XP_074629085.1 across 84 RNA-seq samples of Acropora palmata. This gene has no row in the species' RNA-seq expression matrix, so every value below is shown as zero — the matrix simply does not cover this transcript. 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 |
|---|---|---|---|---|---|
| all_coral_tissue · exposed | 46 | 0 | 0.00 | 0.00 | |
| all_coral_tissue · baseline | 38 | 0 | 0.00 | 0.00 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR8800026 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800027 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800028 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800029 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800033 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800034 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800036 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800038 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800039 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800040 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800042 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800044 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800045 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800047 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800051 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800053 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800056 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800058 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800060 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800061 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800062 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800063 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800065 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800066 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800068 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800071 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800073 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800075 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800077 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800079 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800080 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800083 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800086 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800087 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800088 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800089 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800091 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800092 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800093 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800094 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800095 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800097 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800099 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800100 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800105 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800107 | all_coral_tissue · exposed | all_coral_tissue | not recorded | exposed | SRP189781 | 0.00 |
| SRR8800030 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800031 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800032 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800035 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800037 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800041 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800043 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800046 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800048 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800049 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800050 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800052 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800054 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800055 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800057 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800059 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800064 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800067 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800069 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800070 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800072 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800074 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800076 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800078 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800081 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800082 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800084 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800085 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800090 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800096 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800098 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800101 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800102 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800103 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800104 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800106 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800108 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
| SRR8800109 | all_coral_tissue · baseline | all_coral_tissue | not recorded | baseline | SRP189781 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (APALM_TPM,
StringTie quantification over 84 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 palmata 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 | 0 | not in this network | - |
This gene has no edge at all in the Acropora palmata network, in either direction — it is not one of the genes the network was built from (the network covers genes with enough expression variation across the transcriptome samples). The counts above are a property of the network, not a failed lookup.
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 palmata, 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 |
|---|---|
| Polyp_Underside_Control_2 | open |
| Polyp_Underside_Control_3 | open |
| Polyp_Underside_Treatment_1 | open |
| Polyp_Upperside_Control_1 | open |
| Polyp_Upperside_Treatment_3 | open |
| Polyp_Upperside_Treatment_4 | 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. | no expression matrix | – |
| 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 → |
