Genomic Location: NC_064038.1:1048578...1051355
NR annotation: XP_001623735.2, repulsive guidance molecule B [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families
| CDS |
| LOC5502564 |
| Transcript |
| rna-XM_001623685.3 |
| Protein |
| XP_001623735.2 |
| UniProt accession | Description |
|---|---|
| Q6NW40 | Repulsive guidance molecule B OS=Homo sapiens OX=9606 GN=RGMB PE=1 SV=3 |
| Q7TQ33 | Repulsive guidance molecule B OS=Mus musculus OX=10090 GN=Rgmb PE=1 SV=1 |
| Q9N0A6 | Repulsive guidance molecule A OS=Macaca fascicularis OX=9541 GN=RGMA PE=2 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0008115 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF06534 all species → | RGM_C | Repulsive guidance molecule (RGM) C-terminus | Family | Interproscan |
| PF06535 all species → | RGM_N | Repulsive guidance molecule (RGM) N-terminus | Family | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR009496 all species → | Domain | Repulsive guidance molecule, C-terminal | Interproscan |
| IPR040287 all species → | Family | Repulsive guidance molecule | Interproscan |
| IPR010536 all species → | Domain | Repulsive guidance molecule, N-terminal | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR31428 all species → | RGM DOMAIN FAMILY MEMBER DRAG-1 | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0005886 all species → | Cellular Component | plasma membrane | Interproscan |
| GO:0015026 all species → | Molecular Function | coreceptor activity | Interproscan |
| GO:0030509 all species → | Biological Process | BMP signaling pathway | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K23096 | RGMA; repulsive guidance molecule A | - | Axon guidance | ko04360 | deepkoala |
Transcript abundance of XP_001623735.2 across 48 RNA-seq samples of Nematostella vectensis. 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 |
|---|---|---|---|---|---|
| whole 6 week old aboral regenerate · regenerate 96hpa | 3 | 3 | 51.26 | 63.44 | |
| whole 6 week old aboral regenerate · regenerate 144hpa | 3 | 3 | 50.80 | 62.38 | |
| whole 6 week old aboral regenerate · regenerate 0hpa | 3 | 3 | 28.75 | 32.42 | |
| whole 6 week old aboral regenerate · regenerate 2hpa | 3 | 3 | 24.26 | 26.76 | |
| whole 6 week old aboral regenerate · regenerate uncut | 3 | 3 | 65.90 | 75.01 | |
| whole 6 week old aboral regenerate · regenerate 4hpa | 3 | 2 | 16.53 | 27.83 | |
| whole 6 week old aboral regenerate · regenerate 120hpa | 3 | 3 | 58.39 | 59.06 | |
| whole 6 week old aboral regenerate · regenerate 36hpa | 3 | 3 | 33.71 | 39.04 | |
| whole 6 week old aboral regenerate · regenerate 24hpa | 3 | 3 | 35.88 | 38.13 | |
| whole 6 week old aboral regenerate · regenerate 20hpa | 3 | 3 | 33.33 | 38.80 | |
| whole 6 week old aboral regenerate · regenerate 16hpa | 3 | 3 | 29.51 | 34.64 | |
| whole 6 week old aboral regenerate · regenerate 72hpa | 3 | 3 | 45.95 | 55.76 | |
| whole 6 week old aboral regenerate · regenerate 60hpa | 3 | 3 | 36.09 | 40.81 | |
| whole 6 week old aboral regenerate · regenerate 48hpa | 3 | 3 | 32.41 | 39.18 | |
| whole 6 week old aboral regenerate · regenerate 8hpa | 3 | 3 | 25.34 | 28.85 | |
| whole 6 week old aboral regenerate · regenerate 12hpa | 3 | 2 | 19.42 | 32.05 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR6320863 | whole 6 week old aboral regenerate · regenerate 96hpa | whole 6 week old aboral regenerate | six weeks | regenerate 96hpa | SRP125570 | 63.44 |
| SRR6320836 | whole 6 week old aboral regenerate · regenerate 96hpa | whole 6 week old aboral regenerate | six weeks | regenerate 96hpa | SRP125570 | 49.65 |
| SRR6320837 | whole 6 week old aboral regenerate · regenerate 96hpa | whole 6 week old aboral regenerate | six weeks | regenerate 96hpa | SRP125570 | 40.70 |
| SRR6320847 | whole 6 week old aboral regenerate · regenerate 144hpa | whole 6 week old aboral regenerate | six weeks | regenerate 144hpa | SRP125570 | 62.38 |
| SRR6320838 | whole 6 week old aboral regenerate · regenerate 144hpa | whole 6 week old aboral regenerate | six weeks | regenerate 144hpa | SRP125570 | 45.87 |
| SRR6320841 | whole 6 week old aboral regenerate · regenerate 144hpa | whole 6 week old aboral regenerate | six weeks | regenerate 144hpa | SRP125570 | 44.14 |
| SRR6320846 | whole 6 week old aboral regenerate · regenerate 0hpa | whole 6 week old aboral regenerate | six weeks | regenerate 0hpa | SRP125570 | 32.42 |
| SRR6320840 | whole 6 week old aboral regenerate · regenerate 0hpa | whole 6 week old aboral regenerate | six weeks | regenerate 0hpa | SRP125570 | 29.80 |
| SRR6320839 | whole 6 week old aboral regenerate · regenerate 0hpa | whole 6 week old aboral regenerate | six weeks | regenerate 0hpa | SRP125570 | 24.04 |
| SRR6320861 | whole 6 week old aboral regenerate · regenerate 2hpa | whole 6 week old aboral regenerate | six weeks | regenerate 2hpa | SRP125570 | 26.76 |
| SRR6320842 | whole 6 week old aboral regenerate · regenerate 2hpa | whole 6 week old aboral regenerate | six weeks | regenerate 2hpa | SRP125570 | 24.82 |
| SRR6320848 | whole 6 week old aboral regenerate · regenerate 2hpa | whole 6 week old aboral regenerate | six weeks | regenerate 2hpa | SRP125570 | 21.20 |
| SRR6320844 | whole 6 week old aboral regenerate · regenerate uncut | whole 6 week old aboral regenerate | six weeks | regenerate uncut | SRP125570 | 75.01 |
| SRR6320843 | whole 6 week old aboral regenerate · regenerate uncut | whole 6 week old aboral regenerate | six weeks | regenerate uncut | SRP125570 | 63.02 |
| SRR6320845 | whole 6 week old aboral regenerate · regenerate uncut | whole 6 week old aboral regenerate | six weeks | regenerate uncut | SRP125570 | 59.68 |
| SRR6320849 | whole 6 week old aboral regenerate · regenerate 4hpa | whole 6 week old aboral regenerate | six weeks | regenerate 4hpa | SRP125570 | 27.83 |
| SRR6320872 | whole 6 week old aboral regenerate · regenerate 4hpa | whole 6 week old aboral regenerate | six weeks | regenerate 4hpa | SRP125570 | 21.75 |
| SRR6320873 | whole 6 week old aboral regenerate · regenerate 4hpa | whole 6 week old aboral regenerate | six weeks | regenerate 4hpa | SRP125570 | 0.00 |
| SRR6320882 | whole 6 week old aboral regenerate · regenerate 120hpa | whole 6 week old aboral regenerate | six weeks | regenerate 120hpa | SRP125570 | 59.06 |
| SRR6320850 | whole 6 week old aboral regenerate · regenerate 120hpa | whole 6 week old aboral regenerate | six weeks | regenerate 120hpa | SRP125570 | 58.45 |
| SRR6320883 | whole 6 week old aboral regenerate · regenerate 120hpa | whole 6 week old aboral regenerate | six weeks | regenerate 120hpa | SRP125570 | 57.65 |
| SRR6320851 | whole 6 week old aboral regenerate · regenerate 36hpa | whole 6 week old aboral regenerate | six weeks | regenerate 36hpa | SRP125570 | 39.04 |
| SRR6320852 | whole 6 week old aboral regenerate · regenerate 36hpa | whole 6 week old aboral regenerate | six weeks | regenerate 36hpa | SRP125570 | 32.92 |
| SRR6320855 | whole 6 week old aboral regenerate · regenerate 36hpa | whole 6 week old aboral regenerate | six weeks | regenerate 36hpa | SRP125570 | 29.16 |
| SRR6320854 | whole 6 week old aboral regenerate · regenerate 24hpa | whole 6 week old aboral regenerate | six weeks | regenerate 24hpa | SRP125570 | 38.13 |
| SRR6320853 | whole 6 week old aboral regenerate · regenerate 24hpa | whole 6 week old aboral regenerate | six weeks | regenerate 24hpa | SRP125570 | 34.96 |
| SRR6320856 | whole 6 week old aboral regenerate · regenerate 24hpa | whole 6 week old aboral regenerate | six weeks | regenerate 24hpa | SRP125570 | 34.55 |
| SRR6320859 | whole 6 week old aboral regenerate · regenerate 20hpa | whole 6 week old aboral regenerate | six weeks | regenerate 20hpa | SRP125570 | 38.80 |
| SRR6320860 | whole 6 week old aboral regenerate · regenerate 20hpa | whole 6 week old aboral regenerate | six weeks | regenerate 20hpa | SRP125570 | 31.07 |
| SRR6320857 | whole 6 week old aboral regenerate · regenerate 20hpa | whole 6 week old aboral regenerate | six weeks | regenerate 20hpa | SRP125570 | 30.13 |
| SRR6320880 | whole 6 week old aboral regenerate · regenerate 16hpa | whole 6 week old aboral regenerate | six weeks | regenerate 16hpa | SRP125570 | 34.64 |
| SRR6320858 | whole 6 week old aboral regenerate · regenerate 16hpa | whole 6 week old aboral regenerate | six weeks | regenerate 16hpa | SRP125570 | 29.23 |
| SRR6320881 | whole 6 week old aboral regenerate · regenerate 16hpa | whole 6 week old aboral regenerate | six weeks | regenerate 16hpa | SRP125570 | 24.65 |
| SRR6320864 | whole 6 week old aboral regenerate · regenerate 72hpa | whole 6 week old aboral regenerate | six weeks | regenerate 72hpa | SRP125570 | 55.76 |
| SRR6320862 | whole 6 week old aboral regenerate · regenerate 72hpa | whole 6 week old aboral regenerate | six weeks | regenerate 72hpa | SRP125570 | 44.55 |
| SRR6320865 | whole 6 week old aboral regenerate · regenerate 72hpa | whole 6 week old aboral regenerate | six weeks | regenerate 72hpa | SRP125570 | 37.53 |
| SRR6320867 | whole 6 week old aboral regenerate · regenerate 60hpa | whole 6 week old aboral regenerate | six weeks | regenerate 60hpa | SRP125570 | 40.81 |
| SRR6320866 | whole 6 week old aboral regenerate · regenerate 60hpa | whole 6 week old aboral regenerate | six weeks | regenerate 60hpa | SRP125570 | 38.78 |
| SRR6320869 | whole 6 week old aboral regenerate · regenerate 60hpa | whole 6 week old aboral regenerate | six weeks | regenerate 60hpa | SRP125570 | 28.67 |
| SRR6320870 | whole 6 week old aboral regenerate · regenerate 48hpa | whole 6 week old aboral regenerate | six weeks | regenerate 48hpa | SRP125570 | 39.18 |
| SRR6320871 | whole 6 week old aboral regenerate · regenerate 48hpa | whole 6 week old aboral regenerate | six weeks | regenerate 48hpa | SRP125570 | 34.15 |
| SRR6320868 | whole 6 week old aboral regenerate · regenerate 48hpa | whole 6 week old aboral regenerate | six weeks | regenerate 48hpa | SRP125570 | 23.89 |
| SRR6320874 | whole 6 week old aboral regenerate · regenerate 8hpa | whole 6 week old aboral regenerate | six weeks | regenerate 8hpa | SRP125570 | 28.85 |
| SRR6320876 | whole 6 week old aboral regenerate · regenerate 8hpa | whole 6 week old aboral regenerate | six weeks | regenerate 8hpa | SRP125570 | 24.83 |
| SRR6320875 | whole 6 week old aboral regenerate · regenerate 8hpa | whole 6 week old aboral regenerate | six weeks | regenerate 8hpa | SRP125570 | 22.35 |
| SRR6320877 | whole 6 week old aboral regenerate · regenerate 12hpa | whole 6 week old aboral regenerate | six weeks | regenerate 12hpa | SRP125570 | 32.05 |
| SRR6320879 | whole 6 week old aboral regenerate · regenerate 12hpa | whole 6 week old aboral regenerate | six weeks | regenerate 12hpa | SRP125570 | 26.22 |
| SRR6320878 | whole 6 week old aboral regenerate · regenerate 12hpa | whole 6 week old aboral regenerate | six weeks | regenerate 12hpa | SRP125570 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (NVECT_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.
Peptides from this gene's protein product were identified in 1 re-processed proteomic dataset at a false discovery rate of q ≤ 0.01 (Comet + Percolator).
| Dataset | Species | Tissue / condition | Peptides | PSMs | Coverage | Best q | |
|---|---|---|---|---|---|---|---|
| PXD033068 | Nematostella vectensis | Embryos | 1 | 2 |
18.5%
|
0.0000678288 | peptides |
|
K.GSTGSGQWATPGGHLEFGEEWDECAAR.E q=0.0000678288
| |||||||
Search parameters for this evidence: Comet 2026.01,
precursor 10 ppm, fragment 0.02 Da,
fixed C+57.021464, variable M+15.9949,
PSM-level q ≤ 0.01 against
.
·
all proteins for Nematostella vectensis
Genes whose expression across the transcriptome samples of Nematostella vectensis 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 | 15 | XP_032220851.2 | 0.865035467282093 |
| Negatively correlated | 44 | XP_048587361.1 | -0.797391563065409 |
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 Nematostella vectensis, 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.
| Dataset | Tissue / stage | Cells | Cell types | This gene | Marker of |
|---|---|---|---|---|---|
| NVECT_2month | 2 month animal · Adult tissues/organs | 1,614 | 23 | not in this dataset | – |
| NVECT_bodywall | body wall with mesenteries · 6-8 weeks adults | 11,742 | 13 | not in this dataset | – |
| NVECT_embryo | embryos · 8, 10 and 12 h after fertilisation (deposit labels 8h/10h/12h) | 9,711 | 17 | in viewer | Cluster 12 (2.438, 0.834%) |
| NVECT_gastrula | Blastula-gastrula intermediate · Developmental stages | 49,166 | 27 | not in this dataset | – |
| NVECT_gastruloid | dissociated and reaggregated embryos · 4-48 hpa | 36,550 | 8 | not in this dataset | – |
| NVECT_neoplasm | neoplasm · Adult tissues/organs | 2,532 | 16 | not in this dataset | – |
| NVECT_nervous | Gastrula Cells · nervous system | 16,590 | 27 | unmapped | – |
| NVECT_notch48h | embryos treated 24-48 hpf (DMSO vs LY411575) · 48 hpf | 19,044 | 7 | not in this dataset | – |
| NVECT_tentacle | tentacle · Adult tissues/organs | 7,977 | 19 | not in this dataset | – |
Opening a dataset shows the UMAP with this gene coloured and the violin plot of its expression per cell type. A gene is in viewer when the dataset ships a per-cell expression vector for it; marker only means it is in the dataset’s ranked marker table but no vector was exported, so the atlas cannot draw it; not in this dataset means the dataset’s own gene-ID table does not list it, so no expression claim can be made for that dataset. unmapped is deliberately weaker still: the dataset has no gene-ID table on CnidoSite yet, so nothing is claimed in either direction. Where markers are listed, the numbers are log2 fold change and the percentage of cells of that type in which the gene was detected.
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.
| Assay | Sample | Peaks | Region |
|---|---|---|---|
| ChIP-seq | H3K27ac_gastrulae_24h | 4 | Promoter (<=1kb) 2 · Promoter (2-3kb) 1 · Distal Intergenic 1 |
| H3K27ac_planulae_4days | 2 | Promoter (<=1kb) 2 | |
| H3K4me2_gastrulae_24h | 7 | Promoter (<=1kb) 3 · Distal Intergenic 2 · Promoter (1-2kb) 1 · Promoter (2-3kb) 1 | |
| H3K4me2_planulae_4days | 1 | Promoter (<=1kb) 1 | |
| H3K4me2_polyps | 5 | Promoter (<=1kb) 2 · Distal Intergenic 2 · Promoter (2-3kb) 1 | |
| H3K4me3_gastrulae_24h | 4 | Promoter (<=1kb) 2 · Promoter (2-3kb) 1 · Distal Intergenic 1 | |
| H3K4me3_planulae_4days | 2 | Promoter (<=1kb) 2 | |
| H3K4me3_polyps | 3 | Promoter (<=1kb) 2 · Promoter (2-3kb) 1 | |
| H3K27ac_Ncol3_negative | 4 | Promoter (<=1kb) 1 · Promoter (2-3kb) 1 · Distal Intergenic 1 · Intron 1 | |
| H3K27ac_Ncol3_positive | 3 | Promoter (<=1kb) 1 · Promoter (2-3kb) 1 · Distal Intergenic 1 | |
| H3K27ac_Nep3_negative | 3 | Promoter (<=1kb) 1 · Promoter (1-2kb) 1 · Promoter (2-3kb) 1 | |
| H3K27ac_Nep3_positive | 3 | Promoter (<=1kb) 1 · Promoter (2-3kb) 1 · Distal Intergenic 1 | |
| H3K36me3_gastrulae_24h | 6 | Exon 3 · Intron 2 · Promoter (1-2kb) 1 | |
| H3K36me3_planulae_4days | 2 | Promoter (<=1kb) 1 · 3' UTR 1 | |
| H3K36me3_polyps | 4 | Exon 3 · Promoter (<=1kb) 1 |
7 further sample(s) also have peaks at this gene; open the assay page below to see them all.
Browse the full epigenomic landscape of this species: ChIP-seq · ATAC-seq.
| Sample | Methylation profile |
|---|---|
| Whole_adults | 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. | 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 → |
