Genomic Location: Sc0000373:534...13267
NR annotation: XP_015771093.1, PREDICTED: glycine receptor subunit alpha-1-like isoform X3 [Acropora digitifera]
Species Montipora capitata · all data for this species · gene families
| CDS |
| g11980.t1 |
| Transcript |
| g11980.t1 |
| Protein |
| g11980.t1 |
| UniProt accession | Description |
|---|---|
| P07727 | Glycine receptor subunit alpha-1 OS=Rattus norvegicus OX=10116 GN=Glra1 PE=1 SV=4 |
| P57695 | Glycine receptor subunit alpha-1 OS=Bos taurus OX=9913 GN=GLRA1 PE=1 SV=1 |
| P23415 | Glycine receptor subunit alpha-1 OS=Homo sapiens OX=9606 GN=GLRA1 PE=1 SV=2 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0000070 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF02932 all species → | Neur_chan_memb | Neurotransmitter-gated ion-channel transmembrane region | Family | Interproscan |
| PF02931 all species → | Neur_chan_LBD | Neurotransmitter-gated ion-channel ligand binding domain | Family | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR006201 all species → | Family | Neurotransmitter-gated ion-channel | Interproscan |
| IPR006028 all species → | Family | Gamma-aminobutyric acid A receptor/Glycine receptor alpha | Interproscan |
| IPR036734 all species → | Homologous_superfamily | Neurotransmitter-gated ion-channel ligand-binding domain superfamily | Interproscan |
| IPR006029 all species → | Domain | Neurotransmitter-gated ion-channel transmembrane domain | Interproscan |
| IPR018000 all species → | Conserved_site | Neurotransmitter-gated ion-channel, conserved site | Interproscan |
| IPR036719 all species → | Homologous_superfamily | Neurotransmitter-gated ion-channel transmembrane domain superfamily | Interproscan |
| IPR006202 all species → | Domain | Neurotransmitter-gated ion-channel ligand-binding domain | Interproscan |
| IPR002289 all species → | Family | Gamma-aminobutyric-acid A receptor, beta subunit | Interproscan |
| IPR038050 all species → | Homologous_superfamily | Neuronal acetylcholine receptor | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR18945 all species → | NEUROTRANSMITTER GATED ION CHANNEL | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0004888 all species → | Molecular Function | transmembrane signaling receptor activity | Interproscan |
| GO:0005216 all species → | Molecular Function | monoatomic ion channel activity | Interproscan |
| GO:0005231 all species → | Molecular Function | excitatory extracellular ligand-gated monoatomic ion channel activity | Interproscan |
| GO:0005254 all species → | Molecular Function | chloride channel activity | Interproscan |
| GO:0005887 all species → | Cellular Component | plasma membrane | Interproscan |
| GO:0007165 all species → | Biological Process | signal transduction | Interproscan |
| GO:0007268 all species → | Biological Process | chemical synaptic transmission | Interproscan |
| GO:0016020 all species → | Cellular Component | membrane | Interproscan |
| GO:0030594 all species → | Molecular Function | neurotransmitter receptor activity | Interproscan |
| GO:0034220 all species → | Biological Process | monoatomic ion transmembrane transport | Interproscan |
| GO:0042391 all species → | Biological Process | regulation of membrane potential | Interproscan |
| GO:0043005 all species → | Cellular Component | neuron projection | Interproscan |
| GO:0045202 all species → | Cellular Component | synapse | Interproscan |
| GO:0050877 all species → | Biological Process | nervous system process | Interproscan |
| GO:1902476 all species → | Biological Process | chloride transmembrane transport | Interproscan |
| GO:1904315 all species → | Molecular Function | transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential | Interproscan |
| GO:0005230 all species → | Molecular Function | extracellular ligand-gated monoatomic ion channel activity | Interproscan |
| GO:0006811 all species → | Biological Process | monoatomic ion transport | Interproscan |
| GO:0004890 all species → | Molecular Function | GABA-A receptor activity | Interproscan |
g11980.t1.Transcript abundance of g11980.t1 across 48 RNA-seq samples of Montipora capitata. 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 organisms · ambient pH treatment | 21 | 15 | 1.45 | 6.42 | |
| whole organisms · low pH treatment | 15 | 12 | 1.55 | 3.77 | |
| whole organisms · extra low pH treatment pH treatment | 12 | 8 | 1.70 | 5.42 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR11452228 | whole organisms · ambient pH treatment | whole organisms | planulae | ambient pH treatment | SRP254626 | 6.42 |
| SRR11452230 | whole organisms · ambient pH treatment | whole organisms | planulae | ambient pH treatment | SRP254626 | 4.80 |
| SRR11452222 | whole organisms · ambient pH treatment | whole organisms | planulae | ambient pH treatment | SRP254626 | 3.38 |
| SRR11452250 | whole organisms · ambient pH treatment | whole organisms | prawn chip | ambient pH treatment | SRP254626 | 3.36 |
| SRR11452252 | whole organisms · ambient pH treatment | whole organisms | prawn chip | ambient pH treatment | SRP254626 | 2.72 |
| SRR11452263 | whole organisms · ambient pH treatment | whole organisms | egg | ambient pH treatment | SRP254626 | 1.84 |
| SRR11452246 | whole organisms · ambient pH treatment | whole organisms | prawn chip | ambient pH treatment | SRP254626 | 1.39 |
| SRR11452243 | whole organisms · ambient pH treatment | whole organisms | gastrula | ambient pH treatment | SRP254626 | 1.28 |
| SRR11452237 | whole organisms · ambient pH treatment | whole organisms | gastrula | ambient pH treatment | SRP254626 | 1.17 |
| SRR11452262 | whole organisms · ambient pH treatment | whole organisms | egg | ambient pH treatment | SRP254626 | 0.93 |
| SRR11452260 | whole organisms · ambient pH treatment | whole organisms | cleavage | ambient pH treatment | SRP254626 | 0.87 |
| SRR11452242 | whole organisms · ambient pH treatment | whole organisms | gastrula | ambient pH treatment | SRP254626 | 0.80 |
| SRR11452232 | whole organisms · ambient pH treatment | whole organisms | blastula | ambient pH treatment | SRP254626 | 0.61 |
| SRR11452217 | whole organisms · ambient pH treatment | whole organisms | fertilized embryo | ambient pH treatment | SRP254626 | 0.55 |
| SRR11452233 | whole organisms · ambient pH treatment | whole organisms | morula | ambient pH treatment | SRP254626 | 0.25 |
| SRR11452231 | whole organisms · ambient pH treatment | whole organisms | blastula | ambient pH treatment | SRP254626 | 0.00 |
| SRR11452234 | whole organisms · ambient pH treatment | whole organisms | morula | ambient pH treatment | SRP254626 | 0.00 |
| SRR11452240 | whole organisms · ambient pH treatment | whole organisms | fertilized embryo | ambient pH treatment | SRP254626 | 0.00 |
| SRR11452251 | whole organisms · ambient pH treatment | whole organisms | egg | ambient pH treatment | SRP254626 | 0.00 |
| SRR11452254 | whole organisms · ambient pH treatment | whole organisms | cleavage | ambient pH treatment | SRP254626 | 0.00 |
| SRR11452259 | whole organisms · ambient pH treatment | whole organisms | cleavage | ambient pH treatment | SRP254626 | 0.00 |
| SRR11452221 | whole organisms · low pH treatment | whole organisms | planulae | low pH treatment | SRP254626 | 3.77 |
| SRR11452229 | whole organisms · low pH treatment | whole organisms | fertilized embryo | low pH treatment | SRP254626 | 3.29 |
| SRR11452224 | whole organisms · low pH treatment | whole organisms | planulae | low pH treatment | SRP254626 | 3.27 |
| SRR11452223 | whole organisms · low pH treatment | whole organisms | planulae | low pH treatment | SRP254626 | 2.41 |
| SRR11452249 | whole organisms · low pH treatment | whole organisms | prawn chip | low pH treatment | SRP254626 | 2.29 |
| SRR11452247 | whole organisms · low pH treatment | whole organisms | prawn chip | low pH treatment | SRP254626 | 1.69 |
| SRR11452245 | whole organisms · low pH treatment | whole organisms | prawn chip | low pH treatment | SRP254626 | 1.69 |
| SRR11452238 | whole organisms · low pH treatment | whole organisms | gastrula | low pH treatment | SRP254626 | 1.43 |
| SRR11452216 | whole organisms · low pH treatment | whole organisms | fertilized embryo | low pH treatment | SRP254626 | 1.10 |
| SRR11452241 | whole organisms · low pH treatment | whole organisms | gastrula | low pH treatment | SRP254626 | 0.96 |
| SRR11452236 | whole organisms · low pH treatment | whole organisms | gastrula | low pH treatment | SRP254626 | 0.83 |
| SRR11452258 | whole organisms · low pH treatment | whole organisms | cleavage | low pH treatment | SRP254626 | 0.57 |
| SRR11452218 | whole organisms · low pH treatment | whole organisms | fertilized embryo | low pH treatment | SRP254626 | 0.00 |
| SRR11452253 | whole organisms · low pH treatment | whole organisms | cleavage | low pH treatment | SRP254626 | 0.00 |
| SRR11452255 | whole organisms · low pH treatment | whole organisms | cleavage | low pH treatment | SRP254626 | 0.00 |
| SRR11452225 | whole organisms · extra low pH treatment pH treatment | whole organisms | planulae | extra low pH treatment pH treatment | SRP254626 | 5.42 |
| SRR11452226 | whole organisms · extra low pH treatment pH treatment | whole organisms | planulae | extra low pH treatment pH treatment | SRP254626 | 4.40 |
| SRR11452227 | whole organisms · extra low pH treatment pH treatment | whole organisms | planulae | extra low pH treatment pH treatment | SRP254626 | 3.66 |
| SRR11452248 | whole organisms · extra low pH treatment pH treatment | whole organisms | prawn chip | extra low pH treatment pH treatment | SRP254626 | 2.25 |
| SRR11452244 | whole organisms · extra low pH treatment pH treatment | whole organisms | prawn chip | extra low pH treatment pH treatment | SRP254626 | 2.14 |
| SRR11452219 | whole organisms · extra low pH treatment pH treatment | whole organisms | fertilized embryo | extra low pH treatment pH treatment | SRP254626 | 1.47 |
| SRR11452261 | whole organisms · extra low pH treatment pH treatment | whole organisms | fertilized embryo | extra low pH treatment pH treatment | SRP254626 | 0.72 |
| SRR11452239 | whole organisms · extra low pH treatment pH treatment | whole organisms | gastrula | extra low pH treatment pH treatment | SRP254626 | 0.38 |
| SRR11452220 | whole organisms · extra low pH treatment pH treatment | whole organisms | fertilized embryo | extra low pH treatment pH treatment | SRP254626 | 0.00 |
| SRR11452235 | whole organisms · extra low pH treatment pH treatment | whole organisms | gastrula | extra low pH treatment pH treatment | SRP254626 | 0.00 |
| SRR11452256 | whole organisms · extra low pH treatment pH treatment | whole organisms | cleavage | extra low pH treatment pH treatment | SRP254626 | 0.00 |
| SRR11452257 | whole organisms · extra low pH treatment pH treatment | whole organisms | cleavage | extra low pH treatment pH treatment | SRP254626 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (MCAPI_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 Montipora capitata 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 | 4 | g23536.t1 | 0.889429585110037 |
| Negatively correlated | 3 | g20217.t1 | -0.801037240631124 |
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 Montipora capitata, 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 → |
