Genomic Location: Sc0000020:40309...57239
NR annotation: XP_044163987.1, nuclear receptor subfamily 2 group E member 1-like [Acropora millepora]
Species Montipora capitata · all data for this species · gene families
| CDS |
| g1533.t1 |
| Transcript |
| g1533.t1 |
| Protein |
| g1533.t1 |
| UniProt accession | Description |
|---|---|
| Q9TTF0 | Photoreceptor-specific nuclear receptor OS=Bos taurus OX=9913 GN=NR2E3 PE=1 SV=2 |
| Q9Y5X4 | Photoreceptor-specific nuclear receptor OS=Homo sapiens OX=9606 GN=NR2E3 PE=1 SV=1 |
| Q91379 | Nuclear receptor subfamily 2 group E member 1 OS=Gallus gallus OX=9031 GN=NR2E1 PE=2 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0000188 (this species only) · gene tree & orthology |
| Transcription factor family | ESR-like · all TF in this species |
| Transcription factor family | Miscellaneous · all TF in this species |
| Transcription factor family | NGFIB-like · all TF in this species |
| Transcription factor family | RXR-like · all TF in this species |
| Transcription factor family | SF-like · all TF in this species |
| Transcription factor family | THR-like · all TF in this species |
| Transcription factor family | GCNF-like · all TF in this species |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF00104 all species → | Hormone_recep | Ligand-binding domain of nuclear hormone receptor | Domain | Interproscan |
| PF00105 all species → | zf-C4 | Zinc finger, C4 type (two domains) | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR013088 all species → | Homologous_superfamily | Zinc finger, NHR/GATA-type | Interproscan |
| IPR000536 all species → | Domain | Nuclear hormone receptor, ligand-binding domain | Interproscan |
| IPR035500 all species → | Homologous_superfamily | Nuclear hormone receptor-like domain superfamily | Interproscan |
| IPR000003 all species → | Family | Retinoid X receptor/HNF4 | Interproscan |
| IPR001628 all species → | Domain | Zinc finger, nuclear hormone receptor-type | Interproscan |
| IPR050274 all species → | Family | Nuclear hormone receptor family NR2 subfamily | Interproscan |
| IPR001723 all species → | Family | Nuclear hormone receptor | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR24083 all species → | NUCLEAR HORMONE RECEPTOR | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0006355 all species → | Biological Process | regulation of DNA-templated transcription | Interproscan |
| GO:0008270 all species → | Molecular Function | zinc ion binding | Interproscan |
| GO:0003677 all species → | Molecular Function | DNA binding | Interproscan |
| GO:0003707 all species → | Molecular Function | nuclear steroid receptor activity | Interproscan |
| GO:0005634 all species → | Cellular Component | nucleus | Interproscan |
| GO:0003700 all species → | Molecular Function | DNA-binding transcription factor activity | Interproscan |
| GO:0043565 all species → | Molecular Function | sequence-specific DNA binding | Interproscan |
| GO:0000978 all species → | Molecular Function | RNA polymerase II cis-regulatory region sequence-specific DNA binding | Interproscan |
| GO:0004879 all species → | Molecular Function | nuclear receptor activity | Interproscan |
| GO:0006357 all species → | Biological Process | regulation of transcription by RNA polymerase II | Interproscan |
| GO:0030154 all species → | Biological Process | cell differentiation | Interproscan |
| GO:0048856 all species → | Biological Process | anatomical structure development | Interproscan |
g1533.t1.Transcript abundance of g1533.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 | 7 | 1.24 | 7.82 | |
| whole organisms · low pH treatment | 15 | 4 | 0.87 | 4.83 | |
| whole organisms · extra low pH treatment pH treatment | 12 | 4 | 1.32 | 5.96 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR11452230 | whole organisms · ambient pH treatment | whole organisms | planulae | ambient pH treatment | SRP254626 | 7.82 |
| SRR11452228 | whole organisms · ambient pH treatment | whole organisms | planulae | ambient pH treatment | SRP254626 | 6.58 |
| SRR11452222 | whole organisms · ambient pH treatment | whole organisms | planulae | ambient pH treatment | SRP254626 | 5.94 |
| SRR11452232 | whole organisms · ambient pH treatment | whole organisms | blastula | ambient pH treatment | SRP254626 | 2.80 |
| SRR11452231 | whole organisms · ambient pH treatment | whole organisms | blastula | ambient pH treatment | SRP254626 | 1.48 |
| SRR11452237 | whole organisms · ambient pH treatment | whole organisms | gastrula | ambient pH treatment | SRP254626 | 0.83 |
| SRR11452234 | whole organisms · ambient pH treatment | whole organisms | morula | ambient pH treatment | SRP254626 | 0.66 |
| SRR11452217 | whole organisms · ambient pH treatment | whole organisms | fertilized embryo | ambient pH treatment | SRP254626 | 0.00 |
| SRR11452233 | 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 |
| SRR11452242 | whole organisms · ambient pH treatment | whole organisms | gastrula | ambient pH treatment | SRP254626 | 0.00 |
| SRR11452243 | whole organisms · ambient pH treatment | whole organisms | gastrula | ambient pH treatment | SRP254626 | 0.00 |
| SRR11452246 | whole organisms · ambient pH treatment | whole organisms | prawn chip | ambient pH treatment | SRP254626 | 0.00 |
| SRR11452250 | whole organisms · ambient pH treatment | whole organisms | prawn chip | ambient pH treatment | SRP254626 | 0.00 |
| SRR11452251 | whole organisms · ambient pH treatment | whole organisms | egg | ambient pH treatment | SRP254626 | 0.00 |
| SRR11452252 | whole organisms · ambient pH treatment | whole organisms | prawn chip | 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 |
| SRR11452260 | whole organisms · ambient pH treatment | whole organisms | cleavage | ambient pH treatment | SRP254626 | 0.00 |
| SRR11452262 | whole organisms · ambient pH treatment | whole organisms | egg | ambient pH treatment | SRP254626 | 0.00 |
| SRR11452263 | whole organisms · ambient pH treatment | whole organisms | egg | ambient pH treatment | SRP254626 | 0.00 |
| SRR11452223 | whole organisms · low pH treatment | whole organisms | planulae | low pH treatment | SRP254626 | 4.83 |
| SRR11452224 | whole organisms · low pH treatment | whole organisms | planulae | low pH treatment | SRP254626 | 3.97 |
| SRR11452221 | whole organisms · low pH treatment | whole organisms | planulae | low pH treatment | SRP254626 | 3.57 |
| SRR11452241 | whole organisms · low pH treatment | whole organisms | gastrula | low pH treatment | SRP254626 | 0.65 |
| SRR11452216 | whole organisms · low pH treatment | whole organisms | fertilized embryo | low pH treatment | SRP254626 | 0.00 |
| SRR11452218 | whole organisms · low pH treatment | whole organisms | fertilized embryo | low pH treatment | SRP254626 | 0.00 |
| SRR11452229 | whole organisms · low pH treatment | whole organisms | fertilized embryo | low pH treatment | SRP254626 | 0.00 |
| SRR11452236 | whole organisms · low pH treatment | whole organisms | gastrula | low pH treatment | SRP254626 | 0.00 |
| SRR11452238 | whole organisms · low pH treatment | whole organisms | gastrula | low pH treatment | SRP254626 | 0.00 |
| SRR11452245 | whole organisms · low pH treatment | whole organisms | prawn chip | low pH treatment | SRP254626 | 0.00 |
| SRR11452247 | whole organisms · low pH treatment | whole organisms | prawn chip | low pH treatment | SRP254626 | 0.00 |
| SRR11452249 | whole organisms · low pH treatment | whole organisms | prawn chip | 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 |
| SRR11452258 | whole organisms · low pH treatment | whole organisms | cleavage | low pH treatment | SRP254626 | 0.00 |
| SRR11452227 | whole organisms · extra low pH treatment pH treatment | whole organisms | planulae | extra low pH treatment pH treatment | SRP254626 | 5.96 |
| SRR11452226 | whole organisms · extra low pH treatment pH treatment | whole organisms | planulae | extra low pH treatment pH treatment | SRP254626 | 5.40 |
| SRR11452225 | whole organisms · extra low pH treatment pH treatment | whole organisms | planulae | extra low pH treatment pH treatment | SRP254626 | 3.84 |
| SRR11452239 | whole organisms · extra low pH treatment pH treatment | whole organisms | gastrula | extra low pH treatment pH treatment | SRP254626 | 0.68 |
| SRR11452219 | whole organisms · extra low pH treatment pH treatment | whole organisms | fertilized embryo | extra low pH treatment pH treatment | SRP254626 | 0.00 |
| 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 |
| SRR11452244 | whole organisms · extra low pH treatment pH treatment | whole organisms | prawn chip | extra low pH treatment pH treatment | SRP254626 | 0.00 |
| SRR11452248 | whole organisms · extra low pH treatment pH treatment | whole organisms | prawn chip | 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 |
| SRR11452261 | whole organisms · extra low pH treatment pH treatment | whole organisms | fertilized embryo | 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 | 13 | g19186.t1 | 0.989853375129627 |
| Negatively correlated | 3 | g6649.t1 | -0.899362037820796 |
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 → |
