Genomic Location: sc0000039_pilon:460831...472828
NR annotation: XP_015767881.1, PREDICTED: photoreceptor-specific nuclear receptor-like [Acropora digitifera]
Species Acropora gemmifera · all data for this species · gene families
| CDS |
| agem_s0039.g34.t1 |
| Transcript |
| agem_s0039.g34.t1 |
| Protein |
| agem_s0039.g34.t1 |
| UniProt accession | Description |
|---|---|
| Q9TTF0 | Photoreceptor-specific nuclear receptor OS=Bos taurus OX=9913 GN=NR2E3 PE=1 SV=2 |
| Q9QXZ7 | Photoreceptor-specific nuclear receptor OS=Mus musculus OX=10090 GN=Nr2e3 PE=1 SV=1 |
| Q9Y5X4 | Photoreceptor-specific nuclear receptor OS=Homo sapiens OX=9606 GN=NR2E3 PE=1 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0009786 (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 |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF00105 all species → | zf-C4 | Zinc finger, C4 type (two domains) | Domain | Interproscan |
| PF00104 all species → | Hormone_recep | Ligand-binding domain of nuclear hormone receptor | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR001628 all species → | Domain | Zinc finger, nuclear hormone receptor-type | Interproscan |
| IPR000536 all species → | Domain | Nuclear hormone receptor, ligand-binding domain | Interproscan |
| IPR013088 all species → | Homologous_superfamily | Zinc finger, NHR/GATA-type | Interproscan |
| IPR035500 all species → | Homologous_superfamily | Nuclear hormone receptor-like domain superfamily | Interproscan |
| IPR001723 all species → | Family | Nuclear hormone receptor | Interproscan |
| IPR050274 all species → | Family | Nuclear hormone receptor family NR2 subfamily | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR24083 all species → | NUCLEAR HORMONE RECEPTOR | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0003700 all species → | Molecular Function | DNA-binding transcription factor activity | Interproscan |
| GO:0006355 all species → | Biological Process | regulation of DNA-templated transcription | Interproscan |
| GO:0008270 all species → | Molecular Function | zinc ion binding | 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 |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K08546 | NR2E3, PNR; nuclear receptor subfamily 2 group E member 3 | - | Nuclear receptors | ko03310 | deepkoala |
Transcript abundance of agem_s0039.g34.t1 across 48 RNA-seq samples of Acropora gemmifera. 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 |
|---|---|---|---|---|---|
| branch tip | 48 | 2 | 0.53 | 14.18 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR3223317 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 14.18 |
| SRR3223319 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 11.11 |
| SRR2169558 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169421 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169422 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169423 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169425 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169426 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169518 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169527 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169528 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169529 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169530 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169531 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169532 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169533 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169534 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169535 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169536 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169537 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169538 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169539 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169540 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169541 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182410 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182448 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182557 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182684 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182685 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182686 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182775 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182776 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182777 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182778 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182779 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182780 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182781 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182784 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182785 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182786 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182787 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182788 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182789 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182790 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182791 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182792 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182793 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182794 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (AGEMM_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 Acropora gemmifera 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 | 9 | agem_s0049.g32.t1 | 0.999999961045859 |
| Negatively correlated | 3 | agem_s0028.g73.t1 | -0.499005603946196 |
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 gemmifera, 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 → |
