Genomic Location: sc0004126_pilon:1...2325
NR annotation: XP_015769289.1, PREDICTED: isocitrate dehydrogenase [NAD] subunit beta, mitochondrial-like [Acropora digitifera]
Species Acropora selago · all data for this species · gene families
| CDS |
| asel_s4126.g1.t1 |
| Transcript |
| asel_s4126.g1.t1 |
| Protein |
| asel_s4126.g1.t1 |
| UniProt accession | Description |
|---|---|
| O77784 | Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial OS=Bos taurus OX=9913 GN=IDH3B PE=2 SV=2 |
| O43837 | Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial OS=Homo sapiens OX=9606 GN=IDH3B PE=1 SV=2 |
| Q28479 | Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial OS=Macaca fascicularis OX=9541 GN=IDH3B PE=2 SV=2 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0001138 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF00180 all species → | Iso_dh | Isocitrate/isopropylmalate dehydrogenase | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR024084 all species → | Domain | Isopropylmalate dehydrogenase-like domain | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR11835 all species → | DECARBOXYLATING DEHYDROGENASES-ISOCITRATE, ISOPROPYLMALATE, TARTRATE | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0005739 all species → | Cellular Component | mitochondrion | Interproscan |
| GO:0006099 all species → | Biological Process | tricarboxylic acid cycle | Interproscan |
| GO:0006102 all species → | Biological Process | isocitrate metabolic process | Interproscan |
asel_s4126.g1.t1.Transcript abundance of asel_s4126.g1.t1 across 24 RNA-seq samples of Acropora selago. 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 |
|---|---|---|---|---|---|
| coral larvae | 24 | 22 | 130.07 | 198.51 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR14308004 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 198.51 |
| SRR14308008 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 185.48 |
| SRR14308026 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 183.84 |
| SRR14308015 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 179.47 |
| SRR14308022 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 158.09 |
| SRR14308018 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 156.46 |
| SRR14308011 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 153.93 |
| SRR14308007 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 149.73 |
| SRR14308027 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 146.15 |
| SRR14308012 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 145.12 |
| SRR14308010 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 139.65 |
| SRR14308014 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 134.68 |
| SRR14308006 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 134.50 |
| SRR14308021 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 128.77 |
| SRR14308023 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 127.72 |
| SRR14308024 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 125.74 |
| SRR14308017 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 120.52 |
| SRR14308013 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 116.67 |
| SRR14308019 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 114.76 |
| SRR14308016 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 111.03 |
| SRR14308025 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 108.89 |
| SRR14308020 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 101.98 |
| SRR14308005 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 0.00 |
| SRR14308009 | coral larvae | coral larvae | not recorded | not recorded | SRP315987 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (ASELA_TPM,
StringTie quantification over 24 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 selago 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 | 36 | asel_s0067.g38.t1 | 0.934098326764287 |
| Negatively correlated | 6 | asel_s0176.g29.t1 | -0.833559998011287 |
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 selago, 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 |
|---|---|
| Coral_Fragment_Parent | open |
| Larval_Pool_Offspring | 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 → |
