Genomic Location: sc0000291_pilon:211586...252306
NR annotation: XP_044164572.1, exosome RNA helicase MTR4-like [Acropora millepora]
Species Acropora muricata · all data for this species · gene families
| CDS |
| amur_s0291.g21.t2 |
| Transcript |
| amur_s0291.g21.t2 |
| Protein |
| amur_s0291.g21.t2 |
| UniProt accession | Description |
|---|---|
| Q9CZU3 | Exosome RNA helicase MTR4 OS=Mus musculus OX=10090 GN=Mtrex PE=1 SV=1 |
| P42285 | Exosome RNA helicase MTR4 OS=Homo sapiens OX=9606 GN=MTREX PE=1 SV=3 |
| O14232 | ATP-dependent RNA helicase mtr4 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=mtr4 PE=1 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0001220 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF00271 all species → | Helicase_C | Helicase conserved C-terminal domain | Domain | Interproscan |
| PF08148 all species → | DSHCT | DSHCT (NUC185) domain | Domain | Interproscan |
| PF00270 all species → | DEAD | DEAD/DEAH box helicase | Domain | Interproscan |
| PF21408 all species → | MTR4-like_stalk | Exosome RNA helicase MTR4-like, stalk | Domain | Interproscan |
| PF13234 all species → | MTR4_beta-barrel | Mtr4-like, beta-barrel domain | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR014001 all species → | Domain | Helicase superfamily 1/2, ATP-binding domain | Interproscan |
| IPR027417 all species → | Homologous_superfamily | P-loop containing nucleoside triphosphate hydrolase | Interproscan |
| IPR001650 all species → | Domain | Helicase, C-terminal domain-like | Interproscan |
| IPR012961 all species → | Domain | ATP-dependent RNA helicase Ski2/MTR4, C-terminal | Interproscan |
| IPR011545 all species → | Domain | DEAD/DEAH box helicase domain | Interproscan |
| IPR048392 all species → | Domain | Exosome RNA helicase MTR4-like, stalk | Interproscan |
| IPR050699 all species → | Family | RNA/DNA Helicase | Interproscan |
| IPR016438 all species → | Family | ATP-dependent RNA helicase SKI2-like | Interproscan |
| IPR025696 all species → | Domain | Exosome RNA helicase MTR4-like, beta-barrel domain | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR12131 all species → | ATP-DEPENDENT RNA AND DNA HELICASE | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0003676 all species → | Molecular Function | nucleic acid binding | Interproscan |
| GO:0005524 all species → | Molecular Function | ATP binding | Interproscan |
| GO:0000460 all species → | Biological Process | maturation of 5.8S rRNA | Interproscan |
| GO:0003724 all species → | Molecular Function | RNA helicase activity | Interproscan |
| GO:0005634 all species → | Cellular Component | nucleus | Interproscan |
| GO:0006401 all species → | Biological Process | RNA catabolic process | Interproscan |
| GO:0003723 all species → | Molecular Function | RNA binding | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K12598 | MTR4, SKIV2L2; ATP-dependent RNA helicase DOB1 | EC:5.6.2.6 | Transfer RNA biogenesis | ko03016 | deepkoala |
Transcript abundance of amur_s0291.g21.t2 across 82 RNA-seq samples of Acropora muricata. This gene has no row in the species' RNA-seq expression matrix, so every value below is shown as zero — the matrix simply does not cover this transcript. 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 |
|---|---|---|---|---|---|
| Polyps | 79 | 0 | 0.00 | 0.00 | |
| Severed branch | 3 | 0 | 0.00 | 0.00 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR12710849 | Polyps | Polyps | OA 2 day3 | not recorded | SRP199550 | 0.00 |
| SRR12710850 | Polyps | Polyps | OA 2 day3 | not recorded | SRP199550 | 0.00 |
| SRR12710851 | Polyps | Polyps | OA 2 day3 | not recorded | SRP199550 | 0.00 |
| SRR12710859 | Polyps | Polyps | OA 2 day9 | not recorded | SRP199550 | 0.00 |
| SRR12710860 | Polyps | Polyps | OA 2 day9 | not recorded | SRP199550 | 0.00 |
| SRR12710861 | Polyps | Polyps | OA 2 day9 | not recorded | SRP199550 | 0.00 |
| SRR12786899 | Polyps | Polyps | OA 2 day0 | not recorded | SRP199550 | 0.00 |
| SRR12786900 | Polyps | Polyps | OA 2 day0 | not recorded | SRP199550 | 0.00 |
| SRR12786901 | Polyps | Polyps | OA 2 day0 | not recorded | SRP199550 | 0.00 |
| SRR12807382 | Polyps | Polyps | OA2 day0 | not recorded | SRP199550 | 0.00 |
| SRR12904784 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 0.00 |
| SRR12904785 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 0.00 |
| SRR12904786 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 0.00 |
| SRR12927881 | Polyps | Polyps | E2 day0 | not recorded | SRP199550 | 0.00 |
| SRR12959191 | Polyps | polyps | E2 day21 | not recorded | SRP199550 | 0.00 |
| SRR12959192 | Polyps | Polyps | E2 day21 | not recorded | SRP199550 | 0.00 |
| SRR12959193 | Polyps | Polyps | E2 day21 | not recorded | SRP199550 | 0.00 |
| SRR12959195 | Polyps | Polyps | E2 day0 | not recorded | SRP199550 | 0.00 |
| SRR12959204 | Polyps | Polyps | E2 day15 | not recorded | SRP199550 | 0.00 |
| SRR12959205 | Polyps | Polyps | E2 day15 | not recorded | SRP199550 | 0.00 |
| SRR12959206 | Polyps | Polyps | E2 day0 | not recorded | SRP199550 | 0.00 |
| SRR12959207 | Polyps | Polyps | E2 day15 | not recorded | SRP199550 | 0.00 |
| SRR12959217 | Polyps | Polyps | E2 day0 | not recorded | SRP199550 | 0.00 |
| SRR12959218 | Polyps | Polyps | E2 day9 | not recorded | SRP199550 | 0.00 |
| SRR12959219 | Polyps | Polyps | E2 day9 | not recorded | SRP199550 | 0.00 |
| SRR12959220 | Polyps | Polyps | E2 day9 | not recorded | SRP199550 | 0.00 |
| SRR12959231 | Polyps | Polyps | E2 day3 | not recorded | SRP199550 | 0.00 |
| SRR12959232 | Polyps | Polyps | E2 day3 | not recorded | SRP199550 | 0.00 |
| SRR12959233 | Polyps | Polyps | E2 day3 | not recorded | SRP199550 | 0.00 |
| SRR27868158 | Polyps | Polyps | regeneration day6 | not recorded | SRP199550 | 0.00 |
| SRR27868159 | Polyps | Polyps | regeneration day6 | not recorded | SRP199550 | 0.00 |
| SRR27868160 | Polyps | Polyps | regeneration day6 | not recorded | SRP199550 | 0.00 |
| SRR27868165 | Polyps | Polyps | regeneration day3 | not recorded | SRP199550 | 0.00 |
| SRR27868174 | Polyps | Polyps | regeneration day39 | not recorded | SRP199550 | 0.00 |
| SRR27868175 | Polyps | Polyps | regeneration day39 | not recorded | SRP199550 | 0.00 |
| SRR27868176 | Polyps | Polyps | regeneration day3 | not recorded | SRP199550 | 0.00 |
| SRR27868177 | Polyps | Polyps | regeneration day39 | not recorded | SRP199550 | 0.00 |
| SRR27868178 | Polyps | Polyps | regeneration day36 | not recorded | SRP199550 | 0.00 |
| SRR27868179 | Polyps | Polyps | regeneration day36 | not recorded | SRP199550 | 0.00 |
| SRR27868180 | Polyps | Polyps | regeneration day36 | not recorded | SRP199550 | 0.00 |
| SRR27868181 | Polyps | Polyps | regeneration day33 | not recorded | SRP199550 | 0.00 |
| SRR27868182 | Polyps | Polyps | regeneration day33 | not recorded | SRP199550 | 0.00 |
| SRR27868183 | Polyps | Polyps | regeneration day33 | not recorded | SRP199550 | 0.00 |
| SRR27868184 | Polyps | Polyps | regeneration day30 | not recorded | SRP199550 | 0.00 |
| SRR27868185 | Polyps | Polyps | regeneration day30 | not recorded | SRP199550 | 0.00 |
| SRR27868186 | Polyps | Polyps | regeneration day30 | not recorded | SRP199550 | 0.00 |
| SRR27868187 | Polyps | Polyps | regeneration day3 | not recorded | SRP199550 | 0.00 |
| SRR27868188 | Polyps | Polyps | regeneration day27 | not recorded | SRP199550 | 0.00 |
| SRR27868189 | Polyps | Polyps | regeneration day27 | not recorded | SRP199550 | 0.00 |
| SRR27868190 | Polyps | Polyps | regeneration day27 | not recorded | SRP199550 | 0.00 |
| SRR27868191 | Polyps | Polyps | regeneration day24 | not recorded | SRP199550 | 0.00 |
| SRR27868192 | Polyps | Polyps | regeneration day24 | not recorded | SRP199550 | 0.00 |
| SRR27868193 | Polyps | Polyps | regeneration day24 | not recorded | SRP199550 | 0.00 |
| SRR27868194 | Polyps | Polyps | regeneration day21 | not recorded | SRP199550 | 0.00 |
| SRR27868195 | Polyps | Polyps | regeneration day21 | not recorded | SRP199550 | 0.00 |
| SRR27868196 | Polyps | Polyps | regeneration day21 | not recorded | SRP199550 | 0.00 |
| SRR27868197 | Polyps | Polyps | regeneration day18 | not recorded | SRP199550 | 0.00 |
| SRR27868198 | Polyps | Polyps | regeneration day0 | not recorded | SRP199550 | 0.00 |
| SRR27868199 | Polyps | Polyps | regeneration day18 | not recorded | SRP199550 | 0.00 |
| SRR27868200 | Polyps | Polyps | regeneration day18 | not recorded | SRP199550 | 0.00 |
| SRR27868201 | Polyps | Polyps | regeneration day15 | not recorded | SRP199550 | 0.00 |
| SRR27868202 | Polyps | Polyps | regeneration day15 | not recorded | SRP199550 | 0.00 |
| SRR27868203 | Polyps | Polyps | regeneration day15 | not recorded | SRP199550 | 0.00 |
| SRR27868204 | Polyps | Polyps | regeneration day12 | not recorded | SRP199550 | 0.00 |
| SRR27868205 | Polyps | Polyps | regeneration day12 | not recorded | SRP199550 | 0.00 |
| SRR27868206 | Polyps | Polyps | regeneration day12 | not recorded | SRP199550 | 0.00 |
| SRR27868207 | Polyps | Polyps | regeneration day9 | not recorded | SRP199550 | 0.00 |
| SRR27868208 | Polyps | Polyps | regeneration day9 | not recorded | SRP199550 | 0.00 |
| SRR27868209 | Polyps | Polyps | regeneration day0 | not recorded | SRP199550 | 0.00 |
| SRR27868210 | Polyps | Polyps | regeneration day0 | not recorded | SRP199550 | 0.00 |
| SRR27940222 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 0.00 |
| SRR27940224 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 0.00 |
| SRR27940225 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 0.00 |
| SRR27940226 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 0.00 |
| SRR27940227 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 0.00 |
| SRR27940228 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 0.00 |
| SRR27940229 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 0.00 |
| SRR9613488 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 0.00 |
| SRR9613516 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 0.00 |
| SRR12995717 | Severed branch | Severed branch | regeneration day0 | not recorded | SRP199550 | 0.00 |
| SRR12996627 | Severed branch | Severed branch | regeneration day0 | not recorded | SRP199550 | 0.00 |
| SRR12996628 | Severed branch | Severed branch | regeneration High gene expression | not recorded | SRP199550 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (AMURI_TPM,
StringTie quantification over 82 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 muricata 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 | 0 | not in this network | - |
| Negatively correlated | 0 | not in this network | - |
This gene has no edge at all in the Acropora muricata network, in either direction — it is not one of the genes the network was built from (the network covers genes with enough expression variation across the transcriptome samples). The counts above are a property of the network, not a failed lookup.
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 muricata, 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 |
|---|---|---|---|---|---|
| AMURI_regen | Polyps · regeneration | 8,721 | 28 | unmapped | – |
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.
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. | no expression matrix | – |
| 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 → |
