Genomic Location: sc0000188_pilon:354926...365315
NR annotation: XP_044175028.1, ATP-dependent RNA helicase DEAH12, chloroplastic-like [Acropora millepora]
Species Acropora gemmifera · all data for this species · gene families
| CDS |
| agem_s0188.g24.t1 |
| Transcript |
| agem_s0188.g24.t1 |
| Protein |
| agem_s0188.g24.t1 |
| UniProt accession | Description |
|---|---|
| F4KGU4 | ATP-dependent RNA helicase DEAH12, chloroplastic OS=Arabidopsis thaliana OX=3702 GN=At5g10370 PE=3 SV=1 |
| P0CE10 | ATP-dependent RNA helicase DEAH11, chloroplastic OS=Arabidopsis thaliana OX=3702 GN=At4g01020 PE=3 SV=1 |
| Q14562 | ATP-dependent RNA helicase DHX8 OS=Homo sapiens OX=9606 GN=DHX8 PE=1 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0000322 (this species only) · gene tree & orthology |
| Ubiquitin family | E3|E3 activity|RBR · all ubiquitin genes in this species |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF04408 all species → | HA2_N | Helicase associated domain (HA2), winged-helix | Domain | Interproscan |
| PF01485 all species → | IBR | IBR domain, a half RING-finger domain | Domain | Interproscan |
| PF07717 all species → | OB_NTP_bind | Oligonucleotide/oligosaccharide-binding (OB)-fold | Domain | Interproscan |
| PF00270 all species → | DEAD | DEAD/DEAH box helicase | Domain | Interproscan |
| PF00271 all species → | Helicase_C | Helicase conserved C-terminal domain | Domain | Interproscan |
| PF21010 all species → | HA2_C | Helicase associated domain (HA2), ratchet-like | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR014001 all species → | Domain | Helicase superfamily 1/2, ATP-binding domain | Interproscan |
| IPR007502 all species → | Domain | Helicase-associated domain | Interproscan |
| IPR048333 all species → | Domain | Helicase associated domain (HA2), winged-helix domain | Interproscan |
| IPR002867 all species → | Domain | IBR domain | Interproscan |
| IPR001650 all species → | Domain | Helicase, C-terminal domain-like | Interproscan |
| IPR027417 all species → | Homologous_superfamily | P-loop containing nucleoside triphosphate hydrolase | Interproscan |
| IPR011709 all species → | Domain | DEAD-box helicase, OB fold | Interproscan |
| IPR044066 all species → | Domain | TRIAD supradomain | Interproscan |
| IPR011545 all species → | Domain | DEAD/DEAH box helicase domain | Interproscan |
| IPR002464 all species → | Conserved_site | DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site | Interproscan |
| IPR013083 all species → | Homologous_superfamily | Zinc finger, RING/FYVE/PHD-type | Interproscan |
| IPR035979 all species → | Homologous_superfamily | RNA-binding domain superfamily | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR18934 all species → | ATP-DEPENDENT RNA HELICASE | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0008270 all species → | Molecular Function | zinc ion binding | Interproscan |
| GO:0003676 all species → | Molecular Function | nucleic acid binding | Interproscan |
| GO:0005524 all species → | Molecular Function | ATP binding | Interproscan |
| GO:0003723 all species → | Molecular Function | RNA binding | Interproscan |
| GO:0004386 all species → | Molecular Function | helicase activity | Interproscan |
| GO:0005622 all species → | Cellular Component | intracellular anatomical structure | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K12818 | DHX8, PRP22; ATP-dependent RNA helicase DHX8/PRP22 | EC:5.6.2.6 | Spliceosome | ko03041 | deepkoala |
Transcript abundance of agem_s0188.g24.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 | 3 | 1.32 | 28.86 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR2169558 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 28.86 |
| SRR3223317 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 23.19 |
| SRR3223319 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 11.38 |
| 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 | 11 | agem_s0246.g32.t1 | 0.999999993413428 |
| Negatively correlated | 3 | agem_s0028.g73.t1 | -0.583474450770835 |
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 → |
