Genomic Location: Ap8:3045749...3058124
NR annotation: XP_020608399.1, H/ACA ribonucleoprotein complex subunit 4-like [Orbicella faveolata]
Species Astrangia poculata · all data for this species · gene families
| CDS |
| evm.model.Ap8.295.1.5f15e5ce |
| Transcript |
| evm.model.Ap8.295.1.5f15e5ce |
| Protein |
| evm.model.Ap8.295.1.5f15e5ce |
| UniProt accession | Description |
|---|---|
| Q5ZJH9 | H/ACA ribonucleoprotein complex subunit DKC1 OS=Gallus gallus OX=9031 GN=DKC1 PE=2 SV=1 |
| Q9ESX5 | H/ACA ribonucleoprotein complex subunit DKC1 OS=Mus musculus OX=10090 GN=Dkc1 PE=1 SV=4 |
| F1Q749 | H/ACA ribonucleoprotein complex subunit DKC1 OS=Danio rerio OX=7955 GN=dkc1 PE=2 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0004107 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF16198 all species → | TruB_C_2 | tRNA pseudouridylate synthase B C-terminal domain | Family | Interproscan |
| PF08068 all species → | DKCLD | DKCLD (NUC011) domain | Domain | Interproscan |
| PF01509 all species → | TruB_N | TruB family pseudouridylate synthase (N terminal domain) | Family | Interproscan |
| PF01472 all species → | PUA | PUA domain | Family | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR036974 all species → | Homologous_superfamily | PUA domain superfamily | Interproscan |
| IPR015947 all species → | Homologous_superfamily | PUA-like superfamily | Interproscan |
| IPR004521 all species → | Domain | Uncharacterised domain CHP00451 | Interproscan |
| IPR012960 all species → | Domain | Dyskerin-like | Interproscan |
| IPR032819 all species → | Domain | tRNA pseudouridylate synthase B, C-terminal | Interproscan |
| IPR004802 all species → | Family | tRNA pseudouridine synthase B family | Interproscan |
| IPR002501 all species → | Domain | Pseudouridine synthase II, N-terminal | Interproscan |
| IPR002478 all species → | Domain | PUA domain | Interproscan |
| IPR020103 all species → | Homologous_superfamily | Pseudouridine synthase, catalytic domain superfamily | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR23127 all species → | CENTROMERE/MICROTUBULE BINDING PROTEIN CBF5 | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0003723 all species → | Molecular Function | RNA binding | Interproscan |
| GO:0006396 all species → | Biological Process | RNA processing | Interproscan |
| GO:0000495 all species → | Biological Process | box H/ACA sno(s)RNA 3'-end processing | Interproscan |
| GO:0009982 all species → | Molecular Function | pseudouridine synthase activity | Interproscan |
| GO:0031118 all species → | Biological Process | rRNA pseudouridine synthesis | Interproscan |
| GO:0031120 all species → | Biological Process | snRNA pseudouridine synthesis | Interproscan |
| GO:0031429 all species → | Cellular Component | box H/ACA snoRNP complex | Interproscan |
| GO:1990481 all species → | Biological Process | mRNA pseudouridine synthesis | Interproscan |
| GO:0001522 all species → | Biological Process | pseudouridine synthesis | Interproscan |
| GO:0009451 all species → | Biological Process | RNA modification | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K11131 | DKC1, NOLA4, CBF5; H/ACA ribonucleoprotein complex subunit 4 | EC:5.4.99.- | DNA replication proteins | ko03032 | deepkoala |
Transcript abundance of evm.model.Ap8.295.1.5f15e5ce across 49 RNA-seq samples of Astrangia poculata. 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 |
|---|---|---|---|---|---|
| whole organism · cold control | 14 | 0 | 0.00 | 0.00 | |
| whole organism · heat control | 12 | 0 | 0.00 | 0.00 | |
| whole organism · cold challenge | 12 | 0 | 0.00 | 0.00 | |
| whole organism · heat challenge | 11 | 0 | 0.00 | 0.00 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR10674714 | whole organism · cold control | whole organism | not recorded | cold control | SRP237293 | 0.00 |
| SRR10674715 | whole organism · cold control | whole organism | not recorded | cold control | SRP237293 | 0.00 |
| SRR10674724 | whole organism · cold control | whole organism | not recorded | cold control | SRP237293 | 0.00 |
| SRR10674733 | whole organism · cold control | whole organism | not recorded | cold control | SRP237293 | 0.00 |
| SRR10674734 | whole organism · cold control | whole organism | not recorded | cold control | SRP237293 | 0.00 |
| SRR10674735 | whole organism · cold control | whole organism | not recorded | cold control | SRP237293 | 0.00 |
| SRR10674736 | whole organism · cold control | whole organism | not recorded | cold control | SRP237293 | 0.00 |
| SRR10674737 | whole organism · cold control | whole organism | not recorded | cold control | SRP237293 | 0.00 |
| SRR10674739 | whole organism · cold control | whole organism | not recorded | cold control | SRP237293 | 0.00 |
| SRR10674743 | whole organism · cold control | whole organism | not recorded | cold control | SRP237293 | 0.00 |
| SRR10674746 | whole organism · cold control | whole organism | not recorded | cold control | SRP237293 | 0.00 |
| SRR10674747 | whole organism · cold control | whole organism | not recorded | cold control | SRP237293 | 0.00 |
| SRR10674748 | whole organism · cold control | whole organism | not recorded | cold control | SRP237293 | 0.00 |
| SRR10674750 | whole organism · cold control | whole organism | not recorded | cold control | SRP237293 | 0.00 |
| SRR10674706 | whole organism · heat control | whole organism | not recorded | heat control | SRP237293 | 0.00 |
| SRR10674707 | whole organism · heat control | whole organism | not recorded | heat control | SRP237293 | 0.00 |
| SRR10674708 | whole organism · heat control | whole organism | not recorded | heat control | SRP237293 | 0.00 |
| SRR10674717 | whole organism · heat control | whole organism | not recorded | heat control | SRP237293 | 0.00 |
| SRR10674718 | whole organism · heat control | whole organism | not recorded | heat control | SRP237293 | 0.00 |
| SRR10674720 | whole organism · heat control | whole organism | not recorded | heat control | SRP237293 | 0.00 |
| SRR10674721 | whole organism · heat control | whole organism | not recorded | heat control | SRP237293 | 0.00 |
| SRR10674725 | whole organism · heat control | whole organism | not recorded | heat control | SRP237293 | 0.00 |
| SRR10674731 | whole organism · heat control | whole organism | not recorded | heat control | SRP237293 | 0.00 |
| SRR10674741 | whole organism · heat control | whole organism | not recorded | heat control | SRP237293 | 0.00 |
| SRR10674752 | whole organism · heat control | whole organism | not recorded | heat control | SRP237293 | 0.00 |
| SRR10674753 | whole organism · heat control | whole organism | not recorded | heat control | SRP237293 | 0.00 |
| SRR10674711 | whole organism · cold challenge | whole organism | not recorded | cold challenge | SRP237293 | 0.00 |
| SRR10674712 | whole organism · cold challenge | whole organism | not recorded | cold challenge | SRP237293 | 0.00 |
| SRR10674713 | whole organism · cold challenge | whole organism | not recorded | cold challenge | SRP237293 | 0.00 |
| SRR10674722 | whole organism · cold challenge | whole organism | not recorded | cold challenge | SRP237293 | 0.00 |
| SRR10674723 | whole organism · cold challenge | whole organism | not recorded | cold challenge | SRP237293 | 0.00 |
| SRR10674730 | whole organism · cold challenge | whole organism | not recorded | cold challenge | SRP237293 | 0.00 |
| SRR10674732 | whole organism · cold challenge | whole organism | not recorded | cold challenge | SRP237293 | 0.00 |
| SRR10674738 | whole organism · cold challenge | whole organism | not recorded | cold challenge | SRP237293 | 0.00 |
| SRR10674740 | whole organism · cold challenge | whole organism | not recorded | cold challenge | SRP237293 | 0.00 |
| SRR10674744 | whole organism · cold challenge | whole organism | not recorded | cold challenge | SRP237293 | 0.00 |
| SRR10674745 | whole organism · cold challenge | whole organism | not recorded | cold challenge | SRP237293 | 0.00 |
| SRR10674749 | whole organism · cold challenge | whole organism | not recorded | cold challenge | SRP237293 | 0.00 |
| SRR10674709 | whole organism · heat challenge | whole organism | not recorded | heat challenge | SRP237293 | 0.00 |
| SRR10674710 | whole organism · heat challenge | whole organism | not recorded | heat challenge | SRP237293 | 0.00 |
| SRR10674716 | whole organism · heat challenge | whole organism | not recorded | heat challenge | SRP237293 | 0.00 |
| SRR10674719 | whole organism · heat challenge | whole organism | not recorded | heat challenge | SRP237293 | 0.00 |
| SRR10674726 | whole organism · heat challenge | whole organism | not recorded | heat challenge | SRP237293 | 0.00 |
| SRR10674727 | whole organism · heat challenge | whole organism | not recorded | heat challenge | SRP237293 | 0.00 |
| SRR10674728 | whole organism · heat challenge | whole organism | not recorded | heat challenge | SRP237293 | 0.00 |
| SRR10674729 | whole organism · heat challenge | whole organism | not recorded | heat challenge | SRP237293 | 0.00 |
| SRR10674742 | whole organism · heat challenge | whole organism | not recorded | heat challenge | SRP237293 | 0.00 |
| SRR10674751 | whole organism · heat challenge | whole organism | not recorded | heat challenge | SRP237293 | 0.00 |
| SRR10674754 | whole organism · heat challenge | whole organism | not recorded | heat challenge | SRP237293 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (APOCU_TPM,
StringTie quantification over 49 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 Astrangia poculata 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 Astrangia poculata 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 Astrangia poculata, 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. | 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 → |
