Genomic Location: chr4:15363578...15373639
NR annotation: CAB3993443.1, H ACA ribonucleo complex subunit 4-like [Paramuricea clavata]
Species Eunicella cavolini · all data for this species · gene families
| CDS |
| ENSLDHT00000040841 |
| Protein |
| ENSLDHP00000037595.1 |
| UniProt accession | Description |
|---|---|
| Q9ESX5 | H/ACA ribonucleoprotein complex subunit DKC1 OS=Mus musculus OX=10090 GN=Dkc1 PE=1 SV=4 |
| Q9LD90 | H/ACA ribonucleoprotein complex subunit 4 OS=Arabidopsis thaliana OX=3702 GN=CBF5 PE=1 SV=1 |
| O43102 | H/ACA ribonucleoprotein complex subunit cbf5 OS=Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293) OX=330879 GN=cbf5 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 |
| PF01509 all species → | TruB_N | TruB family pseudouridylate synthase (N terminal domain) | Family | Interproscan |
| PF01472 all species → | PUA | PUA domain | Family | Interproscan |
| PF08068 all species → | DKCLD | DKCLD (NUC011) domain | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR036974 all species → | Homologous_superfamily | PUA domain superfamily | Interproscan |
| IPR015947 all species → | Homologous_superfamily | PUA-like superfamily | Interproscan |
| IPR004802 all species → | Family | tRNA pseudouridine synthase B family | Interproscan |
| IPR012960 all species → | Domain | Dyskerin-like | Interproscan |
| IPR020103 all species → | Homologous_superfamily | Pseudouridine synthase, catalytic domain superfamily | Interproscan |
| IPR032819 all species → | Domain | tRNA pseudouridylate synthase B, C-terminal | Interproscan |
| IPR002501 all species → | Domain | Pseudouridine synthase II, N-terminal | Interproscan |
| IPR004521 all species → | Domain | Uncharacterised domain CHP00451 | Interproscan |
| IPR002478 all species → | Domain | PUA domain | 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:0001522 all species → | Biological Process | pseudouridine synthesis | Interproscan |
| GO:0009451 all species → | Biological Process | RNA modification | Interproscan |
| GO:0009982 all species → | Molecular Function | pseudouridine synthase activity | Interproscan |
| GO:0000495 all species → | Biological Process | box H/ACA sno(s)RNA 3'-end processing | 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 |
| 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 |
Genes whose expression across the transcriptome samples of Eunicella cavolini 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.
No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.
Whether this gene can be visualised in the single-cell atlases of Eunicella cavolini, 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 → |
