Genomic Location: chr8:52057803...52063183
NR annotation: XP_029196064.1, CCA tRNA nucleotidyltransferase 1, mitochondrial-like [Acropora millepora]
Species Montipora foliosa · all data for this species · gene families
| CDS |
| LOC137967633 |
| Transcript |
| rna-XM_068814151.1 |
| Protein |
| XP_068670252.1 |
| UniProt accession | Description |
|---|---|
| F6NXI9 | CCA tRNA nucleotidyltransferase 1, mitochondrial OS=Danio rerio OX=7955 GN=trnt1 PE=2 SV=1 |
| Q8K1J6 | CCA tRNA nucleotidyltransferase 1, mitochondrial OS=Mus musculus OX=10090 GN=Trnt1 PE=1 SV=1 |
| Q96Q11 | CCA tRNA nucleotidyltransferase 1, mitochondrial OS=Homo sapiens OX=9606 GN=TRNT1 PE=1 SV=2 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0007822 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF12627 all species → | PolyA_pol_RNAbd | Probable RNA and SrmB- binding site of polymerase A | Domain | Interproscan |
| PF01743 all species → | PolyA_pol | Poly A polymerase head domain | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR032828 all species → | Domain | tRNA nucleotidyltransferase/poly(A) polymerase, RNA and SrmB- binding domain | Interproscan |
| IPR043519 all species → | Homologous_superfamily | Nucleotidyltransferase superfamily | Interproscan |
| IPR002646 all species → | Domain | Poly A polymerase, head domain | Interproscan |
| IPR050264 all species → | Family | Bacterial CCA-adding enzyme type 3 subfamily | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR46173 all species → | CCA TRNA NUCLEOTIDYLTRANSFERASE 1, MITOCHONDRIAL | 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:0016779 all species → | Molecular Function | nucleotidyltransferase activity | Interproscan |
| GO:0000049 all species → | Molecular Function | tRNA binding | Interproscan |
| GO:0001680 all species → | Biological Process | tRNA 3'-terminal CCA addition | Interproscan |
| GO:0005739 all species → | Cellular Component | mitochondrion | Interproscan |
| GO:0008033 all species → | Biological Process | tRNA processing | Interproscan |
| GO:1990180 all species → | Biological Process | mitochondrial tRNA 3'-end processing | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K00974 | cca; tRNA nucleotidyltransferase (CCA-adding enzyme) | EC:2.7.7.72 EC:3.1.3.- EC:3.1.4.- | Transfer RNA biogenesis | ko03016 | deepkoala |
Transcript abundance of XP_068670252.1 across 36 RNA-seq samples of Montipora foliosa. 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 | 36 | 26 | 7.65 | 13.72 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR12959226 | Polyps | Polyps | E4 day3 | not recorded | SRP199550 | 13.72 |
| SRR12710866 | Polyps | Polyps | OA4 day3 | not recorded | SRP199550 | 13.63 |
| SRR12710865 | Polyps | Polyps | OA4 day3 | not recorded | SRP199550 | 13.06 |
| SRR12710845 | Polyps | Polyps | OA4 day3 | not recorded | SRP199550 | 12.89 |
| SRR12959212 | Polyps | Polyps | E4 day9 | not recorded | SRP199550 | 12.52 |
| SRR12786895 | Polyps | Polyps | OA4 day0 | not recorded | SRP199550 | 12.07 |
| SRR12904780 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 11.86 |
| SRR27940180 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 11.71 |
| SRR12786904 | Polyps | Polyps | OA4 day0 | not recorded | SRP199550 | 11.69 |
| SRR12959225 | Polyps | Polyps | E4 day3 | not recorded | SRP199550 | 11.66 |
| SRR12904791 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 10.58 |
| SRR27940177 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 10.46 |
| SRR12959200 | Polyps | Polyps | E4 day15 | not recorded | SRP199550 | 10.31 |
| SRR12959224 | Polyps | Polyps | E4 day3 | not recorded | SRP199550 | 10.27 |
| SRR12959213 | Polyps | Polyps | E4 day9 | not recorded | SRP199550 | 10.22 |
| SRR12959198 | Polyps | Polyps | E4 day15 | not recorded | SRP199550 | 10.14 |
| SRR27940179 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 10.11 |
| SRR12710852 | Polyps | Polyps | OA4 day9 | not recorded | SRP199550 | 10.10 |
| SRR12959238 | Polyps | Polyps | E4 day0 | not recorded | SRP199550 | 10.06 |
| SRR12904792 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 9.98 |
| SRR12959181 | Polyps | Polyps | E4 day0 | not recorded | SRP199550 | 9.87 |
| SRR12959199 | Polyps | Polyps | E4 day15 | not recorded | SRP199550 | 9.57 |
| SRR12959237 | Polyps | Polyps | E4 day0 | not recorded | SRP199550 | 9.44 |
| SRR12710853 | Polyps | Polyps | OA4 day9 | not recorded | SRP199550 | 7.01 |
| SRR12959187 | Polyps | Polyps | E4 day21 | not recorded | SRP199550 | 6.49 |
| SRR12959185 | Polyps | Polyps | E4 day21 | not recorded | SRP199550 | 6.04 |
| SRR12710854 | Polyps | Polyps | OA4 day9 | not recorded | SRP199550 | 0.00 |
| SRR12786903 | Polyps | Polyps | OA4 day0 | not recorded | SRP199550 | 0.00 |
| SRR12807380 | Polyps | Polyps | OA4 day0 | not recorded | SRP199550 | 0.00 |
| SRR12849112 | Polyps | Polyps | OA4 day0 | not recorded | SRP199550 | 0.00 |
| SRR12927879 | Polyps | Polyps | E4 day0 | not recorded | SRP199550 | 0.00 |
| SRR12959186 | Polyps | Polyps | E4 day21 | not recorded | SRP199550 | 0.00 |
| SRR12959211 | Polyps | Polyps | E4 day9 | not recorded | SRP199550 | 0.00 |
| SRR12963483 | Polyps | Polyps | E4 day0 | not recorded | SRP199550 | 0.00 |
| SRR9129315 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 0.00 |
| SRR9613518 | Polyps | Polyps | not recorded | not recorded | SRP199550 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (MFOLI_TPM,
StringTie quantification over 36 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 Montipora foliosa 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 | 24 | XP_068713691.1 | 0.944202338936967 |
| Negatively correlated | 3 | XP_068681185.1 | -0.42596079460201 |
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 Montipora foliosa, 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 → |
