Genomic Location: JASJOG010000057.1:843573...858560
NR annotation: XP_028393087.1, LOW QUALITY PROTEIN: DNA ligase 4-like [Dendronephthya gigantea]
Species Heliopora coerulea · all data for this species · gene families
| CDS |
| ENSBQFT00000029776 |
| Protein |
| ENSBQFP00000026603.1 |
| UniProt accession | Description |
|---|---|
| Q90YB1 | DNA ligase 4 OS=Gallus gallus OX=9031 GN=LIG4 PE=2 SV=2 |
| P49917 | DNA ligase 4 OS=Homo sapiens OX=9606 GN=LIG4 PE=1 SV=2 |
| Q5R6L3 | DNA ligase 4 OS=Pongo abelii OX=9601 GN=LIG4 PE=2 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0002879 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF04675 all species → | DNA_ligase_A_N | DNA ligase N terminus | Family | Interproscan |
| PF04679 all species → | DNA_ligase_A_C | ATP dependent DNA ligase C terminal region | Family | Interproscan |
| PF11411 all species → | DNA_ligase_IV | DNA ligase IV | Family | Interproscan |
| PF01068 all species → | DNA_ligase_A_M | ATP dependent DNA ligase domain | Domain | Interproscan |
| PF16589 all species → | BRCT_2 | BRCT domain, a BRCA1 C-terminus domain | Family | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR012340 all species → | Homologous_superfamily | Nucleic acid-binding, OB-fold | Interproscan |
| IPR012308 all species → | Domain | DNA ligase, ATP-dependent, N-terminal | Interproscan |
| IPR036420 all species → | Homologous_superfamily | BRCT domain superfamily | Interproscan |
| IPR036599 all species → | Homologous_superfamily | DNA ligase, ATP-dependent, N-terminal domain superfamily | Interproscan |
| IPR001357 all species → | Domain | BRCT domain | Interproscan |
| IPR012309 all species → | Domain | DNA ligase, ATP-dependent, C-terminal | Interproscan |
| IPR044125 all species → | Domain | DNA Ligase 4, adenylation domain | Interproscan |
| IPR000977 all species → | Family | DNA ligase, ATP-dependent | Interproscan |
| IPR029710 all species → | Family | DNA ligase 4 | Interproscan |
| IPR021536 all species → | Domain | DNA ligase IV domain | Interproscan |
| IPR012310 all species → | Domain | DNA ligase, ATP-dependent, central | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR45997 all species → | DNA LIGASE 4 | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0003677 all species → | Molecular Function | DNA binding | Interproscan |
| GO:0003910 all species → | Molecular Function | DNA ligase (ATP) activity | Interproscan |
| GO:0006281 all species → | Biological Process | DNA repair | Interproscan |
| GO:0006310 all species → | Biological Process | DNA recombination | Interproscan |
| GO:0005524 all species → | Molecular Function | ATP binding | Interproscan |
| GO:0071897 all species → | Biological Process | DNA biosynthetic process | Interproscan |
| GO:0005958 all species → | Cellular Component | DNA-dependent protein kinase-DNA ligase 4 complex | Interproscan |
| GO:0006297 all species → | Biological Process | nucleotide-excision repair, DNA gap filling | Interproscan |
| GO:0006303 all species → | Biological Process | double-strand break repair via nonhomologous end joining | Interproscan |
| GO:0032807 all species → | Cellular Component | DNA ligase IV complex | Interproscan |
| GO:0051103 all species → | Biological Process | DNA ligation involved in DNA repair | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K10777 | LIG4, DNL4; DNA ligase 4 | EC:6.5.1.1 | DNA repair and recombination proteins | ko03400 | deepkoala |
Transcript abundance of ENSBQFP00000026603.1 across 37 RNA-seq samples of Heliopora coerulea. 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 coral | 17 | 0 | 0.00 | 0.00 | |
| polyp and skeleton · 31C, 3week | 6 | 0 | 0.00 | 0.00 | |
| polyp and skeleton · 28C, 3week | 6 | 0 | 0.00 | 0.00 | |
| polyp and skeleton · 26C, 3week | 4 | 0 | 0.00 | 0.00 | |
| polyp and skeleton · 28C, 24hr | 2 | 0 | 0.00 | 0.00 | |
| polyp and skeleton · 31C, 24hr | 2 | 0 | 0.00 | 0.00 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| ERR6178387 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178388 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178389 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178770 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178771 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178772 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178773 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178774 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178775 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178776 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178777 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178778 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178779 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178780 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178781 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178782 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178783 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| SRR12578065 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 0.00 |
| SRR12578066 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 0.00 |
| SRR12578068 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 0.00 |
| SRR12587799 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 0.00 |
| SRR12587800 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 0.00 |
| SRR12587804 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 0.00 |
| SRR12578067 | polyp and skeleton · 28C, 3week | polyp and skeleton | not recorded | 28C, 3week | SRP115860 | 0.00 |
| SRR12587802 | polyp and skeleton · 28C, 3week | polyp and skeleton | not recorded | 28C, 3week | SRP115860 | 0.00 |
| SRR12587803 | polyp and skeleton · 28C, 3week | polyp and skeleton | not recorded | 28C, 3week | SRP115860 | 0.00 |
| SRR12587807 | polyp and skeleton · 28C, 3week | polyp and skeleton | not recorded | 28C, 3week | SRP115860 | 0.00 |
| SRR12587808 | polyp and skeleton · 28C, 3week | polyp and skeleton | not recorded | 28C, 3week | SRP115860 | 0.00 |
| SRR5949849 | polyp and skeleton · 28C, 3week | polyp and skeleton | not recorded | 28C, 3week | SRP115860 | 0.00 |
| SRR12587798 | polyp and skeleton · 26C, 3week | polyp and skeleton | not recorded | 26C, 3week | SRP115860 | 0.00 |
| SRR12587801 | polyp and skeleton · 26C, 3week | polyp and skeleton | not recorded | 26C, 3week | SRP115860 | 0.00 |
| SRR12587805 | polyp and skeleton · 26C, 3week | polyp and skeleton | not recorded | 26C, 3week | SRP115860 | 0.00 |
| SRR12587806 | polyp and skeleton · 26C, 3week | polyp and skeleton | not recorded | 26C, 3week | SRP115860 | 0.00 |
| SRR12578063 | polyp and skeleton · 28C, 24hr | polyp and skeleton | not recorded | 28C, 24hr | SRP115860 | 0.00 |
| SRR5949850 | polyp and skeleton · 28C, 24hr | polyp and skeleton | not recorded | 28C, 24hr | SRP115860 | 0.00 |
| SRR12578064 | polyp and skeleton · 31C, 24hr | polyp and skeleton | not recorded | 31C, 24hr | SRP115860 | 0.00 |
| SRR5949848 | polyp and skeleton · 31C, 24hr | polyp and skeleton | not recorded | 31C, 24hr | SRP115860 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (HCOER_TPM,
StringTie quantification over 37 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 Heliopora coerulea 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 Heliopora coerulea 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 Heliopora coerulea, 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 → |
