Genomic Location: JASJOG010000020.1:2828085...2841997
NR annotation: XP_053405230.1, DNA mismatch repair protein Msh3-like isoform X3 [Mercenaria mercenaria]
Species Heliopora coerulea · all data for this species · gene families
| CDS |
| ENSBQFT00000012544 |
| Protein |
| ENSBQFP00000011306.1 |
| UniProt accession | Description |
|---|---|
| P13705 | DNA mismatch repair protein Msh3 OS=Mus musculus OX=10090 GN=Msh3 PE=2 SV=3 |
| P20585 | DNA mismatch repair protein Msh3 OS=Homo sapiens OX=9606 GN=MSH3 PE=1 SV=4 |
| A4R0R0 | DNA mismatch repair protein MSH3 OS=Pyricularia oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) OX=242507 GN=MSH3 PE=3 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0004789 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF05188 all species → | MutS_II | MutS domain II | Domain | Interproscan |
| PF01624 all species → | MutS_I | MutS domain I | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR045076 all species → | Family | DNA mismatch repair MutS family | Interproscan |
| IPR007860 all species → | Domain | DNA mismatch repair protein MutS, connector domain | Interproscan |
| IPR016151 all species → | Homologous_superfamily | DNA mismatch repair protein MutS, N-terminal | Interproscan |
| IPR036678 all species → | Homologous_superfamily | MutS, connector domain superfamily | Interproscan |
| IPR007695 all species → | Domain | DNA mismatch repair protein MutS-like, N-terminal | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR11361 all species → | DNA MISMATCH REPAIR PROTEIN MUTS FAMILY MEMBER | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0003690 all species → | Molecular Function | double-stranded DNA binding | Interproscan |
| GO:0005524 all species → | Molecular Function | ATP binding | Interproscan |
| GO:0005634 all species → | Cellular Component | nucleus | Interproscan |
| GO:0006298 all species → | Biological Process | mismatch repair | Interproscan |
| GO:0006312 all species → | Biological Process | mitotic recombination | Interproscan |
| GO:0030983 all species → | Molecular Function | mismatched DNA binding | Interproscan |
| GO:0140664 all species → | Molecular Function | ATP-dependent DNA damage sensor activity | Interproscan |
ENSBQFP00000011306.1.Transcript abundance of ENSBQFP00000011306.1 across 37 RNA-seq samples of Heliopora coerulea. 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 | 10 | 1.99 | 5.11 | |
| polyp and skeleton · 31C, 3week | 6 | 6 | 5.41 | 8.95 | |
| polyp and skeleton · 28C, 3week | 6 | 4 | 3.82 | 7.16 | |
| polyp and skeleton · 26C, 3week | 4 | 2 | 3.60 | 10.11 | |
| polyp and skeleton · 28C, 24hr | 2 | 2 | 6.54 | 8.55 | |
| polyp and skeleton · 31C, 24hr | 2 | 1 | 2.90 | 5.81 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| ERR6178388 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 5.11 |
| ERR6178770 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 3.83 |
| ERR6178783 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 3.73 |
| ERR6178389 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 3.62 |
| ERR6178776 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 3.41 |
| ERR6178778 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 3.40 |
| ERR6178773 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 3.21 |
| ERR6178781 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 2.55 |
| ERR6178774 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 2.50 |
| ERR6178779 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 2.43 |
| ERR6178387 | 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 |
| ERR6178775 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178777 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178780 | Whole coral | Whole coral | not recorded | not recorded | ERP120267 | 0.00 |
| ERR6178782 | 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 | 8.95 |
| SRR12587804 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 6.62 |
| SRR12578068 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 6.32 |
| SRR12578066 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 3.82 |
| SRR12587799 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 3.49 |
| SRR12587800 | polyp and skeleton · 31C, 3week | polyp and skeleton | not recorded | 31C, 3week | SRP115860 | 3.27 |
| SRR12587802 | polyp and skeleton · 28C, 3week | polyp and skeleton | not recorded | 28C, 3week | SRP115860 | 7.16 |
| SRR12587803 | polyp and skeleton · 28C, 3week | polyp and skeleton | not recorded | 28C, 3week | SRP115860 | 6.41 |
| SRR12587807 | polyp and skeleton · 28C, 3week | polyp and skeleton | not recorded | 28C, 3week | SRP115860 | 5.31 |
| SRR12587808 | polyp and skeleton · 28C, 3week | polyp and skeleton | not recorded | 28C, 3week | SRP115860 | 4.02 |
| SRR12578067 | 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 | 10.11 |
| SRR12587805 | polyp and skeleton · 26C, 3week | polyp and skeleton | not recorded | 26C, 3week | SRP115860 | 4.28 |
| SRR12587801 | 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 |
| SRR5949850 | polyp and skeleton · 28C, 24hr | polyp and skeleton | not recorded | 28C, 24hr | SRP115860 | 8.55 |
| SRR12578063 | polyp and skeleton · 28C, 24hr | polyp and skeleton | not recorded | 28C, 24hr | SRP115860 | 4.52 |
| SRR12578064 | polyp and skeleton · 31C, 24hr | polyp and skeleton | not recorded | 31C, 24hr | SRP115860 | 5.81 |
| 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 | 22 | ENSBQFP00000050438 | 0.881475131039109 |
| Negatively correlated | 5 | ENSBQFP00000034671 | -0.694324796387231 |
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. Partner counts were matched on ENSBQFP00000011306, the spelling this network uses.
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. | 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 → |
