Genomic Location: chr12Alt:7146285...7163507
NR annotation: XP_029201075.2, polycomb protein Scm-like isoform X1 [Acropora millepora]
Species Acropora digitifera · all data for this species · gene families
| CDS |
| g25550.t2 |
| Transcript |
| chr12Alt.g25550.t2 |
| Protein |
| chr12Alt.g25550.t2 |
| UniProt accession | Description |
|---|---|
| Q8K214 | Polycomb protein SCMH1 OS=Mus musculus OX=10090 GN=Scmh1 PE=1 SV=1 |
| Q96GD3 | Polycomb protein SCMH1 OS=Homo sapiens OX=9606 GN=SCMH1 PE=1 SV=1 |
| Q9UQR0 | Sex comb on midleg-like protein 2 OS=Homo sapiens OX=9606 GN=SCML2 PE=1 SV=1 |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF00536 all species → | SAM_1 | SAM domain (Sterile alpha motif) | Domain | Interproscan |
| PF12140 all species → | SLED | SLED domain | Domain | Interproscan |
| PF02820 all species → | MBT | mbt repeat | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR001660 all species → | Domain | Sterile alpha motif domain | Interproscan |
| IPR004092 all species → | Repeat | Mbt repeat | Interproscan |
| IPR050548 all species → | Family | Polycomb group and chromatin remodeling factors | Interproscan |
| IPR038348 all species → | Homologous_superfamily | SLED domain superfamily | Interproscan |
| IPR021987 all species → | Domain | SLED domain | Interproscan |
| IPR013761 all species → | Homologous_superfamily | Sterile alpha motif/pointed domain superfamily | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR12247 all species → | POLYCOMB GROUP PROTEIN | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0005515 all species → | Molecular Function | protein binding | Interproscan |
| GO:0005634 all species → | Cellular Component | nucleus | Interproscan |
| GO:0006355 all species → | Biological Process | regulation of DNA-templated transcription | Interproscan |
| GO:0003682 all species → | Molecular Function | chromatin binding | Interproscan |
| GO:0042393 all species → | Molecular Function | histone binding | Interproscan |
| GO:0045892 all species → | Biological Process | negative regulation of DNA-templated transcription | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K11461 | SCMH1; polycomb protein SCMH1 | - | Chromosome and associated proteins | ko03036 | deepkoala |
Transcript abundance of g25550.t2 across 39 RNA-seq samples of Acropora digitifera. 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 |
|---|---|---|---|---|---|
| Coral branch | 39 | 0 | 0.00 | 0.00 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR23047206 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047207 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047208 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047209 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047210 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047211 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047212 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047213 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047214 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047215 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047216 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047217 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047218 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047219 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047220 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047221 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047222 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047223 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047224 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047225 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047226 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047227 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047228 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047229 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047230 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047231 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047232 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047233 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047234 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047235 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047236 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047237 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047238 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047239 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047240 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047241 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047242 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047243 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
| SRR23047244 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (ADIGI_TPM,
StringTie quantification over 39 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 Acropora digitifera 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 Acropora digitifera 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 Acropora digitifera, 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.
| Assay | Sample | Peaks | Region |
|---|
No called peak overlaps this gene in 1 available assay. Either the gene is not near an accessible or marked region in those samples, or it is not represented in the peak caller’s annotation.
Browse the full epigenomic landscape of this species: DNase-seq (DHS).
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 → |
