Genomic Location: chr12Alt:948593...956272
NR annotation: XP_015773193.1, PREDICTED: zinc finger CCHC-type and RNA-binding motif-containing protein 1-like [Acropora digitifera]
Species Acropora digitifera · all data for this species · gene families
| CDS |
| g25048.t1 |
| Transcript |
| chr12Alt.g25048.t1 |
| Protein |
| chr12Alt.g25048.t1 |
| UniProt accession | Description |
|---|---|
| Q499V6 | Zinc finger CCHC-type and RNA-binding motif-containing protein 1 OS=Rattus norvegicus OX=10116 GN=Zcrb1 PE=2 SV=1 |
| Q6DJI9 | Zinc finger CCHC-type and RNA-binding motif-containing protein 1 OS=Xenopus laevis OX=8355 GN=zcrb1 PE=2 SV=1 |
| Q9CZ96 | Zinc finger CCHC-type and RNA-binding motif-containing protein 1 OS=Mus musculus OX=10090 GN=Zcrb1 PE=1 SV=1 |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF00098 all species → | zf-CCHC | Zinc knuckle | Domain | Interproscan |
| PF00076 all species → | RRM_1 | RNA recognition motif | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR001878 all species → | Domain | Zinc finger, CCHC-type | Interproscan |
| IPR036875 all species → | Homologous_superfamily | Zinc finger, CCHC-type superfamily | Interproscan |
| IPR044598 all species → | Family | Zinc finger CCHC-type and RNA-binding motif-containing protein 1 | Interproscan |
| IPR000504 all species → | Domain | RNA recognition motif domain | Interproscan |
| IPR012677 all species → | Homologous_superfamily | Nucleotide-binding alpha-beta plait domain superfamily | Interproscan |
| IPR034219 all species → | Domain | ZCRB1, RNA recognition motif | Interproscan |
| IPR035979 all species → | Homologous_superfamily | RNA-binding domain superfamily | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR46259 all species → | ZINC FINGER CCHC-TYPE AND RNA-BINDING MOTIF-CONTAINING PROTEIN 1 | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0003676 all species → | Molecular Function | nucleic acid binding | Interproscan |
| GO:0008270 all species → | Molecular Function | zinc ion binding | Interproscan |
| GO:0000398 all species → | Biological Process | mRNA splicing, via spliceosome | Interproscan |
| GO:0005689 all species → | Cellular Component | U12-type spliceosomal complex | Interproscan |
| GO:0003723 all species → | Molecular Function | RNA binding | Interproscan |
| KO | Enzyme | Enzyme ID | Pathway | Map ID | Source |
|---|---|---|---|---|---|
| K13154 | ZCRB1; U11/U12 small nuclear ribonucleoprotein 31 kDa protein | - | Spliceosome | ko03041 | deepkoala |
Transcript abundance of g25048.t1 across 39 RNA-seq samples of Acropora digitifera. 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 | 39 | 62.41 | 90.87 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR23047244 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 90.87 |
| SRR23047222 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 83.83 |
| SRR23047243 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 83.51 |
| SRR23047220 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 81.39 |
| SRR23047210 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 79.99 |
| SRR23047221 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 74.56 |
| SRR23047237 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 74.12 |
| SRR23047208 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 73.73 |
| SRR23047236 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 73.62 |
| SRR23047207 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 72.65 |
| SRR23047216 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 72.04 |
| SRR23047219 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 71.86 |
| SRR23047223 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 69.62 |
| SRR23047213 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 65.40 |
| SRR23047226 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 64.29 |
| SRR23047218 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 63.89 |
| SRR23047239 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 63.10 |
| SRR23047209 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 60.17 |
| SRR23047233 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 59.41 |
| SRR23047211 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 58.74 |
| SRR23047232 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 58.73 |
| SRR23047224 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 58.60 |
| SRR23047228 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 57.21 |
| SRR23047225 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 56.21 |
| SRR23047238 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 56.15 |
| SRR23047235 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 55.59 |
| SRR23047212 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 55.59 |
| SRR23047242 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 54.01 |
| SRR23047229 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 53.87 |
| SRR23047240 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 52.24 |
| SRR23047234 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 51.85 |
| SRR23047214 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 51.23 |
| SRR23047241 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 50.61 |
| SRR23047217 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 50.56 |
| SRR23047227 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 50.48 |
| SRR23047206 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 48.10 |
| SRR23047215 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 47.97 |
| SRR23047231 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 46.69 |
| SRR23047230 | Coral branch | Coral branch | adult | not recorded | SRP416931 | 41.49 |
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 | 21 | g7924.t1 | 0.839189108382968 |
| Negatively correlated | 36 | g16226.t1 | -0.855480569061067 |
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. | 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 → |
