Genomic Location: sc0000002_pilon:2861037...2873121
NR annotation: XP_044173668.1, LOW QUALITY PROTEIN: protocadherin Fat 4-like [Acropora millepora]
Species Acropora gemmifera · all data for this species · gene families
| CDS |
| agem_s0002.g218.t1 |
| Transcript |
| agem_s0002.g218.t1 |
| Protein |
| agem_s0002.g218.t1 |
| UniProt accession | Description |
|---|---|
| C0HL13 | Low-density lipoprotein receptor-related protein 2 OS=Sus scrofa OX=9823 GN=LRP2 PE=1 SV=1 |
| G3V928 | Prolow-density lipoprotein receptor-related protein 1 OS=Rattus norvegicus OX=10116 GN=Lrp1 PE=1 SV=1 |
| P98157 | Low-density lipoprotein receptor-related protein 1 OS=Gallus gallus OX=9031 GN=LRP1 PE=2 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0009736 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF00028 all species → | Cadherin | Cadherin domain | Domain | Interproscan |
| PF12662 all species → | cEGF | Complement Clr-like EGF-like | Domain | Interproscan |
| PF12947 all species → | EGF_3 | EGF domain | Domain | Interproscan |
| PF14670 all species → | FXa_inhibition | Coagulation Factor Xa inhibitory site | Domain | Interproscan |
| PF00008 all species → | EGF | EGF-like domain | Domain | Interproscan |
| PF07645 all species → | EGF_CA | Calcium-binding EGF domain | Domain | Interproscan |
| PF00058 all species → | Ldl_recept_b | Low-density lipoprotein receptor repeat class B | Repeat | Interproscan |
| PF12661 all species → | hEGF | Human growth factor-like EGF | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR039808 all species → | Family | Cadherin | Interproscan |
| IPR011042 all species → | Homologous_superfamily | Six-bladed beta-propeller, TolB-like | Interproscan |
| IPR000742 all species → | Domain | EGF-like domain | Interproscan |
| IPR015919 all species → | Homologous_superfamily | Cadherin-like superfamily | Interproscan |
| IPR002126 all species → | Domain | Cadherin-like | Interproscan |
| IPR026823 all species → | Domain | Complement Clr-like EGF domain | Interproscan |
| IPR000152 all species → | PTM | EGF-type aspartate/asparagine hydroxylation site | Interproscan |
| IPR009030 all species → | Homologous_superfamily | Growth factor receptor cysteine-rich domain superfamily | Interproscan |
| IPR000436 all species → | Domain | Sushi/SCR/CCP domain | Interproscan |
| IPR000033 all species → | Repeat | LDLR class B repeat | Interproscan |
| IPR018097 all species → | Conserved_site | EGF-like calcium-binding, conserved site | Interproscan |
| IPR024731 all species → | Domain | EGF domain | Interproscan |
| IPR002049 all species → | Domain | Laminin-type EGF domain | Interproscan |
| IPR035976 all species → | Homologous_superfamily | Sushi/SCR/CCP superfamily | Interproscan |
| IPR049883 all species → | Domain | NOTCH1 EGF-like calcium-binding domain | Interproscan |
| IPR001881 all species → | Domain | EGF-like calcium-binding domain | Interproscan |
| IPR013032 all species → | Conserved_site | EGF-like, conserved site | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR24027 all species → | CADHERIN-23 | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0000902 all species → | Biological Process | cell morphogenesis | Interproscan |
| GO:0005509 all species → | Molecular Function | calcium ion binding | Interproscan |
| GO:0005912 all species → | Cellular Component | adherens junction | Interproscan |
| GO:0007043 all species → | Biological Process | cell-cell junction assembly | Interproscan |
| GO:0007275 all species → | Biological Process | multicellular organism development | Interproscan |
| GO:0016339 all species → | Biological Process | calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules | Interproscan |
| GO:0016342 all species → | Cellular Component | catenin complex | Interproscan |
| GO:0034332 all species → | Biological Process | adherens junction organization | Interproscan |
| GO:0044331 all species → | Biological Process | cell-cell adhesion mediated by cadherin | Interproscan |
| GO:0045296 all species → | Molecular Function | cadherin binding | Interproscan |
| GO:0098609 all species → | Biological Process | cell-cell adhesion | Interproscan |
| GO:0098742 all species → | Biological Process | cell-cell adhesion via plasma-membrane adhesion molecules | Interproscan |
| GO:0016020 all species → | Cellular Component | membrane | Interproscan |
| GO:0007156 all species → | Biological Process | homophilic cell adhesion via plasma membrane adhesion molecules | Interproscan |
agem_s0002.g218.t1.Transcript abundance of agem_s0002.g218.t1 across 48 RNA-seq samples of Acropora gemmifera. 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 |
|---|---|---|---|---|---|
| branch tip | 48 | 3 | 1.25 | 24.40 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR2169558 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 24.40 |
| SRR3223317 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 22.04 |
| SRR3223319 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 13.33 |
| SRR3169421 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169422 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169423 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169425 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169426 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169518 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169527 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169528 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169529 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169530 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169531 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169532 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169533 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169534 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169535 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169536 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169537 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169538 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169539 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169540 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3169541 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182410 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182448 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182557 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182684 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182685 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182686 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182775 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182776 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182777 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182778 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182779 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182780 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182781 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182784 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182785 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182786 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182787 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182788 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182789 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182790 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182791 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182792 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182793 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
| SRR3182794 | branch tip | branch tip | not recorded | not recorded | SRP062488 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (AGEMM_TPM,
StringTie quantification over 48 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 gemmifera 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 | 12 | agem_s0017.g136.t1 | 0.999999766691773 |
| Negatively correlated | 3 | agem_s0028.g73.t1 | -0.60164883131578 |
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 gemmifera, 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 → |
