Genomic Location: QPEY01000017.1:323645...342924
NR annotation: CRX73263.1, Hemicentin 1-like 2 [Hydra vulgaris]
Species Hydra viridissima · all data for this species · gene families
| CDS |
| BRAKERKRET00000005338 |
| Transcript |
| BRAKERKRET00000005338 |
| Protein |
| BRAKERKREP00000005338.1 |
| UniProt accession | Description |
|---|---|
| Q05793 | Basement membrane-specific heparan sulfate proteoglycan core protein OS=Mus musculus OX=10090 GN=Hspg2 PE=1 SV=1 |
| P98160 | Basement membrane-specific heparan sulfate proteoglycan core protein OS=Homo sapiens OX=9606 GN=HSPG2 PE=1 SV=4 |
| Q06561 | Basement membrane proteoglycan OS=Caenorhabditis elegans OX=6239 GN=unc-52 PE=1 SV=2 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0001076 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF13927 all species → | Ig_3 | Immunoglobulin domain | Domain | Interproscan |
| PF07679 all species → | I-set | Immunoglobulin I-set domain | Domain | Interproscan |
| PF13385 all species → | Laminin_G_3 | Concanavalin A-like lectin/glucanases superfamily | Domain | Interproscan |
| PF00053 all species → | Laminin_EGF | Laminin EGF domain | Domain | Interproscan |
| PF00052 all species → | Laminin_B | Laminin B (Domain IV) | Domain | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR013320 all species → | Homologous_superfamily | Concanavalin A-like lectin/glucanase domain superfamily | Interproscan |
| IPR002049 all species → | Domain | Laminin-type EGF domain | Interproscan |
| IPR013783 all species → | Homologous_superfamily | Immunoglobulin-like fold | Interproscan |
| IPR036179 all species → | Homologous_superfamily | Immunoglobulin-like domain superfamily | Interproscan |
| IPR036116 all species → | Homologous_superfamily | Fibronectin type III superfamily | Interproscan |
| IPR003598 all species → | Domain | Immunoglobulin subtype 2 | Interproscan |
| IPR003599 all species → | Domain | Immunoglobulin subtype | Interproscan |
| IPR007110 all species → | Domain | Immunoglobulin-like domain | Interproscan |
| IPR013098 all species → | Domain | Immunoglobulin I-set | Interproscan |
| IPR000742 all species → | Domain | EGF-like domain | Interproscan |
| IPR000034 all species → | Domain | Laminin IV | Interproscan |
| IPR050440 all species → | Family | Laminin/Netrin Extracellular Matrix | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR10574 all species → | NETRIN/LAMININ-RELATED | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0005515 all species → | Molecular Function | protein binding | Interproscan |
| GO:0001738 all species → | Biological Process | morphogenesis of a polarized epithelium | Interproscan |
| GO:0005178 all species → | Molecular Function | integrin binding | Interproscan |
| GO:0005604 all species → | Cellular Component | basement membrane | Interproscan |
| GO:0005610 all species → | Cellular Component | laminin-5 complex | Interproscan |
| GO:0009887 all species → | Biological Process | animal organ morphogenesis | Interproscan |
| GO:0009888 all species → | Biological Process | tissue development | Interproscan |
| GO:0016477 all species → | Biological Process | cell migration | Interproscan |
| GO:0098609 all species → | Biological Process | cell-cell adhesion | Interproscan |
BRAKERKREP00000005338.1.Transcript abundance of BRAKERKREP00000005338.1 across 29 RNA-seq samples of Hydra viridissima. 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 body | 18 | 9 | 4.74 | 27.42 | |
| Whole | 6 | 6 | 12.96 | 16.30 | |
| aposymbioic hydra M9 strain · aposymbioic hydra rep1 | 1 | 1 | 14.52 | 14.52 | |
| aposymbioic hydra M9 strain · aposymbioic hydra rep2 | 1 | 1 | 11.42 | 11.42 | |
| symbioic hydra M9 strain · symbioic hydra rep1 | 1 | 1 | 5.67 | 5.67 | |
| symbioic hydra M9 strain · symbioic hydra rep2 | 1 | 1 | 5.57 | 5.57 | |
| unannotated | 1 | 0 | 0.00 | 0.00 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| SRR21134050 | whole body | whole body | not recorded | not recorded | SRP392977 | 27.42 |
| SRR21134060 | whole body | whole body | not recorded | not recorded | SRP392977 | 13.93 |
| SRR21134052 | whole body | whole body | not recorded | not recorded | SRP392977 | 12.86 |
| SRR21134064 | whole body | whole body | not recorded | not recorded | SRP392977 | 11.54 |
| SRR21134057 | whole body | whole body | not recorded | not recorded | SRP392977 | 6.60 |
| SRR21134066 | whole body | whole body | not recorded | not recorded | SRP392977 | 4.89 |
| SRR21134054 | whole body | whole body | not recorded | not recorded | SRP392977 | 3.46 |
| SRR21134055 | whole body | whole body | not recorded | not recorded | SRP392977 | 2.96 |
| SRR21134056 | whole body | whole body | not recorded | not recorded | SRP392977 | 1.71 |
| SRR21134051 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134053 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134058 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134059 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134061 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134062 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134063 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134065 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR21134067 | whole body | whole body | not recorded | not recorded | SRP392977 | 0.00 |
| SRR10058803 | Whole | Whole | not recorded | not recorded | SRP220397 | 16.30 |
| SRR10058807 | Whole | Whole | not recorded | not recorded | SRP220397 | 14.09 |
| SRR10058804 | Whole | Whole | not recorded | not recorded | SRP220397 | 13.88 |
| SRR10058806 | Whole | Whole | not recorded | not recorded | SRP220397 | 13.48 |
| SRR10058805 | Whole | Whole | not recorded | not recorded | SRP220397 | 12.89 |
| SRR10058802 | Whole | Whole | not recorded | not recorded | SRP220397 | 7.09 |
| DRR048593 | aposymbioic hydra M9 strain · aposymbioic hydra rep1 | not recorded | not recorded | aposymbioic hydra rep1 | DRP003902 | 14.52 |
| DRR048594 | aposymbioic hydra M9 strain · aposymbioic hydra rep2 | not recorded | not recorded | aposymbioic hydra rep2 | DRP003902 | 11.42 |
| DRR048595 | symbioic hydra M9 strain · symbioic hydra rep1 | not recorded | not recorded | symbioic hydra rep1 | DRP003902 | 5.67 |
| DRR048596 | symbioic hydra M9 strain · symbioic hydra rep2 | not recorded | not recorded | symbioic hydra rep2 | DRP003902 | 5.57 |
| ERR13389755 | unannotated | not recorded | not recorded | not recorded | ERP162636 | 0.00 |
Source: CnidoSite RNA-seq expression matrices (HVIRI_TPM,
StringTie quantification over 29 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 Hydra viridissima 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 | 14 | 23954_g | 0.931241408146213 |
| Negatively correlated | 3 | BRAKERKREP00000024112.1 | -0.656355621718544 |
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 Hydra viridissima, 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 → |
