Genomic Location: NW_027103566.1:297598...299712
NR annotation: MBM78604.1, D-alanine--D-alanine ligase [Crocinitomicaceae bacterium]
Species Clytia hemisphaerica · all data for this species · gene families
| CDS |
| XP_066913774.1 |
| Protein |
| XP_066913774.1 |
| UniProt accession | Description |
|---|---|
| Q5LI31 | D-alanine--D-alanine ligase OS=Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2) OX=272559 GN=ddl PE=3 SV=1 |
| Q64Z37 | D-alanine--D-alanine ligase OS=Bacteroides fragilis (strain YCH46) OX=295405 GN=ddl PE=3 SV=1 |
| A6LFD0 | D-alanine--D-alanine ligase OS=Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152) OX=435591 GN=ddl PE=3 SV=1 |
| Family type | Membership / link |
|---|---|
| Orthogroup (gene family) | OG0018304 (this species only) · gene tree & orthology |
| Pfam accession | Pfam name | Description | Type | Source |
|---|---|---|---|---|
| PF07478 all species → | Dala_Dala_lig_C | D-ala D-ala ligase C-terminus | Family | Interproscan |
| PF01820 all species → | Dala_Dala_lig_N | D-ala D-ala ligase N-terminus | Family | Interproscan |
| InterPro term | Type | Description | Source |
|---|---|---|---|
| IPR005905 all species → | Family | D-alanine--D-alanine ligase | Interproscan |
| IPR000291 all species → | Conserved_site | D-alanine--D-alanine ligase/VANA/B/C, conserved site | Interproscan |
| IPR011095 all species → | Domain | D-alanine--D-alanine ligase, C-terminal | Interproscan |
| IPR013815 all species → | Homologous_superfamily | ATP-grasp fold, subdomain 1 | Interproscan |
| IPR011127 all species → | Domain | D-alanine--D-alanine ligase, N-terminal domain | Interproscan |
| IPR011761 all species → | Domain | ATP-grasp fold | Interproscan |
| IPR016185 all species → | Homologous_superfamily | Pre-ATP-grasp domain superfamily | Interproscan |
| PANTHER term | Description | Source |
|---|---|---|
| PTHR23132 all species → | D-ALANINE--D-ALANINE LIGASE | Interproscan |
| GO term | Category | Description | Source |
|---|---|---|---|
| GO:0005524 all species → | Molecular Function | ATP binding | Interproscan |
| GO:0005737 all species → | Cellular Component | cytoplasm | Interproscan |
| GO:0008716 all species → | Molecular Function | D-alanine-D-alanine ligase activity | Interproscan |
| GO:0009252 all species → | Biological Process | peptidoglycan biosynthetic process | Interproscan |
| GO:0046872 all species → | Molecular Function | metal ion binding | Interproscan |
XP_066913774.1.Transcript abundance of XP_066913774.1 across 40 RNA-seq samples of Clytia hemisphaerica. 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 |
|---|---|---|---|---|---|
| Mature medusa | 5 | 4 | 3.01 | 7.88 | |
| medusa · Experiment Condition A1 | 4 | 0 | 0.00 | 0.00 | |
| medusa · Experiment Condition A2 | 4 | 0 | 0.00 | 0.00 | |
| medusa · Experiment Condition A3 | 4 | 0 | 0.00 | 0.00 | |
| Early gastrula | 2 | 2 | 0.88 | 0.89 | |
| Planula 24hpf | 2 | 1 | 0.10 | 0.20 | |
| Planula 48hpf | 2 | 2 | 0.91 | 1.16 | |
| Planula 72hpf | 2 | 1 | 0.42 | 0.85 | |
| Primary polyp | 2 | 2 | 0.47 | 0.55 | |
| Gastrozooid | 2 | 1 | 0.34 | 0.68 | |
| Gonozooid | 2 | 2 | 1.48 | 1.64 | |
| Stolon | 2 | 2 | 0.57 | 0.72 | |
| Baby medusa | 2 | 2 | 0.53 | 0.67 | |
| medusa · Experiment Condition B1 | 2 | 0 | 0.00 | 0.00 | |
| medusa · Experiment Condition B2 | 2 | 0 | 0.00 | 0.00 | |
| Mixed | 1 | 1 | 2.23 | 2.23 |
| SRA run | Condition | Tissue | Developmental stage | Treatment | Study | TPM |
|---|---|---|---|---|---|---|
| ERR2816248 | Mature medusa | not recorded | Mature medusa | not recorded | ERP110164 | 7.88 |
| ERR2816249 | Mature medusa | not recorded | Mature medusa | not recorded | ERP110164 | 5.55 |
| ERR2862245 | Mature medusa | not recorded | Mature medusa | not recorded | ERP110164 | 1.56 |
| ERR2816251 | Mature medusa | not recorded | Mature medusa | not recorded | ERP110164 | 0.05 |
| ERR2816250 | Mature medusa | not recorded | Mature medusa | not recorded | ERP110164 | 0.00 |
| ERR3299475 | medusa · Experiment Condition A1 | not recorded | medusa | Experiment Condition A1 | ERP115020 | 0.00 |
| ERR3299476 | medusa · Experiment Condition A1 | not recorded | medusa | Experiment Condition A1 | ERP115020 | 0.00 |
| ERR3299477 | medusa · Experiment Condition A1 | not recorded | medusa | Experiment Condition A1 | ERP115020 | 0.00 |
| ERR3299478 | medusa · Experiment Condition A1 | not recorded | medusa | Experiment Condition A1 | ERP115020 | 0.00 |
| ERR3299479 | medusa · Experiment Condition A2 | not recorded | medusa | Experiment Condition A2 | ERP115020 | 0.00 |
| ERR3299480 | medusa · Experiment Condition A2 | not recorded | medusa | Experiment Condition A2 | ERP115020 | 0.00 |
| ERR3299481 | medusa · Experiment Condition A2 | not recorded | medusa | Experiment Condition A2 | ERP115020 | 0.00 |
| ERR3299482 | medusa · Experiment Condition A2 | not recorded | medusa | Experiment Condition A2 | ERP115020 | 0.00 |
| ERR3299483 | medusa · Experiment Condition A3 | not recorded | medusa | Experiment Condition A3 | ERP115020 | 0.00 |
| ERR3299484 | medusa · Experiment Condition A3 | not recorded | medusa | Experiment Condition A3 | ERP115020 | 0.00 |
| ERR3299485 | medusa · Experiment Condition A3 | not recorded | medusa | Experiment Condition A3 | ERP115020 | 0.00 |
| ERR3299486 | medusa · Experiment Condition A3 | not recorded | medusa | Experiment Condition A3 | ERP115020 | 0.00 |
| ERR2816230 | Early gastrula | not recorded | Early gastrula | not recorded | ERP110164 | 0.89 |
| ERR2816231 | Early gastrula | not recorded | Early gastrula | not recorded | ERP110164 | 0.88 |
| ERR2816232 | Planula 24hpf | not recorded | Planula 24hpf | not recorded | ERP110164 | 0.20 |
| ERR2816233 | Planula 24hpf | not recorded | Planula 24hpf | not recorded | ERP110164 | 0.00 |
| ERR2816234 | Planula 48hpf | not recorded | Planula 48hpf | not recorded | ERP110164 | 1.16 |
| ERR2816235 | Planula 48hpf | not recorded | Planula 48hpf | not recorded | ERP110164 | 0.65 |
| ERR2816237 | Planula 72hpf | not recorded | Planula 72hpf | not recorded | ERP110164 | 0.85 |
| ERR2816236 | Planula 72hpf | not recorded | Planula 72hpf | not recorded | ERP110164 | 0.00 |
| ERR2816238 | Primary polyp | not recorded | Primary polyp | not recorded | ERP110164 | 0.55 |
| ERR2816239 | Primary polyp | not recorded | Primary polyp | not recorded | ERP110164 | 0.40 |
| ERR2816241 | Gastrozooid | not recorded | Gastrozooid | not recorded | ERP110164 | 0.68 |
| ERR2816240 | Gastrozooid | not recorded | Gastrozooid | not recorded | ERP110164 | 0.00 |
| ERR2816243 | Gonozooid | not recorded | Gonozooid | not recorded | ERP110164 | 1.64 |
| ERR2816242 | Gonozooid | not recorded | Gonozooid | not recorded | ERP110164 | 1.33 |
| ERR2816245 | Stolon | not recorded | Stolon | not recorded | ERP110164 | 0.72 |
| ERR2816244 | Stolon | not recorded | Stolon | not recorded | ERP110164 | 0.43 |
| ERR2816247 | Baby medusa | not recorded | Baby medusa | not recorded | ERP110164 | 0.67 |
| ERR2816246 | Baby medusa | not recorded | Baby medusa | not recorded | ERP110164 | 0.38 |
| ERR3299471 | medusa · Experiment Condition B1 | not recorded | medusa | Experiment Condition B1 | ERP115020 | 0.00 |
| ERR3299472 | medusa · Experiment Condition B1 | not recorded | medusa | Experiment Condition B1 | ERP115020 | 0.00 |
| ERR3299473 | medusa · Experiment Condition B2 | not recorded | medusa | Experiment Condition B2 | ERP115020 | 0.00 |
| ERR3299474 | medusa · Experiment Condition B2 | not recorded | medusa | Experiment Condition B2 | ERP115020 | 0.00 |
| ERR2862244 | Mixed | not recorded | Mixed | not recorded | ERP110164 | 2.23 |
Source: CnidoSite RNA-seq expression matrices (CHEMI_TPM,
StringTie quantification over 40 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 Clytia hemisphaerica 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 | XP_066932763.1 | 0.984272442547764 |
| Negatively correlated | 4 | XP_066912853.1 | -0.648614058740729 |
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 Clytia hemisphaerica, 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 → |
