Detailed information of Cxam_g2431.t1 in Cassiopea xamachana

Genomic Location: not available for this species
NR annotation: WP_170662098.1, cobalamin biosynthesis protein CobW [Ruegeria sp. SCSIO 43209]
Species Cassiopea xamachana · all data for this species · gene families

 Sequence
Sequence data are not available for Cassiopea xamachana.
Nucleotide and protein sequences are provided for the species whose genome annotation is complete (see annotated genomes); for this species only the assembly is archived. The functional annotation below is likewise unavailable.
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
P29937Zinc chaperone CobW OS=Sinorhizobium sp. OX=42445 GN=cobW PE=3 SV=3
Q9HZQ2Zinc chaperone CobW OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=cobW PE=3 SV=1
O74310Zinc-regulated GTPase metalloprotein activator 1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=zng1 PE=3 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0009435 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF02492
all species →		cobWCobW/HypB/UreG, nucleotide-binding domainDomainInterproscan
PF07683
all species →		CobW_CCobalamin synthesis protein cobW C-terminal domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR003495
all species →		DomainCobW/HypB/UreG, nucleotide-binding domainInterproscan
IPR027417
all species →		Homologous_superfamilyP-loop containing nucleoside triphosphate hydrolaseInterproscan
IPR051316
all species →		FamilyZinc-regulated GTPase metalloprotein activatorInterproscan
IPR012824
all species →		FamilyZinc chaperone CobWInterproscan
IPR036627
all species →		Homologous_superfamilyCobW-like, C-terminal domain superfamilyInterproscan
IPR011629
all species →		DomainZinc chaperone CobW-like, C-terminalInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR13748
all species →		COBW-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005737
all species →		Cellular ComponentcytoplasmInterproscan
GO:0009236
all species →		Biological Processcobalamin biosynthetic processInterproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.
 KEGG pathway
No KEGG orthology assignment for Cxam_g2431.t1.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Co-expression network

Genes whose expression across the transcriptome samples of Cassiopea xamachana 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.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Cassiopea xamachana, 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.

Epigenetic marks

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.

What you can do with this gene

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.

AnalysisWhat it doesStatus
Primer designDesign PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.sequence table not available–
BLASTSearch this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.sequence table not available–
Expression heatmapDraw 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 / orthogroupLook 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 analysisStart a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.open →
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