Detailed information of Cxam_g1586.t1 in Cassiopea xamachana

Genomic Location: not available for this species
NR annotation: WP_010442122.1, pyruvate dehydrogenase complex E1 component subunit beta [Ruegeria conchae]
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
Q9R9N4Pyruvate dehydrogenase E1 component subunit beta OS=Rhizobium meliloti (strain 1021) OX=266834 GN=pdhB PE=3 SV=2
O66113Pyruvate dehydrogenase E1 component subunit beta OS=Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4) OX=264203 GN=pdhB PE=3 SV=2
Q4UKQ7Pyruvate dehydrogenase E1 component subunit beta OS=Rickettsia felis (strain ATCC VR-1525 / URRWXCal2) OX=315456 GN=pdhB PE=3 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0004105 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00364
all species →		Biotin_lipoylBiotin-requiring enzymeDomainInterproscan
PF02780
all species →		Transketolase_CTransketolase, C-terminal domainDomainInterproscan
PF02779
all species →		Transket_pyrTransketolase, pyrimidine binding domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR029061
all species →		Homologous_superfamilyThiamin diphosphate-binding foldInterproscan
IPR003016
all species →		Binding_site2-oxo acid dehydrogenase, lipoyl-binding siteInterproscan
IPR000089
all species →		DomainBiotin/lipoyl attachmentInterproscan
IPR011053
all species →		Homologous_superfamilySingle hybrid motifInterproscan
IPR033248
all species →		DomainTransketolase, C-terminal domainInterproscan
IPR027110
all species →		FamilyPyruvate dehydrogenase E1 component subunit betaInterproscan
IPR009014
all species →		Homologous_superfamilyTransketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain IIInterproscan
IPR005475
all species →		DomainTransketolase-like, pyrimidine-binding domainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR11624
all species →		DEHYDROGENASE RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0004739
all species →		Molecular Functionpyruvate dehydrogenase (acetyl-transferring) activityInterproscan
GO:0006086
all species →		Biological Processacetyl-CoA biosynthetic process from pyruvateInterproscan
GO:0003824
all species →		Molecular Functioncatalytic activityInterproscan

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
KOEnzymeEnzyme IDPathwayMap IDSource
K00162PDHB, pdhB; pyruvate dehydrogenase E1 component subunit betaEC:1.2.4.1
Diabetic cardiomyopathyko05415deepkoala

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 →
TOP