Detailed information of Cxam_g15006.t1 in Cassiopea xamachana

Genomic Location: not available for this species
NR annotation: WP_110984314.1, FADH(2)-oxidizing methylenetetrahydrofolate--tRNA-(uracil(54)-C(5))-methyltransferase TrmFO [Acaryochloris thomasi]
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
B0C6V8Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO OS=Acaryochloris marina (strain MBIC 11017) OX=329726 GN=trmFO PE=3 SV=1
B0JFX8Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO OS=Microcystis aeruginosa (strain NIES-843 / IAM M-2473) OX=449447 GN=trmFO PE=3 SV=1
B1XK17Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO OS=Picosynechococcus sp. (strain ATCC 27264 / PCC 7002 / PR-6) OX=32049 GN=trmFO PE=3 SV=1
 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF01134
all species →		GIDAGlucose inhibited division protein AFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR036188
all species →		Homologous_superfamilyFAD/NAD(P)-binding domain superfamilyInterproscan
IPR040131
all species →		DomainMnmG, N-terminal domainInterproscan
IPR004417
all species →		FamilyMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFOInterproscan
IPR002218
all species →		FamilytRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG-relatedInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR11806
all species →		GLUCOSE INHIBITED DIVISION PROTEIN AInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005737
all species →		Cellular ComponentcytoplasmInterproscan
GO:0008033
all species →		Biological ProcesstRNA processingInterproscan
GO:0047151
all species →		Molecular FunctiontRNA (uracil(54)-C5)-methyltransferase activity, 5,10-methylenetetrahydrofolate-dependentInterproscan
GO:0050660
all species →		Molecular Functionflavin adenine dinucleotide bindingInterproscan
GO:0002098
all species →		Biological ProcesstRNA wobble uridine modificationInterproscan
GO:0005829
all species →		Cellular ComponentcytosolInterproscan
GO:0030488
all species →		Biological ProcesstRNA methylationInterproscan

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
K04094trmFO, gid; methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferaseEC:2.1.1.74
Chromosome and associated proteinsko03036deepkoala

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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