Gene detail

Detailed information of BRAKERMNPP00000006347.1 in Nemopilema nomurai

Genomic Location: scaffold69:47866...68262
NR annotation: XP_047142101.1, pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3 [Hydra vulgaris]
Species Nemopilema nomurai · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERMNPT00000006347

ATGGGGAAGAAACCGAAAATTGGAAAAGCCAGACGGGATAAGTACTATCACCTCGCTAAAGAGACCGGTTACAGAGCAAGGTCTGCATTTAAGCTTATTCAGTTGAACAGAAAGTTCAACTTTCTCTCAAAGTCAAGAGTTCTGATTGATCTTTGCGCTGCTCCTGGAGGATGGCTACAAGTGGCTTCAAATTTTATGCCTTTATCAAGTGTCATTCTTGGTGTTGATCTTGTTCCGATAAAACCTATAAAAAATGTCACTACATTCACATCAGATATTACCACAGAAACATGTAGACAGCATTTGAAAAAGGAGTTAAAAACCTGGAAGGCTGACTGTGTTCTAAATGATGGAGCACCAAATGTTGGGTCAGCTTGGGTGCAGGATGCCTTTGCTCAAGCTCAACTCACTCTGTCAGCCTTGAAGCTAGCTTGTGAGTTTCTCAACAAAGGAGGGTGGTTTATAACAAAGgTTTTTCGATCAAAAGATTATGCCAATCTGTTGGTAGCTTTCCAAGCTCTTTTCAAGAAAGTTCATGCTACAAAACCCCAGGCTTCAAGAAATGAATCAGCagaaatatttgttgtttGCCAGGGCTTTCTGGCACCCGCTAAATTAGACCAGAAATTACTGGATTTGAAGCATGTCTTCAAAGAAACCGAGGAaactaaaaagcaaaagatcGACATCTTCAAGCCGGAGAAACACAAACGCCAAAGGGATGGTTATGAGGAAGGCAATTACACTCTGTTTACATCGAACAAAGTTTCCGATTTCATGTCTTGTGACAATCCCATTGAAATGCTCTCGACGACAAATCAGCTGATTTTGGAtgatgaaaagattttgaatCACCCTTTAACAACGaacgaaataaaaatttgctgCGATGATATAAAAGTTCTTGGAAAGAAAGAACTGAAGGGTATTCTTACGTGGAGGAAGAAGATTCGCAAAGAGGAAGAAGACGCCAAGAAAATAAGTGACGGAGAAACAGAGAATCAATCTGAGAGCGCTaaggaagatgaagaagaaacagaGGAGTCATTAGATAAAATGATTAAAGAtctgaaagaagaagaaaggcaCGAAGCAAAAAGGAAGAAAAGGCGTGATcgtgaaatgaagaaaaaagtgAGCGAGCGATTGGGAAAGAAAGCTGCTGGAGATAACAATGATGCAGTGGAGATGGATCTCTTCAGATTGTCAGCGATAAAGTCAAAGGAGCATTTGGGTAAAGTTGAAAGCAAAGGGGAAGACCAGAATGATGATGCTGATGAAGAACTTTACCACGAAGACGACGAAGATGCCTTGGAATTCGAATCAGATGGCGACTCGGGCAGTagtgatgatgaaaatgagttGTACGATGACGACATGCCCGAAGCTACCAATCCACTATTGGTCAATGCAGACATCCAGGGTGCGACTGGCCAAACATCGCAGTGGTTCAAAAAGGATATTTTCAAGTCTATCGAGGATGAAGAAGAGGCGGCTGAGGACTACGATATTGAGCAAATCATGAAAGATCACAAGAAGAAGGGAGCTGTCATCATCGGTGAACAAACTGGAACAAAGTCTGAAATTGACACGGTGAAGGCTAAAAAGAATCAGCAAAAGCTGAAGTCAAACGCAGAGTTGGTGAATGAAAGGCAAGAAGAAAATGCAGGGAGAAAAACTGTTGAAGACAAGAAAGAGTCGGATGGGAAGCCGGGGTCGTTTGAAGTAGTTTCACAAAAGCATCAAGCCAGCCGATTCCTTACTCCAGAGGCTTTGGCCCTTGGTGCCGCCATGGCTACCTCCAGGAAACGAAAGCGAGATATTGTCGATGATGCATACAACAGATTCTCTTACGGTGATGAAAATCTGCCGGCGTGGTTCGCGGATGAGGAGAAAAAGCACACGTCAATCAAGCTGCCGATTACGAAAGAGGATGTATTCTATTACAAGGAAAGGCTCAAGGCCATTAATGCCAGGCCTATGAAGAAAGTGGTGGAAGCGCAAGCAAGGAAAAAACGAAAGatgatgaagaaaatggAGAAGGTCCGCAAAAAGGCTGACACAATATTGGAAACCCAAGACGtatcagaaaaagaaaagatgtcTCAAATAAAATCGATTTACAAGAACGCTGGGTTACTGAGTAAGAAGAAAATCGAGAGGAAATATGTTGTCGCAAAGAAGGGCCTTGCCGGCAAGAAATATCCGAGGCCATCTGGTGTGAAGGGGCTATACAAAGTTGTTGATCCGAGAATGAAGAAAGACATAAGAGCAATgaagaacaaagaaaagacGAAGAGCCGGGGACGGGGCGGGATTCTTCAAGCACTTGTTAGTAGCTTGGCTTTGTTGTCAGACGACGCCCTTGCAATTGTATTCCGGCAAATGGGTATACCGGCGGAGTACGGTAGGATCTTTGTTGAAAAGAGGTTTGTAAAGGTACCCATTTCAAATGAGGAAAGTGTTCCGATTTCGTTAGAGGAATCTGTGGCTCTAGAGAACTGTACAAAAGGCAAAAAACTCGTCGGTCGACTCTTCGTCAATGAAACAAGCATCGATTGGGAGCAGCTGAAAGAAGAGCTCAAATTCATGCAAAGTGGTGGATCTTATCAACCCCCGGACTGTGTCCCCACAGTAAGAACAGCAATCATCGTTCCTTACCGCGATCGGGAAGAGCACCTGAAATTGCTTCTGCGACAGATCTACCCGATGTTGCAGCGACAGAATATCGCATTCCAAGTGTTCGTCATAGAACAGGCCGATAACGAAAAATTCAACAGAGGGAAACTGATGAACGTCGGCTTCGCAGAGGCATTGAAACGCGCGAACTTCACGTGTTTCATCTTCCACGACGTTGATCTAATACCCGAGGACGATCGAAATTTCTATGGATGTCATCTCTCTCCGGCTCACATGTCCGTGGCGGTGAATAAATTCGAGTACCAGCTCATCTCTGACACGCTATTTGGCGGCGTTGTGATGTTCACAGAAAGCGATTTTTGGAAGATCAATGGCTTTTCAAATGTCTTCTGGGGTTGGGGCGCTGAAGATGACAATCTCTACCAAAGGTTGGTTCAAAATGAACTGACTCTAAAGAGACCGGCAATGGAAAAAGCCCGCTACACAATGATTAAACACAATCAAGCAGAGGTTGACGATGAAAGATTCGATACCCTAGAGAAAGCTGTTGACCACACCGTCAAAGATGGGCTGAATTCTTTACTGTACAAAGTGAAAGACTCGTTCGAGCATGCCCTTTATACAAAAATTTATGTTGATCTAATTAGAAGTTCATCTTTCGATCCCACAAGAAGAGAAAATGATTCCTGA

Transcript

BRAKERMNPT00000006347

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q5RJT2	pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3 OS=Rattus norvegicus OX=10116 GN=Ftsj3 PE=1 SV=1
Q5ZKM1	pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3 OS=Gallus gallus OX=9031 GN=FTSJ3 PE=2 SV=2
Q9DBE9	pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3 OS=Mus musculus OX=10090 GN=Ftsj3 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003939 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02709 all species →	Glyco_transf_7C	N-terminal domain of galactosyltransferase	Family	Interproscan
PF11861 all species →	DUF3381	Ribosomal RNA methyltransferase Spb1, DUF3381	Domain	Interproscan
PF07780 all species →	Spb1_C	Spb1 C-terminal domain	Domain	Interproscan
PF13733 all species →	Glyco_transf_7N	N-terminal region of glycosyl transferase group 7	Domain	Interproscan
PF01728 all species →	FtsJ	FtsJ-like methyltransferase	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR029044 all species →	Homologous_superfamily	Nucleotide-diphospho-sugar transferases	Interproscan
IPR027791 all species →	Domain	Galactosyltransferase, C-terminal	Interproscan
IPR015507 all species →	Family	Ribosomal RNA large subunit methyltransferase E	Interproscan
IPR024576 all species →	Domain	Ribosomal RNA methyltransferase Spb1, domain of unknown function DUF3381	Interproscan
IPR029063 all species →	Homologous_superfamily	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Interproscan
IPR012920 all species →	Domain	Ribosomal RNA methyltransferase, SPB1-like, C-terminal	Interproscan
IPR027995 all species →	Domain	Galactosyltransferase, N-terminal	Interproscan
IPR002877 all species →	Domain	Ribosomal RNA methyltransferase, FtsJ domain	Interproscan
IPR003859 all species →	Family	Beta-1,4-galactosyltransferase	Interproscan
IPR028589 all species →	Family	AdoMet-dependent rRNA methyltransferase SPB1-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR19300 all species →	BETA-1,4-GALACTOSYLTRANSFERASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0001510 all species →	Biological Process	RNA methylation	Interproscan
GO:0008168 all species →	Molecular Function	methyltransferase activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006364 all species →	Biological Process	rRNA processing	Interproscan
GO:0032259 all species →	Biological Process	methylation	Interproscan
GO:0005794 all species →	Cellular Component	Golgi apparatus	Interproscan
GO:0005975 all species →	Biological Process	carbohydrate metabolic process	Interproscan
GO:0008378 all species →	Molecular Function	galactosyltransferase activity	Interproscan
GO:0016757 all species →	Molecular Function	glycosyltransferase activity	Interproscan
GO:0070085 all species →	Biological Process	glycosylation	Interproscan
GO:0008649 all species →	Molecular Function	rRNA methyltransferase activity	Interproscan
GO:0031167 all species →	Biological Process	rRNA methylation	Interproscan

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 BRAKERMNPP00000006347.1.

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 Nemopilema nomurai 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 Nemopilema nomurai, 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.

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.	no expression matrix	–
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 →