Gene detail

Detailed information of BRAKERXEIP00000027495.1 in Muricea muricata

Genomic Location: chr14:10892440...10904193
NR annotation: CAB3988348.1, pre-rRNA processing FTSJ3 [Paramuricea clavata]
Species Muricea muricata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERXEIT00000027495

ATGGGAAAAAAGGGGAAAATTGGAAAGCAAAGACGAGATAAATTTTATCATCTTGCAAAAGAAACAGGTTATCGTGCTCGGTCTGCATTCAAACTCATTCAGCTGAACAGGAAGTTTGAATTCTTGCAGTCATCTCGAGTTTGTATCGATCTATGTGCTGCTCCTGGAGGATGGCTACAGGTTGCCTCAAAATTTATGCCAGTCTCAAGCATTATTATAGGGGTTGACTTGGTCccaataaaacctatagcaaATGTGATTACTTTACAAGACGATATTACCACGCAAAAATGCAGACAGGACATAAAGAAGGAACTAAAAACGTGGAAGGCGGATTGTGTGTTAAATGATGGTGCTCCGAATGTTGGATCCGCCTGGGCGCACGACGCGTTCACGCAAGCGCATCTGACACTGGCCGCTTTAAAACTGGGGTGTGACTTTCTAAACAAAGGCGGATGGTTTGTCACGAAGGTTTTTCGATCAAAAGACTATCAACCCTTGATGTGGGTTTTTAATCAACTCTTCAAGAAAGTTCATGCAACCAAGCCGCAAGCTTCCCGAAATGAATCTGCCGAGATATTTGTTGTCTGTCAGGGTTACAAAGCTCCAGACAAAATCGATCCAAAGTTACTGGATTGGAAATGTATCTTTGAAGAAGTGAACCAGGAGCCTACAAAACAAGCAACTTTGCTTAGTGACAAGAAACGAGCACGCGCTCAAGGTTATGCAGAAGGAGATTatagtttgtttaaaagtttagcCGTCACAGAGTTTGTGAAGAGCTCAAAACCACTGGATTTGTTGAGCTCAGTGAATAAGATTGTTTTCGATGATAAAAGGTATCAACATCACGATCTGACCACGGCAGAAATCCAAGAATGCTGTAAGGATATCAAAGTACTTGGCAAAGGAGAAGTCAGGTTATTGTTGAACTGGCAAGCAAAGTTACACGAGTTGGAAAAGAATGAAGAAGACCTGAGcGTCCAGCCGGATCAAGGAATCACCGAGGAGCCGCAGAAAAGCGTCGAAGAAATGATACAAGACTTGGAAGATGAAGAGGCCGGTGATCAGAAAAGAAAGCGCCGTAAACTGTTTGCGATGAAGAAACAAGCCCGTGAAAGGATGCATGTCGGAGGAGGAGCTACGGCGGATAGCGAAGACGCTGAATTGTTTTCATTGAATAACATCAAGAGTAAGAAGAATTTAGAAAAAGTTGATGAAGGCGAAGTGGTTGATACCAGCGATGATGAAGGGGATAACAGTGATATCGAGGACAGTGGGGATAGCATTGCTGGGGATATCGAGGACGAGGATGATCATGACGTGAACCCACTGTTAGTTAATCCGGATGAAGAGACGGATGAAGCGAGAAAAACTCAACTTTGGTTTGGCAAGGAAATGTTTCAAGGCCTTGAAACGATGGAAGATGAAGATTTTGAAGTGGAACAGATGATAAAAAGACACAAAAAAGCCGGTGGAGTGCTTCTTGGAAAAGATAAAGACGCGAAAACGACGGTGTCGGCCACAAGTGCAGCCAAGGTGGAGACGAACGACTCCGAGAATGAATCGTCAGATTCCGAAAGTGAATCGGAAGATAGCGACTACGCGATGGAACAGCTTGGTGACTCGGAAGCAAATGCTACGAAGAAATCGGAAAATGGATTTGAAGTTGTGCCACAACATTATCTAATGAAAAATATGACCCCGGAGGGACTCGCTTTAGGAGCTCAGATGGCGCtttcaaagaaaagaaaacgagAGATCGAAGATGAAGCATATCACAGATGGACATTTAATGACGATAACCTACCAGAATGGTTTACCCAAGATGAATCCAAACATTATCAACGAAACTTGCCAGTAACTAAGGAGGAAGCCATGGAATACAAAACGAAACTCAGGGAAATTAACGCCAGGCCGATCAAGAAGATCGCTGAAGCCAAAGCAAGGaaaaaacaaaaggaaatgaaacgACTTGAGAAAGCCAGAAAgaaagctgaagttatttgtgATAACGATGATGTTACCGACAAAGAAAAAGCGCAACAACTTAAAAATTTGTATAAAAAGGCCGGGATTGGCAAACGAAAGAAACCCGAGGTCAAATACGTCGTGGCTAAAAAAGGCGTCGCAGGTAAGAGAGCAAAGAGACCAGCGGGTGTAAAAGGTCCGTATAAGATGGTCGATCCAAGAATGAAGAAGGACTTGCGAGGAAAAATGAACAAACAGGCTAAAAATCGTGGCAAAAGGAAGAAATAG

Transcript

BRAKERXEIT00000027495

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
Q5RAS1	pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3 OS=Pongo abelii OX=9601 GN=FTSJ3 PE=2 SV=1
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
PF07780 all species →	Spb1_C	Spb1 C-terminal domain	Domain	Interproscan
PF11861 all species →	DUF3381	Ribosomal RNA methyltransferase Spb1, DUF3381	Domain	Interproscan
PF01728 all species →	FtsJ	FtsJ-like methyltransferase	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR028589 all species →	Family	AdoMet-dependent rRNA methyltransferase SPB1-like	Interproscan
IPR012920 all species →	Domain	Ribosomal RNA methyltransferase, SPB1-like, C-terminal	Interproscan
IPR029063 all species →	Homologous_superfamily	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Interproscan
IPR024576 all species →	Domain	Ribosomal RNA methyltransferase Spb1, domain of unknown function DUF3381	Interproscan
IPR050082 all species →	Family	Ribosomal RNA large subunit methyltransferase RlmE	Interproscan
IPR002877 all species →	Domain	Ribosomal RNA methyltransferase, FtsJ domain	Interproscan
IPR015507 all species →	Family	Ribosomal RNA large subunit methyltransferase E	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10920 all species →	RIBOSOMAL RNA METHYLTRANSFERASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0008649 all species →	Molecular Function	rRNA methyltransferase activity	Interproscan
GO:0031167 all species →	Biological Process	rRNA methylation	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006364 all species →	Biological Process	rRNA processing	Interproscan
GO:0008168 all species →	Molecular Function	methyltransferase activity	Interproscan
GO:0000463 all species →	Biological Process	maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	Interproscan
GO:0000466 all species →	Biological Process	maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	Interproscan
GO:0001510 all species →	Biological Process	RNA methylation	Interproscan
GO:0005730 all species →	Cellular Component	nucleolus	Interproscan
GO:0008173 all species →	Molecular Function	RNA methyltransferase activity	Interproscan
GO:0008650 all species →	Molecular Function	rRNA (uridine-2'-O-)-methyltransferase activity	Interproscan
GO:0016435 all species →	Molecular Function	rRNA (guanine) methyltransferase activity	Interproscan
GO:0030687 all species →	Cellular Component	preribosome, large subunit precursor	Interproscan
GO:0032259 all species →	Biological Process	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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K14857	SPB1, FTSJ3; AdoMet-dependent rRNA methyltransferase SPB1	EC:2.1.1.-	Ribosome biogenesis	ko03009	deepkoala

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 Muricea muricata 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 Muricea muricata, 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 →