Gene detail

Detailed information of asel_s0563.g2.t1 in Acropora selago

Genomic Location: sc0000563_pilon:13016...56089
NR annotation: XP_044169806.1, pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3-like isoform X1 [Acropora millepora]
Species Acropora selago · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

asel_s0563.g2.t1

ATGGGAAGGAAAACTAAAGCCGGAAAGCAAAGGAAAGACAAATTTTACCGTCTTGCCAAAGAAACAGGTTATCGGTCTCGATCAGCTTTCAAGTTGATTCAGCTGAACAGAAAGTTCAGTTTTCTGCAGACGTCAAGATGCTTGATAGATTTATGTGCGGCGCCCGGGGGCTGGTTACAAGTTGCTTCAAAGTTCATGCCAATATCAAATGTAATCATTGGTGTTGATTTGGTTGCTATCAAGCCCATTCGTAAAGTGATAACTTTTCAGGAAGACATAAGATCAGACAAATGTAAACAGCTCATTAAGAAAGAACTTCATACATGGAAAGCTGATTGCGTGTTAAATGATGGATCACCAAACGTTGGCTCAGCTTGGATACAGGATGCATTTTCTCAAGCACAACTTACTCTCAGTGCACTTAAATTGGCTTGTGAGTTCTTAAGAGAAGGAGGCTGGTTTATCACTAAGGTTTTCAGATCCAAAGATTACCAATCACTGTTGTGGGTTTTCCAACAACTGTTCAAGAAAGTGCATTCCACCAAGCCTCAGGCGTCGCGCTCAGAATCGGCAGAGATTTTTGTTGTATGCCAGGGTTACATAGCTCCAGCCAAGATTGATCCAAAGTTCTTGGACCCCAAACACATCTTCAGTGAAGTAGAACCTGAAGACAAGAAGACAGTTAGTCTTTTAAAATTACAGAAAGGGAAGAAGGCCAAAGCTGAAGGATATACACAAGGGGACTATACCCTTTTCCAAACCGCAAAAGTAACTGACTTTCTTCAGGCAAATCATCCTTTGGAAGTGTTAAGTGCAGTAAATGAGATAGTCTTTGATGAAGAAAAGTACAGCAAGCATGTCAATACCACTAATGATATTAAAGAATGTTGCAAAGATGTGAAAGTCCTTGGCAAGACTGAAATAAAGAGTCTTTTAGCCTGGCACAAAACATTAAGGAAAGAGTTCATTGAGGTGGAAAATGAAGATGCAAGTACTCAAGAAAATGGAGAAACCCAAGAAAATGAGGAGGAAAAATTGGATAAGATGATTGAAGGACTTGAAGAAGAGGAGAAAACACGGATAAAAAGGGAAAAGAAGAAGGTTCGGGGACTGAGAAGAAAATTGCAAGAGAGAATGACTTTGAAGAATATGTTACCTGGAGACCAAGGGAACTTGGAACAAGACATAACTGTTTTTTCCCTAACAAATATAAAAAGTAAACAGCATCTGGACGGAATGGATAACCCAGACAATGATGAAACGCTCGAGTTTGAAGATGACGAAGAAGCAGACGAAAATGACGAGCTTGAGTCAGATTCAGCTTCGGAATATAGCGATAATTATGATGAGAATGGTATGGACGACAGTGAGGATGATGAAGAGTTAGAATTTGACAGTGACAATGACGAAGTGGAGTTAACCAAAGATGAAGATGCTGGAGAAAAGAATCCTTTATTAGTAGATTTGCAACCTGAAATGACCCCCTCGGCCAGAGCAAACATGTGGTTTGAAAAGGATGTTTTCAAAGATCTTGAAAATGAAGCTGACGAAGACTTAGAAATTTCACAAATGGTTGAAGAATATAAAAAGCAAGGAGGAGAGATTTTAGGGAAGAATTGTGAAACTCCATCAGCTATTGGAAAGAAGGGAACGAAACGTGGTAAGAAAGAAGAAGGCAAAAAGATGAAAAAAGTTCGCATCGATGAACGCGAAGGTagtgacagtgacagtgacagcgatagtgaaagcgaaagCGGTCGTGTCGCGGAAAGCGCAGAAGAAACATCAAAGAAACGAAAAAAGAAGGAGAAAGTCAAGAAACTTGGCGGCTTTGAGGTGGTGCCAGCCGAAGATAATGCGAAGTACTTGAAGAAGCTCACTCCAGAAGGCCTAGCACTGGGGCATAAAATGGCGTTCTCACGGAAAAATAGAAGAGACATTATTGATGATGGATATCACAGATGGACCTTTAATGACGAAGGTCTTCCTGATTGGTTTGTTTCTGAAGAAGCGATGCATTACCAGAAAGAACTTCCGGTTACCAAAGAAATGGTTGCAGAGTATCGGGCACGAATGAGGGAGATAAATGCCCGACCAATCAAAAAGGTCGCGGAAGCGAAAGCCAGGAAGAAACGAAGGGAAATGAAAGCACTCGAGAAAGCCCGTAAAAAGGCGGAGGCAATCTGTGATACTGTGGACATTTCAGAAAAGGAGAAAATGAGTCAGATACAAAGTTTGTATAAAAAGGCGCTTCTGAAAGGAAAACCCAAAGAAGTTAAATACGTGGTTGCAAGGAAATTCAATGCTGCAAGACGAATGAAGAGGCCGCCAGGGATAAAAGGACGCTATAAAGTAGTAGACCCAAGGATGAAGAAGGATATGAGAAGCCAGAAGTTAAAAGAAAAGAAAAACAAAAAAGCTGGAAAAAAGAGACGATGA

Transcript

asel_s0563.g2.t1

GGTATGGGAGACTCAGGGTACTTTCATATATGACGCATGAACTCTACCCACCGTGGTTGTAATCAACATACATGAGGTAGGTGACGGTGCTGAGGTTACCTCACTTTGCTACTCCGCACGTGGATTTTACTTTGTCGAGAGCAATGGGAAGGAAAACTAAAGCCGGAAAGCAAAGGAAAGACAAATTTTACCGTCTTGCCAAAGAAACAGGTTATCGGTCTCGATCAGCTTTCAAGTTGATTCAGCTGAACAGAAAGTTCAGTTTTCTGCAGACGTCAAGATGCTTGATAGATTTATGTGCGGCGCCCGGGGGCTGGTTACAAGTTGCTTCAAAGTTCATGCCAATATCAAATGTAATCATTGGTGTTGATTTGGTTGCTATCAAGCCCATTCGTAAAGTGATAACTTTTCAGGAAGACATAAGATCAGACAAATGTAAACAGCTCATTAAGAAAGAACTTCATACATGGAAAGCTGATTGCGTGTTAAATGATGGATCACCAAACGTTGGCTCAGCTTGGATACAGGATGCATTTTCTCAAGCACAACTTACTCTCAGTGCACTTAAATTGGCTTGTGAGTTCTTAAGAGAAGGAGGCTGGTTTATCACTAAGGTTTTCAGATCCAAAGATTACCAATCACTGTTGTGGGTTTTCCAACAACTGTTCAAGAAAGTGCATTCCACCAAGCCTCAGGCGTCGCGCTCAGAATCGGCAGAGATTTTTGTTGTATGCCAGGGTTACATAGCTCCAGCCAAGATTGATCCAAAGTTCTTGGACCCCAAACACATCTTCAGTGAAGTAGAACCTGAAGACAAGAAGACAGTTAGTCTTTTAAAATTACAGAAAGGGAAGAAGGCCAAAGCTGAAGGATATACACAAGGGGACTATACCCTTTTCCAAACCGCAAAAGTAACTGACTTTCTTCAGGCAAATCATCCTTTGGAAGTGTTAAGTGCAGTAAATGAGATAGTCTTTGATGAAGAAAAGTACAGCAAGCATGTCAATACCACTAATGATATTAAAGAATGTTGCAAAGATGTGAAAGTCCTTGGCAAGACTGAAATAAAGAGTCTTTTAGCCTGGCACAAAACATTAAGGAAAGAGTTCATTGAGGTGGAAAATGAAGATGCAAGTACTCAAGAAAATGGAGAAACCCAAGAAAATGAGGAGGAAAAATTGGATAAGATGATTGAAGGACTTGAAGAAGAGGAGAAAACACGGATAAAAAGGGAAAAGAAGAAGGTTCGGGGACTGAGAAGAAAATTGCAAGAGAGAATGACTTTGAAGAATATGTTACCTGGAGACCAAGGGAACTTGGAACAAGACATAACTGTTTTTTCCCTAACAAATATAAAAAGTAAACAGCATCTGGACGGAATGGATAACCCAGACAATGATGAAACGCTCGAGTTTGAAGATGACGAAGAAGCAGACGAAAATGACGAGCTTGAGTCAGATTCAGCTTCGGAATATAGCGATAATTATGATGAGAATGGTATGGACGACAGTGAGGATGATGAAGAGTTAGAATTTGACAGTGACAATGACGAAGTGGAGTTAACCAAAGATGAAGATGCTGGAGAAAAGAATCCTTTATTAGTAGATTTGCAACCTGAAATGACCCCCTCGGCCAGAGCAAACATGTGGTTTGAAAAGGATGTTTTCAAAGATCTTGAAAATGAAGCTGACGAAGACTTAGAAATTTCACAAATGGTTGAAGAATATAAAAAGCAAGGAGGAGAGATTTTAGGGAAGAATTGTGAAACTCCATCAGCTATTGGAAAGAAGGGAACGAAACGTGGTAAGAAAGAAGAAGGCAAAAAGATGAAAAAAGTTCGCATCGATGAACGCGAAGGTagtgacagtgacagtgacagcgatagtgaaagcgaaagCGGTCGTGTCGCGGAAAGCGCAGAAGAAACATCAAAGAAACGAAAAAAGAAGGAGAAAGTCAAGAAACTTGGCGGCTTTGAGGTGGTGCCAGCCGAAGATAATGCGAAGTACTTGAAGAAGCTCACTCCAGAAGGCCTAGCACTGGGGCATAAAATGGCGTTCTCACGGAAAAATAGAAGAGACATTATTGATGATGGATATCACAGATGGACCTTTAATGACGAAGGTCTTCCTGATTGGTTTGTTTCTGAAGAAGCGATGCATTACCAGAAAGAACTTCCGGTTACCAAAGAAATGGTTGCAGAGTATCGGGCACGAATGAGGGAGATAAATGCCCGACCAATCAAAAAGGTCGCGGAAGCGAAAGCCAGGAAGAAACGAAGGGAAATGAAAGCACTCGAGAAAGCCCGTAAAAAGGCGGAGGCAATCTGTGATACTGTGGACATTTCAGAAAAGGAGAAAATGAGTCAGATACAAAGTTTGTATAAAAAGGCGCTTCTGAAAGGAAAACCCAAAGAAGTTAAATACGTGGTTGCAAGGAAATTCAATGCTGCAAGACGAATGAAGAGGCCGCCAGGGATAAAAGGACGCTATAAAGTAGTAGACCCAAGGATGAAGAAGGATATGAGAAGCCAGAAGTTAAAAGAAAAGAAAAACAAAAAAGCTGGAAAAAAGAGACGATGATGACCAAATTGAATGTAAAATGTTTTGAACGAAATTGTTTACGTTGCATTTGCAAGTGTTGTGGTAGAGGATTCTGACTGGGAAACAAAGTCCATTGCTACACTCTTGGGCGAGAACAACCTCCTTACAGTCCAAGCTAAGTACGTACCCTGATAGCATGGGTTGGTTAAGTAAAGCTTATCTTCTACATGTAATTCTATTTGGCattatcactttgtcgggcattttggtgcattttcaatgagggtttaaatggcaagtttggagggctaaaatgtattttaacccactgaaataaagcaatgaaaagtgagaatcaaaccatgtaagaagccaatcagaatcgagtagccattaaagtgtttactctatt

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
Q9DBE9	pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3 OS=Mus musculus OX=10090 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

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
PF01728 all species →	FtsJ	FtsJ-like methyltransferase	Family	Interproscan
PF11861 all species →	DUF3381	Ribosomal RNA methyltransferase Spb1, DUF3381	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR050082 all species →	Family	Ribosomal RNA large subunit methyltransferase RlmE	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
IPR015507 all species →	Family	Ribosomal RNA large subunit methyltransferase E	Interproscan
IPR002877 all species →	Domain	Ribosomal RNA methyltransferase, FtsJ domain	Interproscan
IPR028589 all species →	Family	AdoMet-dependent rRNA methyltransferase SPB1-like	Interproscan
IPR024576 all species →	Domain	Ribosomal RNA methyltransferase Spb1, domain of unknown function DUF3381	Interproscan

PANTHER

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

Gene Ontology

GO term	Category	Description	Source
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: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:0032259 all species →	Biological Process	methylation	Interproscan
GO:0008649 all species →	Molecular Function	rRNA methyltransferase activity	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.

Expression pattern (RNA-seq)

Transcript abundance of asel_s0563.g2.t1 across 24 RNA-seq samples of Acropora selago. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

24Samples

21TPM > 0

1Conditions

27.6Max TPM

14.4Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM	Mean, relative to max
coral larvae	24	21	14.44	27.60

Per sample · hover a bar for the full sample record

Show the sample table (24 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR14308027	coral larvae	coral larvae	not recorded	not recorded	SRP315987	27.60
SRR14308012	coral larvae	coral larvae	not recorded	not recorded	SRP315987	21.75
SRR14308019	coral larvae	coral larvae	not recorded	not recorded	SRP315987	20.48
SRR14308015	coral larvae	coral larvae	not recorded	not recorded	SRP315987	19.06
SRR14308011	coral larvae	coral larvae	not recorded	not recorded	SRP315987	19.04
SRR14308004	coral larvae	coral larvae	not recorded	not recorded	SRP315987	18.69
SRR14308007	coral larvae	coral larvae	not recorded	not recorded	SRP315987	17.90
SRR14308010	coral larvae	coral larvae	not recorded	not recorded	SRP315987	17.27
SRR14308024	coral larvae	coral larvae	not recorded	not recorded	SRP315987	16.30
SRR14308017	coral larvae	coral larvae	not recorded	not recorded	SRP315987	15.71
SRR14308021	coral larvae	coral larvae	not recorded	not recorded	SRP315987	15.61
SRR14308006	coral larvae	coral larvae	not recorded	not recorded	SRP315987	15.12
SRR14308013	coral larvae	coral larvae	not recorded	not recorded	SRP315987	14.72
SRR14308014	coral larvae	coral larvae	not recorded	not recorded	SRP315987	14.53
SRR14308008	coral larvae	coral larvae	not recorded	not recorded	SRP315987	13.93
SRR14308022	coral larvae	coral larvae	not recorded	not recorded	SRP315987	13.92
SRR14308025	coral larvae	coral larvae	not recorded	not recorded	SRP315987	13.71
SRR14308023	coral larvae	coral larvae	not recorded	not recorded	SRP315987	13.70
SRR14308026	coral larvae	coral larvae	not recorded	not recorded	SRP315987	13.48
SRR14308016	coral larvae	coral larvae	not recorded	not recorded	SRP315987	12.17
SRR14308020	coral larvae	coral larvae	not recorded	not recorded	SRP315987	11.94
SRR14308005	coral larvae	coral larvae	not recorded	not recorded	SRP315987	0.00
SRR14308009	coral larvae	coral larvae	not recorded	not recorded	SRP315987	0.00
SRR14308018	coral larvae	coral larvae	not recorded	not recorded	SRP315987	0.00

Source: CnidoSite RNA-seq expression matrices (ASELA_TPM, StringTie quantification over 24 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.

Co-expression network

Genes whose expression across the transcriptome samples of Acropora selago 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.

Direction	Partners	Most correlated partner	PCC
Positively correlated	28	asel_s0340.g29.t1	0.958167063921313
Negatively correlated	3	asel_s0014.g24.t1	-0.857376293060145

Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Acropora selago, 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.

DNA methylation (bisulphite samples)

Sample	Methylation profile
Coral_Fragment_Parent	open
Larval_Pool_Offspring	open

The DNA Methylation page locates this gene by scanning the bisulphite table, which holds one row per cytosine. For the largest datasets that scan takes a while to return; it does not mean the link is broken.

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.	ready	open →
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 →