Gene detail

Detailed information of ENSTHXP00000033396.1 in Siderastrea radians

Genomic Location: chr9:18047738...18075866
NR annotation: no NCBI-NR hit recorded
Species Siderastrea radians · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

ENSTHXT00000049895

atggcggacgaagaAGGCAACACTTCTTCGAAATCGCACAGAAAAAAGCAAGCAGGACCTAAAGCTGAGCGAAAAAAGAAGACCAAACACTCCCCAGAAGATGCTAGTGCTCAAAGAAACCCCAAAGCGTTCTCGTTTAAGTCGGCCGTTAGAGCAGCACGGCAATTTCATCGAAAACAAGACGTGGAAACAAAACGACACCATGAGCCAGTTGTTGATCGAACGCCGCTAGAGCCCCCTCCTTACATCGTAGCCGTGGTTGGACCGCCAAAAGTTGGAAAGACGACGCTTATCAACTCGCTACTGAAGAATTTTACGCGTCAGCAGTTGTCTGATGTCAAAGGACCCGTCACCATAGTCTCTGGGAAGAAAAGACGCCTAACTTTACTTGAGTGCAACAATGACATAAACTCTATGATTGATGTGGCAAAAATTGCTGATCTGGTCCTTCTTCTCATTGATGCAAGTTTTGgatttgaaatggaaatttttgAATTTCTGAATGTTTGTCAAGTCCATGGCTTTCCCAAAATCATGGGAGTCTTGACTCACCTTGATTTGTTGAAGAATAACAAAGCTTTGAAAAAGACCAAGAAGAAGTTGAAATCTAGGTTTTGGACAGAAGTTTATCAGGGAGCAAAGCTGTTTTACTTGTCTGGCCTCGTTTATGGTTCTTATCCCAAAGTAGAGGTACATAATCTGGGAAGATTTATTTCAGTGACAAAGTTCAGACCACTGACTTGGCGAGTTTCACATCCTTACTTCTTGGCAGACAgAATGGAAGAGCTGACAGACCCTGAGCTCATTCGTCAAAATCCCAAATGTGATAGGAAGGTGTGTTTGTATGGATATGTGAGAGGCACTCATCTGAAGCACAACTCCAGAGTCCATATCATTGGTTGTGGAGACCACACTCTTGAAGAGATCAGCCTTCTACCTGATCCATGTCCCTTGCCAAGTGCAGAGAAGAAGCGTTCACTGAATGAGAAGGAACGACTTATTTATGCACCTTTCTCTGGAGTTGGAGGAGTGGTGTATGACAAGGATGCTGTCTACATTGATCTTGGTGGAAGTCAGGCTGCAAGAGAAAAATCCAAGTCTTCAGTACAGGTTGAGAGCAGACCAGGTAATGAGCTAGTGTCGTCTTTGATTGACACAAAGCAGACCATTGACACCAAAATGTTGACAAGCCAACTCACATTGTTTAAGGTACAgCACCCCTTCAaatattattttgaattttccaggGATGAAGACCCTTCAAAACCTTTTGAGCAAGTTGTAATAGATGGGAGTGGCCGTGCAAGAAGAAGAGCGGTTTTTGGCGATGAAGGTGACTGGGACCAAGATGATGATACAAATGGTGCTAGCACTGATGATGGGGTCTCAGATGATGACGGTGAAGACATGGAAAAATTTGAAATTGGTGATAAGGATGATGCTGATAGCAATAGTGACACTGGCATTGACGTTGATAACgccgaggaggaggaggaggaggaggaggaggaggagataGAACGagaagaagatgaagaggaTGAAGAAATAGTTTTTAACTTAAAATCTCAAAAGCATACAGGAAAGCAAAAACTGTCAAAGCAACAAACCACACCAATAGAAAGAACTAAGAAAAGTAGTTTGAGTAACAAATTGGAGGACAATTCAGAAGGGGAAAGTGgtgaagatgaagaagaagaaaggaatGGGAAGTGGAGCAAAAATTCAGTTGAACACTCGGATTCAGAGTCAGAAGTACagtttaaaaaaggaaaacgaaaactaAAGCATGATTTGAATGAGGGTAATATTGATGACCGGAGAGTTAAGAAGAAGTTAAAAGAGGAAACACATTCTTTAGAGCACAAGCCGATAAAAGATCTCTTGTCAAGCCGAAAAAATGGTGCCAAGCCCAAGAGCACAAAAGGAATTGGACGTGAAAGGAGTAAGGATACCTCCGAGAAAAAATCCAGCACACAATCTAAAGTAAAGGATGGTAAGGAACTAGTGGATGGTACTGACGACAGCAGTGAAAGTGAAGGAATGGAGGATATGGATGAGGAATTTGATGACGAAGATGATGCAGGTCTGGAAGAGTCAAGTCTTGCGTCTGAAGAAGgtaCACTGAAATGGAAAGAAAACCTTGCACAAAAAGCTGCAGCTGCCTTTCTCCGTCGCCAGCAAGACACCACAAATCTCCAGAAGCTTGTCTACGGAAGTGTGCTTCAGAAACGTGAGGAACAGGATACAGGGGGTGATAGCGATGAAGAAGCCGTGGGAGGTATCTTCAGACTGAAGACCAAGAAGGATTCTCAAAGCTCCGGTACTGTGCACGAGAGAGACTGCTCACTAGAGGTGTGCAGTACATCACTGAGGGACTGGGGCCAACCGGAAGTGCTTGAGAGCATCCGGGACTGTTTTGTTACTGGCAAATGGAGAGATTCAGAAGATGCTGAAAAACTGCTTCAAGACGACGATCAACTGTCAGATGAGGAATTATTTGGAGACTTCGAGGATCTGGAAACGGGTGAAGTACACCTGGCTGAGGCCAAAATCGACCCAGAGGGGGAGGGAGAGGCGTCTGATGAAGAAAGAGGAGACGAGAATGAAGAGAACGAAACTGAAGGAGGGGATAACAGACTTGAGAAAAAGAAGCAGAAGAAAGCTGCTTTTAATGCTGTCTACGACGAAGGAGACGAAACCTCGTATTATGACGAGCTTAAAACACAGATGTCAGAACAGGCACAGCTGAATCAATCCGAGTTCCAAGATATGGATGATGAAACACGTGCGCAGTATGAAGGGTTCAGACCAGGAGTGTACGTCAGAGTGGAGTTGAATGAAATGCCTTGCGAGTTTGTGACTAACTTTGACGCCAAATATCCTGTCATTCTCGGTGGTCTTCTCTCTAGTGAGGACAAGATGGGTTTTCTTCAGGTGCGCCTCAAAAAGCATCGTTGGCACAAACGAATACTCAAGACGCGAGATCCGCTGATCATGTCTGTTGGCTGGCGCAGATTCCAGACGCTTCCCATGTACTCGGTCCAGGATCACAACGGCCGACATCGGCTGCTAAAATACACACCAGAACACTTGCACTGCATGGCGACCTTTTTTGGTCCCATAGCCCCTCCAGGCACTGGTGTTCTCACTATTCAGAGCACAGCGGGCAACATGGCGGACTTTCGCATTTCAGCCACTGGCACGGTGTTGGACTTGGACAAGTCCGTGCAGCTAGTCAAGAAACTAAAGTTAACCGGAACACCGATGAAAATCTTTAAGAACACAGCATTTATCAAGGGAATGTTTAATTCTGCTCTGGAGGTAGCGAAATTTGAAGGTGCTACAATCCGAACTGTCAGCGGTATCAGAGGACAAGTTAAGCGCGCGCTGAAGACACCAGAGGGTGCATTCCGTGCAAcatttgaagacaaaattttgaTCAGTGATATTGTTTTCATAAGAACCTGGTATCCAGTCTCGCTGCCGAACTTCTACAACCCCGTGACGACACTGCTGTTGCCGCCTGACCAGAAGGAGGAATGGCAAGGCATGCGCACAGTAGGTCAGTTAAGGAAAGACCTGGGACTTAAAGTTCCTGTTAACGCGGACTCGTTGTACAAGCCCGTGGAGCGCGTTACTCGCCACTTCAATCCTCTCAAGATTCCCGTCAAGCTTCAGAAGGAGTTGCCATTCAAATCGAAACCGAAACTGATGAAGAAGAGAACAAAACCTACCTTGGAAACCAAGCGGGCTGTTGTCATGGAACCACGCGAAAAATTGGCGTTCACTCTGATGCAACAACTGCTCACGGCAAAcaaggaaaaacaaagaaagcgcaaagAAAAGttacaagaaagaagaaaagttttccGCGCAGAGCAGGAGAAGAAGAACGTAAAACGATTACAGAAACAgagagaagaaagaaagaagatctTCCGAATGATGGGACAGGCCGAGAAacggaaaaagaaaacttaa

Transcript

ENSTHXT00000049895

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003831 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08142 all species →	AARP2CN	AARP2CN (NUC121) domain	Domain	Interproscan
PF04950 all species →	RIBIOP_C	40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR030387 all species →	Domain	Bms1/Tsr1-type G domain	Interproscan
IPR039761 all species →	Family	Ribosome biogenesis protein Bms1/Tsr1	Interproscan
IPR012948 all species →	Domain	AARP2CN	Interproscan
IPR007034 all species →	Domain	Ribosome biogenesis protein BMS1/TSR1, C-terminal	Interproscan
IPR037875 all species →	Domain	Ribosome biogenesis protein Bms1, N-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12858 all species →	RIBOSOME BIOGENESIS PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000462 all species →	Biological Process	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	Interproscan
GO:0000479 all species →	Biological Process	endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	Interproscan
GO:0003924 all species →	Molecular Function	GTPase activity	Interproscan
GO:0005525 all species →	Molecular Function	GTP binding	Interproscan
GO:0030686 all species →	Cellular Component	90S preribosome	Interproscan
GO:0034511 all species →	Molecular Function	U3 snoRNA binding	Interproscan
GO:0042254 all species →	Biological Process	ribosome biogenesis	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	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
K14569	BMS1; ribosome biogenesis protein BMS1	-	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 Siderastrea radians 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 Siderastrea radians, 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 →