Detailed information of amic_s0176.g14.t1 in Acropora microphthalma

Genomic Location: sc0000176_pilon:98319...125675
NR annotation: XP_015761935.1, PREDICTED: ribosome biogenesis protein BMS1 homolog isoform X1 [Acropora digitifera]
Species Acropora microphthalma · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q14692Ribosome biogenesis protein BMS1 homolog OS=Homo sapiens OX=9606 GN=BMS1 PE=1 SV=1
O94653Ribosome biogenesis protein bms1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=bms1 PE=1 SV=2
Q08965Ribosome biogenesis protein BMS1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=BMS1 PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0003831 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF04950
all species →
RIBIOP_C40S ribosome biogenesis protein Tsr1 and BMS1 C-terminalFamilyInterproscan
PF08142
all species →
AARP2CNAARP2CN (NUC121) domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR039761
all species →
FamilyRibosome biogenesis protein Bms1/Tsr1Interproscan
IPR027417
all species →
Homologous_superfamilyP-loop containing nucleoside triphosphate hydrolaseInterproscan
IPR007034
all species →
DomainRibosome biogenesis protein BMS1/TSR1, C-terminalInterproscan
IPR012948
all species →
DomainAARP2CNInterproscan
IPR037875
all species →
DomainRibosome biogenesis protein Bms1, N-terminalInterproscan
IPR030387
all species →
DomainBms1/Tsr1-type G domainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR12858
all species →
RIBOSOME BIOGENESIS PROTEINInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0000462
all species →
Biological Processmaturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)Interproscan
GO:0000479
all species →
Biological Processendonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)Interproscan
GO:0003924
all species →
Molecular FunctionGTPase activityInterproscan
GO:0005525
all species →
Molecular FunctionGTP bindingInterproscan
GO:0030686
all species →
Cellular Component90S preribosomeInterproscan
GO:0034511
all species →
Molecular FunctionU3 snoRNA bindingInterproscan
GO:0042254
all species →
Biological Processribosome biogenesisInterproscan
GO:0005634
all species →
Cellular ComponentnucleusInterproscan

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
K14569BMS1; ribosome biogenesis protein BMS1-Ribosome biogenesisko03009deepkoala

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 Acropora microphthalma 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 Acropora microphthalma, 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.template foundopen →
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.template foundopen →
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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