Detailed information of g11.t1 in Acropora digitifera

Genomic Location: chr1Alt:211370...218625
NR annotation: XP_015761936.1, PREDICTED: ribosome biogenesis protein BMS1 homolog isoform X2 [Acropora digitifera]
Species Acropora digitifera · 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
 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF01926
all species →		MMR_HSR150S ribosome-binding GTPaseFamilyInterproscan
PF08142
all species →		AARP2CNAARP2CN (NUC121) domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR006073
all species →		DomainGTP binding domainInterproscan
IPR027417
all species →		Homologous_superfamilyP-loop containing nucleoside triphosphate hydrolaseInterproscan
IPR039761
all species →		FamilyRibosome biogenesis protein Bms1/Tsr1Interproscan
IPR030387
all species →		DomainBms1/Tsr1-type G domainInterproscan
IPR012948
all species →		DomainAARP2CNInterproscan
IPR037875
all species →		DomainRibosome biogenesis protein Bms1, N-terminalInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR12858
all species →		RIBOSOME BIOGENESIS PROTEINInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005525
all species →		Molecular FunctionGTP bindingInterproscan
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: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
No KEGG orthology assignment for g11.t1.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of g11.t1 across 39 RNA-seq samples of Acropora digitifera. 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.

39Samples
39TPM > 0
1Conditions
59.5Max TPM
30.9Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Coral branch 39 39 30.88 59.53

Per sample · hover a bar for the full sample record

Show the sample table (39 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR23047222 Coral branch Coral branch adult not recorded SRP416931 59.53
SRR23047217 Coral branch Coral branch adult not recorded SRP416931 40.62
SRR23047235 Coral branch Coral branch adult not recorded SRP416931 39.74
SRR23047234 Coral branch Coral branch adult not recorded SRP416931 39.74
SRR23047213 Coral branch Coral branch adult not recorded SRP416931 37.38
SRR23047214 Coral branch Coral branch adult not recorded SRP416931 37.18
SRR23047226 Coral branch Coral branch adult not recorded SRP416931 36.89
SRR23047219 Coral branch Coral branch adult not recorded SRP416931 36.64
SRR23047241 Coral branch Coral branch adult not recorded SRP416931 36.23
SRR23047243 Coral branch Coral branch adult not recorded SRP416931 35.77
SRR23047231 Coral branch Coral branch adult not recorded SRP416931 34.56
SRR23047221 Coral branch Coral branch adult not recorded SRP416931 34.47
SRR23047240 Coral branch Coral branch adult not recorded SRP416931 34.03
SRR23047220 Coral branch Coral branch adult not recorded SRP416931 33.33
SRR23047211 Coral branch Coral branch adult not recorded SRP416931 33.31
SRR23047223 Coral branch Coral branch adult not recorded SRP416931 33.01
SRR23047227 Coral branch Coral branch adult not recorded SRP416931 31.94
SRR23047225 Coral branch Coral branch adult not recorded SRP416931 31.70
SRR23047216 Coral branch Coral branch adult not recorded SRP416931 31.52
SRR23047207 Coral branch Coral branch adult not recorded SRP416931 30.03
SRR23047206 Coral branch Coral branch adult not recorded SRP416931 29.94
SRR23047224 Coral branch Coral branch adult not recorded SRP416931 29.19
SRR23047208 Coral branch Coral branch adult not recorded SRP416931 28.72
SRR23047212 Coral branch Coral branch adult not recorded SRP416931 27.88
SRR23047215 Coral branch Coral branch adult not recorded SRP416931 27.35
SRR23047210 Coral branch Coral branch adult not recorded SRP416931 27.33
SRR23047238 Coral branch Coral branch adult not recorded SRP416931 27.29
SRR23047233 Coral branch Coral branch adult not recorded SRP416931 26.74
SRR23047242 Coral branch Coral branch adult not recorded SRP416931 26.10
SRR23047218 Coral branch Coral branch adult not recorded SRP416931 25.98
SRR23047239 Coral branch Coral branch adult not recorded SRP416931 25.75
SRR23047236 Coral branch Coral branch adult not recorded SRP416931 24.14
SRR23047209 Coral branch Coral branch adult not recorded SRP416931 24.07
SRR23047232 Coral branch Coral branch adult not recorded SRP416931 23.66
SRR23047230 Coral branch Coral branch adult not recorded SRP416931 23.09
SRR23047228 Coral branch Coral branch adult not recorded SRP416931 21.18
SRR23047229 Coral branch Coral branch adult not recorded SRP416931 21.07
SRR23047244 Coral branch Coral branch adult not recorded SRP416931 18.97
SRR23047237 Coral branch Coral branch adult not recorded SRP416931 18.34

Source: CnidoSite RNA-seq expression matrices (ADIGI_TPM, StringTie quantification over 39 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 digitifera 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.

DirectionPartnersMost correlated partnerPCC
Positively correlated6g10.t10.817307639793301
Negatively correlated5g5342.t1-0.563938185860517

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 digitifera, 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.

Peak calls overlapping this gene

AssaySamplePeaksRegion

No called peak overlaps this gene in 1 available assay. Either the gene is not near an accessible or marked region in those samples, or it is not represented in the peak caller’s annotation.

Browse the full epigenomic landscape of this species: DNase-seq (DHS).

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.readyopen →
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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