Detailed information of g4120.t1 in Acropora digitifera

Genomic Location: chr2Alt:21962195...21965636
NR annotation: XP_044183157.1, 40S ribosomal protein S15-like [Acropora millepora]
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
G1U0Q2Small ribosomal subunit protein uS19 OS=Oryctolagus cuniculus OX=9986 GN=RPS15 PE=1 SV=1
P62846Small ribosomal subunit protein uS19 OS=Gallus gallus OX=9031 GN=RPS15 PE=1 SV=2
P62841Small ribosomal subunit protein uS19 OS=Homo sapiens OX=9606 GN=RPS15 PE=1 SV=2
 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00203
all species →		Ribosomal_S19Ribosomal protein S19DomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR002222
all species →		FamilySmall ribosomal subunit protein uS19Interproscan
IPR005713
all species →		FamilySmall ribosomal subunit protein uS19, eukaryotic/archaealInterproscan
IPR023575
all species →		Homologous_superfamilySmall ribosomal subunit protein uS19, superfamilyInterproscan
IPR020934
all species →		Conserved_siteSmall ribosomal subunit protein uS19, conserved siteInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR11880
all species →		RIBOSOMAL PROTEIN S19P FAMILY MEMBERInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003735
all species →		Molecular Functionstructural constituent of ribosomeInterproscan
GO:0005840
all species →		Cellular ComponentribosomeInterproscan
GO:0006412
all species →		Biological ProcesstranslationInterproscan
GO:0015935
all species →		Cellular Componentsmall ribosomal subunitInterproscan
GO:0000028
all species →		Biological Processribosomal small subunit assemblyInterproscan
GO:0022627
all species →		Cellular Componentcytosolic small ribosomal subunitInterproscan
GO:0003723
all species →		Molecular FunctionRNA bindingInterproscan

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
K02958RP-S15e, RPS15; small subunit ribosomal protein S15e-Ribosomeko03011deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g4120.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
1,793.5Max TPM
1,347.4Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Coral branch 39 39 1,347.39 1,793.48

Per sample · hover a bar for the full sample record

Show the sample table (39 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR23047229 Coral branch Coral branch adult not recorded SRP416931 1,793.48
SRR23047243 Coral branch Coral branch adult not recorded SRP416931 1,695.17
SRR23047221 Coral branch Coral branch adult not recorded SRP416931 1,654.97
SRR23047233 Coral branch Coral branch adult not recorded SRP416931 1,653.86
SRR23047239 Coral branch Coral branch adult not recorded SRP416931 1,647.02
SRR23047230 Coral branch Coral branch adult not recorded SRP416931 1,642.20
SRR23047220 Coral branch Coral branch adult not recorded SRP416931 1,591.85
SRR23047207 Coral branch Coral branch adult not recorded SRP416931 1,544.54
SRR23047234 Coral branch Coral branch adult not recorded SRP416931 1,542.98
SRR23047212 Coral branch Coral branch adult not recorded SRP416931 1,539.26
SRR23047244 Coral branch Coral branch adult not recorded SRP416931 1,537.69
SRR23047217 Coral branch Coral branch adult not recorded SRP416931 1,475.94
SRR23047223 Coral branch Coral branch adult not recorded SRP416931 1,471.56
SRR23047226 Coral branch Coral branch adult not recorded SRP416931 1,469.08
SRR23047228 Coral branch Coral branch adult not recorded SRP416931 1,444.69
SRR23047216 Coral branch Coral branch adult not recorded SRP416931 1,429.44
SRR23047213 Coral branch Coral branch adult not recorded SRP416931 1,413.99
SRR23047240 Coral branch Coral branch adult not recorded SRP416931 1,402.83
SRR23047242 Coral branch Coral branch adult not recorded SRP416931 1,387.63
SRR23047238 Coral branch Coral branch adult not recorded SRP416931 1,358.55
SRR23047206 Coral branch Coral branch adult not recorded SRP416931 1,358.17
SRR23047214 Coral branch Coral branch adult not recorded SRP416931 1,356.28
SRR23047215 Coral branch Coral branch adult not recorded SRP416931 1,330.98
SRR23047210 Coral branch Coral branch adult not recorded SRP416931 1,296.99
SRR23047224 Coral branch Coral branch adult not recorded SRP416931 1,291.14
SRR23047225 Coral branch Coral branch adult not recorded SRP416931 1,280.08
SRR23047231 Coral branch Coral branch adult not recorded SRP416931 1,273.27
SRR23047227 Coral branch Coral branch adult not recorded SRP416931 1,270.96
SRR23047241 Coral branch Coral branch adult not recorded SRP416931 1,231.15
SRR23047236 Coral branch Coral branch adult not recorded SRP416931 1,224.74
SRR23047218 Coral branch Coral branch adult not recorded SRP416931 1,164.52
SRR23047208 Coral branch Coral branch adult not recorded SRP416931 1,148.89
SRR23047219 Coral branch Coral branch adult not recorded SRP416931 983.72
SRR23047211 Coral branch Coral branch adult not recorded SRP416931 977.83
SRR23047235 Coral branch Coral branch adult not recorded SRP416931 971.96
SRR23047232 Coral branch Coral branch adult not recorded SRP416931 950.70
SRR23047237 Coral branch Coral branch adult not recorded SRP416931 948.71
SRR23047222 Coral branch Coral branch adult not recorded SRP416931 896.48
SRR23047209 Coral branch Coral branch adult not recorded SRP416931 894.95

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 correlated36g28201.t10.916958477340327
Negatively correlated99g15208.t1-0.821847989102577

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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