Detailed information of g21025.t1 in Acropora digitifera

Genomic Location: chr10Alt:1285777...1288627
NR annotation: XP_029198936.1, 60S ribosomal protein L11-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
A8XJ93Large ribosomal subunit protein uL5B OS=Caenorhabditis briggsae OX=6238 GN=rpl-11.2 PE=3 SV=1
Q19162Large ribosomal subunit protein uL5B OS=Caenorhabditis elegans OX=6239 GN=rpl-11.2 PE=1 SV=1
P46222Large ribosomal subunit protein uL5 OS=Drosophila melanogaster OX=7227 GN=RpL11 PE=1 SV=2
 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00673
all species →		Ribosomal_L5_Cribosomal L5P family C-terminusDomainInterproscan
PF00281
all species →		Ribosomal_L5Ribosomal protein L5DomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR020929
all species →		Conserved_siteLarge ribosomal subunit protein uL5, conserved siteInterproscan
IPR022803
all species →		Homologous_superfamilyLarge ribosomal subunit protein uL5 domain superfamilyInterproscan
IPR031309
all species →		DomainLarge ribosomal subunit protein uL5, C-terminalInterproscan
IPR002132
all species →		FamilyLarge ribosomal subunit protein uL5Interproscan
IPR031310
all species →		DomainLarge ribosomal subunit protein uL5, N-terminalInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR11994
all species →		60S RIBOSOMAL PROTEIN L11-RELATEDInterproscan

 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:0003723
all species →		Molecular FunctionRNA bindingInterproscan
GO:0022625
all species →		Cellular Componentcytosolic large ribosomal subunitInterproscan

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
K02868RP-L11e, RPL11; large subunit ribosomal protein L11e-Ribosomeko03011deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g21025.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
856.2Max TPM
601.0Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Coral branch 39 39 601.01 856.18

Per sample · hover a bar for the full sample record

Show the sample table (39 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR23047239 Coral branch Coral branch adult not recorded SRP416931 856.18
SRR23047244 Coral branch Coral branch adult not recorded SRP416931 829.44
SRR23047212 Coral branch Coral branch adult not recorded SRP416931 796.56
SRR23047233 Coral branch Coral branch adult not recorded SRP416931 739.99
SRR23047243 Coral branch Coral branch adult not recorded SRP416931 736.18
SRR23047215 Coral branch Coral branch adult not recorded SRP416931 728.12
SRR23047228 Coral branch Coral branch adult not recorded SRP416931 724.24
SRR23047229 Coral branch Coral branch adult not recorded SRP416931 720.02
SRR23047238 Coral branch Coral branch adult not recorded SRP416931 713.67
SRR23047221 Coral branch Coral branch adult not recorded SRP416931 703.30
SRR23047223 Coral branch Coral branch adult not recorded SRP416931 688.46
SRR23047230 Coral branch Coral branch adult not recorded SRP416931 674.51
SRR23047242 Coral branch Coral branch adult not recorded SRP416931 662.47
SRR23047220 Coral branch Coral branch adult not recorded SRP416931 660.58
SRR23047225 Coral branch Coral branch adult not recorded SRP416931 660.52
SRR23047240 Coral branch Coral branch adult not recorded SRP416931 636.51
SRR23047216 Coral branch Coral branch adult not recorded SRP416931 633.24
SRR23047222 Coral branch Coral branch adult not recorded SRP416931 623.13
SRR23047213 Coral branch Coral branch adult not recorded SRP416931 622.36
SRR23047241 Coral branch Coral branch adult not recorded SRP416931 613.12
SRR23047231 Coral branch Coral branch adult not recorded SRP416931 606.60
SRR23047236 Coral branch Coral branch adult not recorded SRP416931 597.97
SRR23047210 Coral branch Coral branch adult not recorded SRP416931 592.28
SRR23047207 Coral branch Coral branch adult not recorded SRP416931 590.62
SRR23047214 Coral branch Coral branch adult not recorded SRP416931 574.73
SRR23047234 Coral branch Coral branch adult not recorded SRP416931 558.54
SRR23047206 Coral branch Coral branch adult not recorded SRP416931 540.88
SRR23047217 Coral branch Coral branch adult not recorded SRP416931 527.71
SRR23047218 Coral branch Coral branch adult not recorded SRP416931 526.26
SRR23047209 Coral branch Coral branch adult not recorded SRP416931 520.10
SRR23047226 Coral branch Coral branch adult not recorded SRP416931 516.16
SRR23047224 Coral branch Coral branch adult not recorded SRP416931 477.20
SRR23047208 Coral branch Coral branch adult not recorded SRP416931 470.26
SRR23047211 Coral branch Coral branch adult not recorded SRP416931 444.14
SRR23047227 Coral branch Coral branch adult not recorded SRP416931 425.32
SRR23047235 Coral branch Coral branch adult not recorded SRP416931 374.76
SRR23047232 Coral branch Coral branch adult not recorded SRP416931 365.62
SRR23047219 Coral branch Coral branch adult not recorded SRP416931 364.15
SRR23047237 Coral branch Coral branch adult not recorded SRP416931 343.55

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 correlated23g1935.t10.819062990293572
Negatively correlated70g7057.t1-0.80062063279563

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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