Detailed information of g2728.t1 in Acropora digitifera

Genomic Location: chr2Alt:3696009...3703383
NR annotation: XP_015756332.1, PREDICTED: LOW QUALITY PROTEIN: 60S ribosomal protein L5-like [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
Q26481Large ribosomal subunit protein uL18 OS=Styela clava OX=7725 GN=RPL5 PE=3 SV=3
O76190Large ribosomal subunit protein uL18 OS=Bombyx mori OX=7091 GN=RpL5 PE=2 SV=1
P46777Large ribosomal subunit protein uL18 OS=Homo sapiens OX=9606 GN=RPL5 PE=1 SV=3
 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF14204
all species →		Ribosomal_L18_cRibosomal L18 C-terminal regionDomainInterproscan
PF17144
all species →		Ribosomal_L5eRibosomal large subunit proteins 60S L5, and 50S L18FamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR005485
all species →		FamilyLarge ribosomal subunit protein uL18 eukaryotic/archaealInterproscan
IPR025607
all species →		DomainLarge ribosomal subunit protein uL18, C-terminal, eukaryotesInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR23410
all species →		RIBOSOMAL PROTEIN L5-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:0008097
all species →		Molecular Function5S rRNA bindingInterproscan
GO:0000027
all species →		Biological Processribosomal large subunit assemblyInterproscan
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
K02932RP-L5e, RPL5; large subunit ribosomal protein L5e-Ribosomeko03011deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g2728.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
1,291.5Max TPM
1,008.0Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Coral branch 39 39 1,008.04 1,291.51

Per sample · hover a bar for the full sample record

Show the sample table (39 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR23047230 Coral branch Coral branch adult not recorded SRP416931 1,291.51
SRR23047240 Coral branch Coral branch adult not recorded SRP416931 1,255.11
SRR23047234 Coral branch Coral branch adult not recorded SRP416931 1,236.84
SRR23047244 Coral branch Coral branch adult not recorded SRP416931 1,217.47
SRR23047206 Coral branch Coral branch adult not recorded SRP416931 1,194.61
SRR23047221 Coral branch Coral branch adult not recorded SRP416931 1,188.11
SRR23047214 Coral branch Coral branch adult not recorded SRP416931 1,179.98
SRR23047217 Coral branch Coral branch adult not recorded SRP416931 1,178.78
SRR23047243 Coral branch Coral branch adult not recorded SRP416931 1,167.75
SRR23047239 Coral branch Coral branch adult not recorded SRP416931 1,135.05
SRR23047220 Coral branch Coral branch adult not recorded SRP416931 1,128.24
SRR23047229 Coral branch Coral branch adult not recorded SRP416931 1,123.00
SRR23047207 Coral branch Coral branch adult not recorded SRP416931 1,101.47
SRR23047233 Coral branch Coral branch adult not recorded SRP416931 1,099.40
SRR23047224 Coral branch Coral branch adult not recorded SRP416931 1,069.35
SRR23047227 Coral branch Coral branch adult not recorded SRP416931 1,068.65
SRR23047212 Coral branch Coral branch adult not recorded SRP416931 1,053.47
SRR23047216 Coral branch Coral branch adult not recorded SRP416931 1,016.66
SRR23047226 Coral branch Coral branch adult not recorded SRP416931 1,015.25
SRR23047213 Coral branch Coral branch adult not recorded SRP416931 999.12
SRR23047228 Coral branch Coral branch adult not recorded SRP416931 987.15
SRR23047210 Coral branch Coral branch adult not recorded SRP416931 982.48
SRR23047223 Coral branch Coral branch adult not recorded SRP416931 978.03
SRR23047208 Coral branch Coral branch adult not recorded SRP416931 970.21
SRR23047242 Coral branch Coral branch adult not recorded SRP416931 963.53
SRR23047238 Coral branch Coral branch adult not recorded SRP416931 962.04
SRR23047241 Coral branch Coral branch adult not recorded SRP416931 938.30
SRR23047222 Coral branch Coral branch adult not recorded SRP416931 905.01
SRR23047215 Coral branch Coral branch adult not recorded SRP416931 903.10
SRR23047218 Coral branch Coral branch adult not recorded SRP416931 902.19
SRR23047231 Coral branch Coral branch adult not recorded SRP416931 892.40
SRR23047225 Coral branch Coral branch adult not recorded SRP416931 863.47
SRR23047236 Coral branch Coral branch adult not recorded SRP416931 798.37
SRR23047209 Coral branch Coral branch adult not recorded SRP416931 788.56
SRR23047232 Coral branch Coral branch adult not recorded SRP416931 781.95
SRR23047237 Coral branch Coral branch adult not recorded SRP416931 780.66
SRR23047211 Coral branch Coral branch adult not recorded SRP416931 767.57
SRR23047235 Coral branch Coral branch adult not recorded SRP416931 752.14
SRR23047219 Coral branch Coral branch adult not recorded SRP416931 676.39

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 correlated33g20635.t10.895027523409069
Negatively correlated80g28510.t1-0.838400748040346

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
DNase-seq (DHS)WholeAnimal2Distal Intergenic 2

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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