Detailed information of g3617.t1 in Acropora digitifera

Genomic Location: chr2Alt:15289510...15292512
NR annotation: XP_015757710.1, PREDICTED: 60S ribosomal protein L28-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
P17702Large ribosomal subunit protein eL28 OS=Rattus norvegicus OX=10116 GN=Rpl28 PE=1 SV=4
Q3T0L7Large ribosomal subunit protein eL28 OS=Bos taurus OX=9913 GN=RPL28 PE=2 SV=3
P46779Large ribosomal subunit protein eL28 OS=Homo sapiens OX=9606 GN=RPL28 PE=1 SV=3
 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF01778
all species →		Ribosomal_L28eRibosomal L28e protein familyFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR002672
all species →		FamilyLarge ribosomal subunit protein eL28Interproscan
IPR029004
all species →		DomainRibosomal eL28/Mak16Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR10544
all species →		60S RIBOSOMAL PROTEIN L28Interproscan

 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: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
K02903RP-L28e, RPL28; large subunit ribosomal protein L28e-Ribosomeko03011deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g3617.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
866.8Max TPM
655.2Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Coral branch 39 39 655.24 866.78

Per sample · hover a bar for the full sample record

Show the sample table (39 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR23047244 Coral branch Coral branch adult not recorded SRP416931 866.78
SRR23047239 Coral branch Coral branch adult not recorded SRP416931 865.45
SRR23047229 Coral branch Coral branch adult not recorded SRP416931 845.32
SRR23047207 Coral branch Coral branch adult not recorded SRP416931 829.73
SRR23047233 Coral branch Coral branch adult not recorded SRP416931 817.27
SRR23047212 Coral branch Coral branch adult not recorded SRP416931 756.50
SRR23047221 Coral branch Coral branch adult not recorded SRP416931 755.74
SRR23047226 Coral branch Coral branch adult not recorded SRP416931 733.69
SRR23047230 Coral branch Coral branch adult not recorded SRP416931 727.29
SRR23047242 Coral branch Coral branch adult not recorded SRP416931 722.16
SRR23047216 Coral branch Coral branch adult not recorded SRP416931 717.15
SRR23047223 Coral branch Coral branch adult not recorded SRP416931 714.63
SRR23047215 Coral branch Coral branch adult not recorded SRP416931 699.49
SRR23047213 Coral branch Coral branch adult not recorded SRP416931 694.95
SRR23047240 Coral branch Coral branch adult not recorded SRP416931 674.54
SRR23047243 Coral branch Coral branch adult not recorded SRP416931 673.51
SRR23047206 Coral branch Coral branch adult not recorded SRP416931 667.15
SRR23047234 Coral branch Coral branch adult not recorded SRP416931 663.72
SRR23047238 Coral branch Coral branch adult not recorded SRP416931 656.01
SRR23047217 Coral branch Coral branch adult not recorded SRP416931 649.78
SRR23047228 Coral branch Coral branch adult not recorded SRP416931 639.37
SRR23047210 Coral branch Coral branch adult not recorded SRP416931 637.75
SRR23047220 Coral branch Coral branch adult not recorded SRP416931 633.27
SRR23047231 Coral branch Coral branch adult not recorded SRP416931 630.38
SRR23047236 Coral branch Coral branch adult not recorded SRP416931 628.12
SRR23047225 Coral branch Coral branch adult not recorded SRP416931 604.23
SRR23047241 Coral branch Coral branch adult not recorded SRP416931 599.25
SRR23047224 Coral branch Coral branch adult not recorded SRP416931 588.74
SRR23047214 Coral branch Coral branch adult not recorded SRP416931 588.22
SRR23047232 Coral branch Coral branch adult not recorded SRP416931 565.98
SRR23047208 Coral branch Coral branch adult not recorded SRP416931 556.24
SRR23047222 Coral branch Coral branch adult not recorded SRP416931 555.72
SRR23047211 Coral branch Coral branch adult not recorded SRP416931 548.98
SRR23047209 Coral branch Coral branch adult not recorded SRP416931 546.69
SRR23047218 Coral branch Coral branch adult not recorded SRP416931 529.22
SRR23047227 Coral branch Coral branch adult not recorded SRP416931 527.01
SRR23047237 Coral branch Coral branch adult not recorded SRP416931 519.86
SRR23047235 Coral branch Coral branch adult not recorded SRP416931 484.87
SRR23047219 Coral branch Coral branch adult not recorded SRP416931 439.58

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 correlated26g27199.t10.887625781256838
Negatively correlated72g27333.t1-0.81129295849975

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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