Detailed information of g27367.t1 in Montipora capitata

Genomic Location: xfSc0000020:165382...176391
NR annotation: XP_029202757.1, 40S ribosomal protein S2 [Acropora millepora]
Species Montipora capitata · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q90YS3Small ribosomal subunit protein uS5 OS=Ictalurus punctatus OX=7998 GN=rps2 PE=2 SV=1
P25444Small ribosomal subunit protein uS5 OS=Mus musculus OX=10090 GN=Rps2 PE=1 SV=3
P27952Small ribosomal subunit protein uS5 OS=Rattus norvegicus OX=10116 GN=Rps2 PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0007570 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF03719
all species →		Ribosomal_S5_CRibosomal protein S5, C-terminal domainDomainInterproscan
PF00333
all species →		Ribosomal_S5Ribosomal protein S5, N-terminal domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR005324
all species →		DomainSmall ribosomal subunit protein uS5, C-terminalInterproscan
IPR020568
all species →		Homologous_superfamilyRibosomal protein uS5 domain 2-type superfamilyInterproscan
IPR018192
all species →		Conserved_siteSmall ribosomal subunit protein uS5, N-terminal, conserved siteInterproscan
IPR005711
all species →		FamilySmall ribosomal subunit protein uS5, eukaryotic/archaealInterproscan
IPR014721
all species →		Homologous_superfamilySmall ribosomal subunit protein uS5 domain 2-type fold, subgroupInterproscan
IPR000851
all species →		FamilySmall ribosomal subunit protein uS5Interproscan
IPR013810
all species →		DomainSmall ribosomal subunit protein uS5, N-terminalInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR13718
all species →		RIBOSOMAL S SUBUNITInterproscan

 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:0003723
all species →		Molecular FunctionRNA bindingInterproscan
GO:0022627
all species →		Cellular Componentcytosolic small 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
K02981RP-S2e, RPS2; small subunit ribosomal protein S2e-Ribosomeko03011deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g27367.t1 across 48 RNA-seq samples of Montipora capitata. 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.

48Samples
48TPM > 0
3Conditions
4,478.6Max TPM
1,028.8Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole organisms · ambient pH treatment 21 21 1,182.89 4,478.62
whole organisms · low pH treatment 15 15 862.25 4,087.92
whole organisms · extra low pH treatment pH treatment 12 12 967.25 4,123.57

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR11452228 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 4,478.62
SRR11452231 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 4,229.33
SRR11452222 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 4,099.92
SRR11452230 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 4,011.28
SRR11452232 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 3,289.10
SRR11452233 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 1,729.38
SRR11452234 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 1,571.61
SRR11452242 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 463.50
SRR11452237 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 434.83
SRR11452243 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 323.89
SRR11452262 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 31.14
SRR11452217 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 28.77
SRR11452250 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 25.65
SRR11452251 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 23.86
SRR11452252 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 22.87
SRR11452240 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 20.59
SRR11452263 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 18.30
SRR11452260 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 14.03
SRR11452246 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 9.95
SRR11452254 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 9.27
SRR11452259 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 4.86
SRR11452224 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 4,087.92
SRR11452223 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 3,753.45
SRR11452221 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 3,708.53
SRR11452241 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 478.90
SRR11452238 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 376.27
SRR11452236 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 353.83
SRR11452216 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 43.13
SRR11452218 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 26.69
SRR11452249 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 23.94
SRR11452255 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 23.84
SRR11452229 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 19.14
SRR11452258 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 11.66
SRR11452245 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 8.87
SRR11452247 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 8.86
SRR11452253 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 8.75
SRR11452226 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 4,123.57
SRR11452227 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 3,879.21
SRR11452225 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 2,750.74
SRR11452235 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 381.89
SRR11452239 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 351.38
SRR11452219 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 37.70
SRR11452261 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 20.79
SRR11452220 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 14.95
SRR11452257 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 12.76
SRR11452244 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 12.58
SRR11452256 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 11.00
SRR11452248 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 10.47

Source: CnidoSite RNA-seq expression matrices (MCAPI_TPM, StringTie quantification over 48 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 Montipora capitata 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 correlated36g17708.t10.994723257712983
Negatively correlated10g30757.t1-0.952056440937843

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 Montipora capitata, 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.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

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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