Detailed information of g12053.t1 in Montipora capitata

Genomic Location: Sc0000378:6925...9207
NR annotation: KAJ7377082.1, tRNA pseudouridine synthase 3 [Desmophyllum pertusum]
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
Q3SX07tRNA pseudouridine(38/39) synthase OS=Bos taurus OX=9913 GN=PUS3 PE=2 SV=1
Q9BZE2tRNA pseudouridine(38/39) synthase OS=Homo sapiens OX=9606 GN=PUS3 PE=1 SV=3
Q9JI38tRNA pseudouridine(38/39) synthase OS=Mus musculus OX=10090 GN=Pus3 PE=1 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0006374 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF01416
all species →		PseudoU_synth_1tRNA pseudouridine synthaseDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR020094
all species →		Homologous_superfamilyPseudouridine synthase TruA/RsuA/RluB/E/F, N-terminalInterproscan
IPR020097
all species →		DomainPseudouridine synthase I, TruA, alpha/beta domainInterproscan
IPR020095
all species →		Homologous_superfamilyPseudouridine synthase I, TruA, C-terminalInterproscan
IPR001406
all species →		FamilyPseudouridine synthase I, TruAInterproscan
IPR020103
all species →		Homologous_superfamilyPseudouridine synthase, catalytic domain superfamilyInterproscan
IPR041707
all species →		FamilyPseudouridine synthase Pus3-likeInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR11142
all species →		PSEUDOURIDYLATE SYNTHASEInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003723
all species →		Molecular FunctionRNA bindingInterproscan
GO:0009982
all species →		Molecular Functionpseudouridine synthase activityInterproscan
GO:0001522
all species →		Biological Processpseudouridine synthesisInterproscan
GO:0009451
all species →		Biological ProcessRNA modificationInterproscan
GO:0005634
all species →		Cellular ComponentnucleusInterproscan
GO:0005737
all species →		Cellular ComponentcytoplasmInterproscan
GO:0031119
all species →		Biological ProcesstRNA pseudouridine synthesisInterproscan
GO:1990481
all species →		Biological ProcessmRNA pseudouridine synthesisInterproscan

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
K01855PUS3, DEG1; tRNA pseudouridine38/39 synthaseEC:5.4.99.45
Transfer RNA biogenesisko03016deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g12053.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
47TPM > 0
3Conditions
44.2Max TPM
14.3Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole organisms · ambient pH treatment 21 21 14.14 41.07
whole organisms · low pH treatment 15 14 15.09 44.24
whole organisms · extra low pH treatment pH treatment 12 12 13.66 40.58

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR11452246 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 41.07
SRR11452252 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 39.54
SRR11452250 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 37.37
SRR11452234 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 17.48
SRR11452243 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 16.67
SRR11452240 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 16.16
SRR11452233 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 15.35
SRR11452254 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 13.83
SRR11452259 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 12.43
SRR11452237 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 11.41
SRR11452242 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 10.65
SRR11452230 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 9.41
SRR11452228 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 8.35
SRR11452232 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 8.24
SRR11452263 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 7.46
SRR11452260 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 7.36
SRR11452222 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 6.56
SRR11452231 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 5.89
SRR11452251 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 4.73
SRR11452262 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 4.12
SRR11452217 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 2.90
SRR11452245 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 44.24
SRR11452247 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 37.96
SRR11452249 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 37.37
SRR11452255 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 15.92
SRR11452236 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 13.53
SRR11452258 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 12.60
SRR11452241 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 12.51
SRR11452238 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 12.40
SRR11452253 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 11.92
SRR11452216 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 6.20
SRR11452224 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 5.84
SRR11452223 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 5.39
SRR11452218 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 5.24
SRR11452221 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 5.22
SRR11452229 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 0.00
SRR11452248 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 40.58
SRR11452244 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 35.27
SRR11452256 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 17.23
SRR11452235 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 13.76
SRR11452257 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 9.47
SRR11452239 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 9.31
SRR11452226 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 9.25
SRR11452225 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 8.77
SRR11452227 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 6.13
SRR11452261 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 6.06
SRR11452220 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 4.57
SRR11452219 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 3.55

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 correlated19g21084.t10.963579113659719
Negatively correlated3g6828.t1-0.784728223848237

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 →
TOP