Detailed information of g11795.t1 in Montipora capitata

Genomic Location: Sc0000361:149692...162348
NR annotation: XP_029191845.2, LOW QUALITY PROTEIN: elongation factor Tu-like [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
P49410Elongation factor Tu, mitochondrial OS=Bos taurus OX=9913 GN=TUFM PE=1 SV=1
Q0BUQ2Elongation factor Tu OS=Granulibacter bethesdensis (strain ATCC BAA-1260 / CGDNIH1) OX=391165 GN=tuf PE=3 SV=1
Q2W2H3Elongation factor Tu OS=Paramagnetospirillum magneticum (strain ATCC 700264 / AMB-1) OX=342108 GN=tuf1 PE=3 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0003933 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00009
all species →		GTP_EFTUElongation factor Tu GTP binding domainDomainInterproscan
PF03144
all species →		GTP_EFTU_D2Elongation factor Tu domain 2DomainInterproscan
PF03143
all species →		GTP_EFTU_D3Elongation factor Tu C-terminal domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR004541
all species →		FamilyTranslation elongation factor EFTu/EF1A, bacterial/organelleInterproscan
IPR000795
all species →		DomainTranslational (tr)-type GTP-binding domainInterproscan
IPR033720
all species →		DomainElongation factor Tu, domain 2Interproscan
IPR050055
all species →		FamilyElongation factor Tu GTPaseInterproscan
IPR004161
all species →		DomainTranslation elongation factor EFTu-like, domain 2Interproscan
IPR027417
all species →		Homologous_superfamilyP-loop containing nucleoside triphosphate hydrolaseInterproscan
IPR004160
all species →		DomainTranslation elongation factor EFTu/EF1A, C-terminalInterproscan
IPR041709
all species →		DomainElongation factor Tu (EF-Tu), GTP-binding domainInterproscan
IPR009000
all species →		Homologous_superfamilyTranslation protein, beta-barrel domain superfamilyInterproscan
IPR009001
all species →		Homologous_superfamilyTranslation elongation factor EF1A/initiation factor IF2gamma, C-terminalInterproscan
IPR031157
all species →		Conserved_siteTr-type G domain, conserved siteInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR43721
all species →		ELONGATION FACTOR TU-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003746
all species →		Molecular Functiontranslation elongation factor activityInterproscan
GO:0005525
all species →		Molecular FunctionGTP bindingInterproscan
GO:0006414
all species →		Biological Processtranslational elongationInterproscan
GO:0003924
all species →		Molecular FunctionGTPase activityInterproscan
GO:0005739
all species →		Cellular ComponentmitochondrionInterproscan
GO:0070125
all species →		Biological Processmitochondrial translational elongationInterproscan

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
K02358tuf, TUFM; elongation factor Tu-Exosomeko04147deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g11795.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
162.6Max TPM
105.6Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole organisms · ambient pH treatment 21 21 107.57 162.64
whole organisms · low pH treatment 15 15 107.00 160.62
whole organisms · extra low pH treatment pH treatment 12 12 100.22 160.62

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR11452250 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 162.64
SRR11452252 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 157.23
SRR11452246 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 149.20
SRR11452237 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 144.95
SRR11452231 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 141.42
SRR11452232 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 140.04
SRR11452243 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 138.34
SRR11452242 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 138.04
SRR11452234 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 132.59
SRR11452233 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 127.34
SRR11452230 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 126.04
SRR11452228 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 125.43
SRR11452222 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 98.41
SRR11452254 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 80.74
SRR11452259 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 78.31
SRR11452260 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 74.68
SRR11452240 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 59.21
SRR11452251 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 56.83
SRR11452263 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 48.33
SRR11452217 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 47.58
SRR11452262 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 31.61
SRR11452249 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 160.62
SRR11452238 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 159.37
SRR11452245 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 159.07
SRR11452247 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 148.80
SRR11452241 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 140.36
SRR11452236 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 135.05
SRR11452224 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 116.81
SRR11452221 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 116.37
SRR11452223 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 114.16
SRR11452258 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 80.59
SRR11452255 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 66.20
SRR11452229 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 61.79
SRR11452218 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 55.55
SRR11452253 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 55.20
SRR11452216 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 35.13
SRR11452248 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 160.62
SRR11452244 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 160.11
SRR11452235 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 145.15
SRR11452239 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 139.32
SRR11452226 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 113.85
SRR11452227 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 108.96
SRR11452225 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 106.40
SRR11452256 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 83.68
SRR11452257 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 52.43
SRR11452219 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 46.59
SRR11452220 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 44.04
SRR11452261 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 41.49

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 correlated41g28600.t10.961538521573683
Negatively correlated48g35341.t1-0.947869247696462

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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