Detailed information of g5010.t1 in Acropora digitifera

Genomic Location: chr2Alt:36130389...36143923
NR annotation: XP_015759296.1, PREDICTED: elongation factor 2-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
Q6P3J5Elongation factor 2b OS=Danio rerio OX=7955 GN=eef2b PE=1 SV=1
Q90705Elongation factor 2 OS=Gallus gallus OX=9031 GN=EEF2 PE=1 SV=3
Q3SYU2Elongation factor 2 OS=Bos taurus OX=9913 GN=EEF2 PE=2 SV=3
 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF14492
all species →		EFG_IIIElongation Factor G, domain IIIDomainInterproscan
PF00009
all species →		GTP_EFTUElongation factor Tu GTP binding domainDomainInterproscan
PF03764
all species →		EFG_IVElongation factor G, domain IVDomainInterproscan
PF03144
all species →		GTP_EFTU_D2Elongation factor Tu domain 2DomainInterproscan
PF00679
all species →		EFG_CElongation factor G C-terminusDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR041095
all species →		DomainElongation Factor G, domain IIInterproscan
IPR009000
all species →		Homologous_superfamilyTranslation protein, beta-barrel domain superfamilyInterproscan
IPR000640
all species →		DomainElongation factor EFG, domain V-likeInterproscan
IPR014721
all species →		Homologous_superfamilySmall ribosomal subunit protein uS5 domain 2-type fold, subgroupInterproscan
IPR000795
all species →		DomainTranslational (tr)-type GTP-binding domainInterproscan
IPR005225
all species →		DomainSmall GTP-binding protein domainInterproscan
IPR005517
all species →		DomainTranslation elongation factor EFG/EF2, domain IVInterproscan
IPR035647
all species →		Homologous_superfamilyEF-G domain III/V-likeInterproscan
IPR027417
all species →		Homologous_superfamilyP-loop containing nucleoside triphosphate hydrolaseInterproscan
IPR004161
all species →		DomainTranslation elongation factor EFTu-like, domain 2Interproscan
IPR031157
all species →		Conserved_siteTr-type G domain, conserved siteInterproscan
IPR020568
all species →		Homologous_superfamilyRibosomal protein uS5 domain 2-type superfamilyInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR42908
all species →		TRANSLATION ELONGATION FACTOR-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003924
all species →		Molecular FunctionGTPase activityInterproscan
GO:0005525
all species →		Molecular FunctionGTP bindingInterproscan
GO:0003746
all species →		Molecular Functiontranslation elongation factor activityInterproscan
GO:0005829
all species →		Cellular ComponentcytosolInterproscan
GO:0006414
all species →		Biological Processtranslational elongationInterproscan
GO:0043022
all species →		Molecular Functionribosome bindingInterproscan
GO:1990904
all species →		Cellular Componentribonucleoprotein complexInterproscan

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
K03234EEF2; elongation factor 2-Exosomeko04147deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g5010.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
1,084.6Max TPM
742.6Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Coral branch 39 39 742.58 1,084.56

Per sample · hover a bar for the full sample record

Show the sample table (39 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR23047234 Coral branch Coral branch adult not recorded SRP416931 1,084.56
SRR23047230 Coral branch Coral branch adult not recorded SRP416931 987.73
SRR23047217 Coral branch Coral branch adult not recorded SRP416931 971.18
SRR23047227 Coral branch Coral branch adult not recorded SRP416931 970.11
SRR23047212 Coral branch Coral branch adult not recorded SRP416931 947.99
SRR23047214 Coral branch Coral branch adult not recorded SRP416931 936.00
SRR23047206 Coral branch Coral branch adult not recorded SRP416931 932.51
SRR23047241 Coral branch Coral branch adult not recorded SRP416931 884.76
SRR23047224 Coral branch Coral branch adult not recorded SRP416931 868.40
SRR23047213 Coral branch Coral branch adult not recorded SRP416931 860.81
SRR23047231 Coral branch Coral branch adult not recorded SRP416931 836.77
SRR23047229 Coral branch Coral branch adult not recorded SRP416931 821.08
SRR23047240 Coral branch Coral branch adult not recorded SRP416931 820.88
SRR23047228 Coral branch Coral branch adult not recorded SRP416931 817.97
SRR23047226 Coral branch Coral branch adult not recorded SRP416931 813.90
SRR23047216 Coral branch Coral branch adult not recorded SRP416931 810.40
SRR23047223 Coral branch Coral branch adult not recorded SRP416931 804.52
SRR23047211 Coral branch Coral branch adult not recorded SRP416931 797.00
SRR23047237 Coral branch Coral branch adult not recorded SRP416931 796.80
SRR23047239 Coral branch Coral branch adult not recorded SRP416931 788.97
SRR23047233 Coral branch Coral branch adult not recorded SRP416931 783.25
SRR23047215 Coral branch Coral branch adult not recorded SRP416931 768.71
SRR23047209 Coral branch Coral branch adult not recorded SRP416931 760.26
SRR23047238 Coral branch Coral branch adult not recorded SRP416931 740.36
SRR23047225 Coral branch Coral branch adult not recorded SRP416931 718.76
SRR23047242 Coral branch Coral branch adult not recorded SRP416931 699.66
SRR23047218 Coral branch Coral branch adult not recorded SRP416931 698.52
SRR23047235 Coral branch Coral branch adult not recorded SRP416931 694.06
SRR23047219 Coral branch Coral branch adult not recorded SRP416931 625.22
SRR23047232 Coral branch Coral branch adult not recorded SRP416931 611.05
SRR23047236 Coral branch Coral branch adult not recorded SRP416931 603.13
SRR23047207 Coral branch Coral branch adult not recorded SRP416931 523.91
SRR23047244 Coral branch Coral branch adult not recorded SRP416931 520.46
SRR23047220 Coral branch Coral branch adult not recorded SRP416931 510.59
SRR23047243 Coral branch Coral branch adult not recorded SRP416931 454.58
SRR23047210 Coral branch Coral branch adult not recorded SRP416931 442.52
SRR23047208 Coral branch Coral branch adult not recorded SRP416931 429.82
SRR23047222 Coral branch Coral branch adult not recorded SRP416931 412.54
SRR23047221 Coral branch Coral branch adult not recorded SRP416931 410.83

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 correlated46g2351.t10.88003071434976
Negatively correlated105g7924.t1-0.897466227617549

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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