Detailed information of g7839.t1 in Montipora capitata

Genomic Location: Sc0000184:349133...362340
NR annotation: XP_044174934.1, LOW QUALITY PROTEIN: eukaryotic translation initiation factor 4 gamma 2-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
Q95L46Eukaryotic translation initiation factor 4 gamma 2 OS=Bos taurus OX=9913 GN=EIF4G2 PE=2 SV=2
P78344Eukaryotic translation initiation factor 4 gamma 2 OS=Homo sapiens OX=9606 GN=EIF4G2 PE=1 SV=1
Q5R7J9Eukaryotic translation initiation factor 4 gamma 2 OS=Pongo abelii OX=9601 GN=EIF4G2 PE=2 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0005957 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF02020
all species →		W2eIF4-gamma/eIF5/eIF2-epsilonRepeatInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR016024
all species →		Homologous_superfamilyArmadillo-type foldInterproscan
IPR003307
all species →		DomainW2 domainInterproscan
IPR003891
all species →		DomainInitiation factor eIF-4 gamma, MA3Interproscan
IPR045208
all species →		FamilyInitiation factor 4GInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR23253
all species →		EUKARYOTIC TRANSLATION INITIATION FACTOR 4 GAMMAInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005515
all species →		Molecular Functionprotein bindingInterproscan
GO:0003729
all species →		Molecular FunctionmRNA bindingInterproscan
GO:0003743
all species →		Molecular Functiontranslation initiation factor activityInterproscan
GO:0016281
all species →		Cellular Componenteukaryotic translation initiation factor 4F 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
No KEGG orthology assignment for g7839.t1.

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

Expression pattern (RNA-seq)

Transcript abundance of g7839.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
794.4Max TPM
437.9Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole organisms · ambient pH treatment 21 21 424.15 747.38
whole organisms · low pH treatment 15 15 467.07 794.38
whole organisms · extra low pH treatment pH treatment 12 12 425.60 762.48

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 747.38
SRR11452259 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 739.02
SRR11452254 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 723.42
SRR11452242 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 664.16
SRR11452252 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 661.34
SRR11452260 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 659.73
SRR11452243 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 638.50
SRR11452246 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 636.19
SRR11452237 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 612.77
SRR11452233 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 516.60
SRR11452234 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 417.44
SRR11452232 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 297.91
SRR11452231 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 234.15
SRR11452230 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 213.59
SRR11452222 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 205.24
SRR11452228 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 204.51
SRR11452251 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 195.53
SRR11452263 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 181.06
SRR11452262 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 132.51
SRR11452240 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 116.62
SRR11452217 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 109.57
SRR11452241 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 794.38
SRR11452247 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 714.04
SRR11452249 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 712.78
SRR11452236 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 707.15
SRR11452253 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 680.02
SRR11452238 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 674.19
SRR11452258 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 671.72
SRR11452245 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 639.50
SRR11452255 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 587.42
SRR11452221 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 176.84
SRR11452223 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 169.28
SRR11452224 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 162.61
SRR11452218 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 127.99
SRR11452216 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 97.05
SRR11452229 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 91.04
SRR11452239 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 762.48
SRR11452235 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 733.73
SRR11452248 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 715.66
SRR11452256 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 678.53
SRR11452244 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 656.99
SRR11452257 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 623.62
SRR11452225 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 227.04
SRR11452227 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 221.33
SRR11452226 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 183.71
SRR11452261 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 114.16
SRR11452219 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 101.23
SRR11452220 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 88.77

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 correlated38g35630.t10.980246278505752
Negatively correlated53g11884.t1-0.957030461785778

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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