Detailed information of ENSBQFP00000010668.1 in Heliopora coerulea

Genomic Location: JASJOG010000015.1:2813434...2824575
NR annotation: CAB3977128.1, eukaryotic peptide chain release factor subunit 1 [Paramuricea clavata]
Species Heliopora coerulea · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q9GR88Eukaryotic peptide chain release factor subunit 1 OS=Polyandrocarpa misakiensis OX=7723 GN=ERF1 PE=2 SV=1
P62498Eukaryotic peptide chain release factor subunit 1 OS=Xenopus tropicalis OX=8364 GN=etf1 PE=2 SV=1
Q0VCX5Eukaryotic peptide chain release factor subunit 1 OS=Bos taurus OX=9913 GN=ETF1 PE=2 SV=3
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0005436 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF03463
all species →		eRF1_1eRF1 domain 1DomainInterproscan
PF03464
all species →		eRF1_2eRF1 domain 2DomainInterproscan
PF03465
all species →		eRF1_3eRF1 domain 3DomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR029064
all species →		Homologous_superfamilyRibosomal protein eL30-like superfamilyInterproscan
IPR024049
all species →		Homologous_superfamilyeRF1, domain 1Interproscan
IPR005140
all species →		DomaineRF1 domain 1/Pelota-likeInterproscan
IPR004403
all species →		FamilyPeptide chain release factor eRF1/aRF1Interproscan
IPR005141
all species →		DomaineRF1 domain 2Interproscan
IPR042226
all species →		Homologous_superfamilyeRF1, domain 2 superfamilyInterproscan
IPR005142
all species →		DomaineRF1 domain 3Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR10113
all species →		PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003747
all species →		Molecular Functiontranslation release factor activityInterproscan
GO:0006415
all species →		Biological Processtranslational terminationInterproscan
GO:0002184
all species →		Biological Processcytoplasmic translational terminationInterproscan
GO:0005829
all species →		Cellular ComponentcytosolInterproscan
GO:0016149
all species →		Molecular Functiontranslation release factor activity, codon specificInterproscan
GO:0018444
all species →		Cellular Componenttranslation release factor complexInterproscan
GO:1990825
all species →		Molecular Functionsequence-specific mRNA bindingInterproscan

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
K03265ETF1, ERF1; peptide chain release factor subunit 1-Translation factorsko03012deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of ENSBQFP00000010668.1 across 37 RNA-seq samples of Heliopora coerulea. 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.

37Samples
32TPM > 0
6Conditions
97.8Max TPM
50.8Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Whole coral 17 17 61.39 97.77
polyp and skeleton · 31C, 3week 6 6 48.61 91.71
polyp and skeleton · 28C, 3week 6 4 38.40 62.62
polyp and skeleton · 26C, 3week 4 2 29.68 63.70
polyp and skeleton · 28C, 24hr 2 2 67.31 72.10
polyp and skeleton · 31C, 24hr 2 1 29.37 58.74

Per sample · hover a bar for the full sample record

Show the sample table (37 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
ERR6178780 Whole coral Whole coral not recorded not recorded ERP120267 97.77
ERR6178775 Whole coral Whole coral not recorded not recorded ERP120267 95.74
ERR6178388 Whole coral Whole coral not recorded not recorded ERP120267 91.70
ERR6178779 Whole coral Whole coral not recorded not recorded ERP120267 90.86
ERR6178389 Whole coral Whole coral not recorded not recorded ERP120267 84.82
ERR6178387 Whole coral Whole coral not recorded not recorded ERP120267 83.45
ERR6178773 Whole coral Whole coral not recorded not recorded ERP120267 70.06
ERR6178774 Whole coral Whole coral not recorded not recorded ERP120267 61.10
ERR6178777 Whole coral Whole coral not recorded not recorded ERP120267 57.10
ERR6178772 Whole coral Whole coral not recorded not recorded ERP120267 47.33
ERR6178783 Whole coral Whole coral not recorded not recorded ERP120267 46.77
ERR6178771 Whole coral Whole coral not recorded not recorded ERP120267 44.37
ERR6178770 Whole coral Whole coral not recorded not recorded ERP120267 42.17
ERR6178776 Whole coral Whole coral not recorded not recorded ERP120267 35.57
ERR6178781 Whole coral Whole coral not recorded not recorded ERP120267 33.51
ERR6178782 Whole coral Whole coral not recorded not recorded ERP120267 30.96
ERR6178778 Whole coral Whole coral not recorded not recorded ERP120267 30.39
SRR12578066 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 91.71
SRR12578065 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 66.63
SRR12587800 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 43.25
SRR12587804 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 34.86
SRR12578068 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 29.77
SRR12587799 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 25.46
SRR12587803 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 62.62
SRR12587802 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 58.03
SRR12587807 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 55.89
SRR12587808 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 53.88
SRR12578067 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 0.00
SRR5949849 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 0.00
SRR12587798 polyp and skeleton · 26C, 3week polyp and skeleton not recorded 26C, 3week SRP115860 63.70
SRR12587805 polyp and skeleton · 26C, 3week polyp and skeleton not recorded 26C, 3week SRP115860 55.02
SRR12587801 polyp and skeleton · 26C, 3week polyp and skeleton not recorded 26C, 3week SRP115860 0.00
SRR12587806 polyp and skeleton · 26C, 3week polyp and skeleton not recorded 26C, 3week SRP115860 0.00
SRR12578063 polyp and skeleton · 28C, 24hr polyp and skeleton not recorded 28C, 24hr SRP115860 72.10
SRR5949850 polyp and skeleton · 28C, 24hr polyp and skeleton not recorded 28C, 24hr SRP115860 62.52
SRR12578064 polyp and skeleton · 31C, 24hr polyp and skeleton not recorded 31C, 24hr SRP115860 58.74
SRR5949848 polyp and skeleton · 31C, 24hr polyp and skeleton not recorded 31C, 24hr SRP115860 0.00

Source: CnidoSite RNA-seq expression matrices (HCOER_TPM, StringTie quantification over 37 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 Heliopora coerulea 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 correlated15ENSBQFP000000055060.827593261134928
Negatively correlated5ENSBQFP00000013717-0.735655673211422

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. Partner counts were matched on ENSBQFP00000010668, the spelling this network uses.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Heliopora coerulea, 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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