Detailed information of ENSBQFP00000013490.1 in Heliopora coerulea

Genomic Location: JASJOG010000027.1:1541130...1547545
NR annotation: XP_028415258.1, E3 ubiquitin-protein ligase RNF34-like [Dendronephthya gigantea]
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
Q6AYH3E3 ubiquitin-protein ligase RNF34 OS=Rattus norvegicus OX=10116 GN=Rnf34 PE=1 SV=1
Q99KR6E3 ubiquitin-protein ligase RNF34 OS=Mus musculus OX=10090 GN=Rnf34 PE=1 SV=1
Q969K3E3 ubiquitin-protein ligase RNF34 OS=Homo sapiens OX=9606 GN=RNF34 PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0008710 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF13920
all species →		zf-C3HC4_3Zinc finger, C3HC4 type (RING finger)DomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR051728
all species →		FamilyRING-FYVE domain-containing E3 ubiquitin-protein ligaseInterproscan
IPR036361
all species →		Homologous_superfamilySAP domain superfamilyInterproscan
IPR013083
all species →		Homologous_superfamilyZinc finger, RING/FYVE/PHD-typeInterproscan
IPR011011
all species →		Homologous_superfamilyZinc finger, FYVE/PHD-typeInterproscan
IPR017455
all species →		DomainZinc finger, FYVE-relatedInterproscan
IPR001841
all species →		DomainZinc finger, RING-typeInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR14879
all species →		CASPASE REGULATOR, RING FINGER DOMAIN-CONTAININGInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005737
all species →		Cellular ComponentcytoplasmInterproscan
GO:0005886
all species →		Cellular Componentplasma membraneInterproscan
GO:0043161
all species →		Biological Processproteasome-mediated ubiquitin-dependent protein catabolic processInterproscan
GO:0061630
all species →		Molecular Functionubiquitin protein ligase activityInterproscan
GO:0070936
all species →		Biological Processprotein K48-linked ubiquitinationInterproscan
GO:1902042
all species →		Biological Processnegative regulation of extrinsic apoptotic signaling pathway via death domain receptorsInterproscan
GO:2001271
all species →		Biological Processobsolete negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosisInterproscan

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
K20804RNF34; E3 ubiquitin-protein ligase RNF34EC:2.3.2.31
Ubiquitin systemko04121deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of ENSBQFP00000013490.1 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
31TPM > 0
6Conditions
49.1Max TPM
22.1Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Whole coral 17 16 25.83 49.08
polyp and skeleton · 31C, 3week 6 6 22.07 38.35
polyp and skeleton · 28C, 3week 6 4 18.45 40.71
polyp and skeleton · 26C, 3week 4 2 18.84 42.99
polyp and skeleton · 28C, 24hr 2 2 22.60 23.13
polyp and skeleton · 31C, 24hr 2 1 7.82 15.63

Per sample · hover a bar for the full sample record

Show the sample table (37 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
ERR6178775 Whole coral Whole coral not recorded not recorded ERP120267 49.08
ERR6178771 Whole coral Whole coral not recorded not recorded ERP120267 41.72
ERR6178781 Whole coral Whole coral not recorded not recorded ERP120267 41.58
ERR6178773 Whole coral Whole coral not recorded not recorded ERP120267 29.17
ERR6178770 Whole coral Whole coral not recorded not recorded ERP120267 27.55
ERR6178780 Whole coral Whole coral not recorded not recorded ERP120267 26.97
ERR6178388 Whole coral Whole coral not recorded not recorded ERP120267 25.82
ERR6178776 Whole coral Whole coral not recorded not recorded ERP120267 25.49
ERR6178774 Whole coral Whole coral not recorded not recorded ERP120267 25.48
ERR6178387 Whole coral Whole coral not recorded not recorded ERP120267 25.05
ERR6178778 Whole coral Whole coral not recorded not recorded ERP120267 23.88
ERR6178783 Whole coral Whole coral not recorded not recorded ERP120267 23.12
ERR6178782 Whole coral Whole coral not recorded not recorded ERP120267 21.03
ERR6178772 Whole coral Whole coral not recorded not recorded ERP120267 20.60
ERR6178779 Whole coral Whole coral not recorded not recorded ERP120267 19.28
ERR6178389 Whole coral Whole coral not recorded not recorded ERP120267 13.33
ERR6178777 Whole coral Whole coral not recorded not recorded ERP120267 0.00
SRR12587804 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 38.35
SRR12578068 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 26.75
SRR12578065 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 24.96
SRR12587800 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 18.01
SRR12578066 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 12.70
SRR12587799 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 11.67
SRR12587802 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 40.71
SRR12587808 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 33.60
SRR12587803 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 21.09
SRR12587807 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 15.32
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 42.99
SRR12587805 polyp and skeleton · 26C, 3week polyp and skeleton not recorded 26C, 3week SRP115860 32.37
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
SRR5949850 polyp and skeleton · 28C, 24hr polyp and skeleton not recorded 28C, 24hr SRP115860 23.13
SRR12578063 polyp and skeleton · 28C, 24hr polyp and skeleton not recorded 28C, 24hr SRP115860 22.06
SRR12578064 polyp and skeleton · 31C, 24hr polyp and skeleton not recorded 31C, 24hr SRP115860 15.63
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 correlated17ENSBQFP000000165800.788125053099654
Negatively correlated5ENSBQFP00000028427-0.60513992649486

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 ENSBQFP00000013490, 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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