Detailed information of ENSBQFP00000038219.1 in Heliopora coerulea

Genomic Location: JASJOG010000128.1:292533...325601
NR annotation: CAB3977639.1, lipopolysaccharide-responsive and beige-like anchor, partial [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
Q9ESE1Lipopolysaccharide-responsive and beige-like anchor protein OS=Mus musculus OX=10090 GN=Lrba PE=1 SV=1
P50851Lipopolysaccharide-responsive and beige-like anchor protein OS=Homo sapiens OX=9606 GN=LRBA PE=1 SV=4
Q9EPN1Neurobeachin OS=Mus musculus OX=10090 GN=Nbea PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0002506 (this species only) · gene tree & orthology
Ubiquitin familyUBD|Other|Beta-prp · all ubiquitin genes in this species
Ubiquitin familyE3|E3 adaptor Cullin RING|CDC20 · all ubiquitin genes in this species
Ubiquitin familyE3|E3 adaptor Cullin RING|DWD · all ubiquitin genes in this species

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF20426
all species →		NBCH_WD40Neurobeachin beta propeller domainRepeatInterproscan
PF02138
all species →		BeachBeige/BEACH domainFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR015943
all species →		Homologous_superfamilyWD40/YVTN repeat-like-containing domain superfamilyInterproscan
IPR001680
all species →		RepeatWD40 repeatInterproscan
IPR050865
all species →		FamilyBEACH Domain-ContainingInterproscan
IPR046851
all species →		DomainNeurobeachin, beta-propeller domainInterproscan
IPR000409
all species →		DomainBEACH domainInterproscan
IPR036372
all species →		Homologous_superfamilyBEACH domain superfamilyInterproscan
IPR036322
all species →		Homologous_superfamilyWD40-repeat-containing domain superfamilyInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR13743
all species →		BEIGE/BEACH-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005515
all species →		Molecular Functionprotein bindingInterproscan
GO:0005829
all species →		Cellular ComponentcytosolInterproscan
GO:0008104
all species →		Biological Processprotein localizationInterproscan
GO:0016020
all species →		Cellular ComponentmembraneInterproscan
GO:0019901
all species →		Molecular Functionprotein kinase 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
No KEGG orthology assignment for ENSBQFP00000038219.1.

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

Expression pattern (RNA-seq)

Transcript abundance of ENSBQFP00000038219.1 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
37TPM > 0
6Conditions
110.9Max TPM
70.3Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Whole coral 17 17 78.24 110.88
polyp and skeleton · 31C, 3week 6 6 42.23 74.06
polyp and skeleton · 28C, 3week 6 6 78.93 105.33
polyp and skeleton · 26C, 3week 4 4 71.78 97.36
polyp and skeleton · 28C, 24hr 2 2 72.32 83.58
polyp and skeleton · 31C, 24hr 2 2 56.17 74.04

Per sample · hover a bar for the full sample record

Show the sample table (37 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
ERR6178781 Whole coral Whole coral not recorded not recorded ERP120267 110.88
ERR6178775 Whole coral Whole coral not recorded not recorded ERP120267 96.05
ERR6178387 Whole coral Whole coral not recorded not recorded ERP120267 85.30
ERR6178776 Whole coral Whole coral not recorded not recorded ERP120267 82.30
ERR6178777 Whole coral Whole coral not recorded not recorded ERP120267 82.12
ERR6178782 Whole coral Whole coral not recorded not recorded ERP120267 82.06
ERR6178771 Whole coral Whole coral not recorded not recorded ERP120267 81.87
ERR6178388 Whole coral Whole coral not recorded not recorded ERP120267 81.85
ERR6178772 Whole coral Whole coral not recorded not recorded ERP120267 79.46
ERR6178779 Whole coral Whole coral not recorded not recorded ERP120267 76.75
ERR6178770 Whole coral Whole coral not recorded not recorded ERP120267 72.94
ERR6178773 Whole coral Whole coral not recorded not recorded ERP120267 71.33
ERR6178778 Whole coral Whole coral not recorded not recorded ERP120267 68.10
ERR6178389 Whole coral Whole coral not recorded not recorded ERP120267 65.59
ERR6178783 Whole coral Whole coral not recorded not recorded ERP120267 65.16
ERR6178780 Whole coral Whole coral not recorded not recorded ERP120267 65.08
ERR6178774 Whole coral Whole coral not recorded not recorded ERP120267 63.18
SRR12587800 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 74.06
SRR12578065 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 44.89
SRR12587804 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 40.52
SRR12578068 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 38.66
SRR12578066 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 28.08
SRR12587799 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 27.19
SRR5949849 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 105.33
SRR12587802 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 104.08
SRR12587803 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 97.28
SRR12578067 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 72.38
SRR12587808 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 53.59
SRR12587807 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 40.89
SRR12587806 polyp and skeleton · 26C, 3week polyp and skeleton not recorded 26C, 3week SRP115860 97.36
SRR12587798 polyp and skeleton · 26C, 3week polyp and skeleton not recorded 26C, 3week SRP115860 79.41
SRR12587801 polyp and skeleton · 26C, 3week polyp and skeleton not recorded 26C, 3week SRP115860 60.94
SRR12587805 polyp and skeleton · 26C, 3week polyp and skeleton not recorded 26C, 3week SRP115860 49.39
SRR12578063 polyp and skeleton · 28C, 24hr polyp and skeleton not recorded 28C, 24hr SRP115860 83.58
SRR5949850 polyp and skeleton · 28C, 24hr polyp and skeleton not recorded 28C, 24hr SRP115860 61.06
SRR5949848 polyp and skeleton · 31C, 24hr polyp and skeleton not recorded 31C, 24hr SRP115860 74.04
SRR12578064 polyp and skeleton · 31C, 24hr polyp and skeleton not recorded 31C, 24hr SRP115860 38.29

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 correlated1ENSBQFP000000251280.708684596438364
Negatively correlated175ENSBQFP00000045525-0.710966580378673

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 ENSBQFP00000038219, 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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