Detailed information of ENSBQFP00000030373.1 in Heliopora coerulea

Genomic Location: JASJOG010000101.1:513642...524009
NR annotation: CAB3980084.1, nibrin isoform X2 [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
Q6XV80Nibrin OS=Xenopus laevis OX=8355 GN=nbn.L PE=1 SV=1
Q9DE07Nibrin OS=Gallus gallus OX=9031 GN=NBN PE=1 SV=1
Q5RCV3Nibrin OS=Pongo abelii OX=9601 GN=NBN PE=2 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0004927 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF16508
all species →		NIBRIN_BRCT_IISecond BRCT domain on Nijmegen syndrome breakage proteinDomainInterproscan
PF08599
all species →		Nbs1_CDNA damage repair protein Nbs1FamilyInterproscan
PF00498
all species →		FHAFHA domainFamilyInterproscan
PF00533
all species →		BRCTBRCA1 C Terminus (BRCT) domainFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR000253
all species →		DomainForkhead-associated (FHA) domainInterproscan
IPR032429
all species →		DomainNibrin, second BRCT domainInterproscan
IPR043014
all species →		Homologous_superfamilyNibrin, second BRCT domain superfamilyInterproscan
IPR013908
all species →		DomainNibrin, C-terminalInterproscan
IPR040227
all species →		FamilyNibrin-relatedInterproscan
IPR008984
all species →		Homologous_superfamilySMAD/FHA domain superfamilyInterproscan
IPR036420
all species →		Homologous_superfamilyBRCT domain superfamilyInterproscan
IPR001357
all species →		DomainBRCT domainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR12162
all species →		NIBRIN-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005515
all species →		Molecular Functionprotein bindingInterproscan
GO:0000724
all species →		Biological Processdouble-strand break repair via homologous recombinationInterproscan
GO:0003684
all species →		Molecular Functiondamaged DNA bindingInterproscan
GO:0006302
all species →		Biological Processdouble-strand break repairInterproscan
GO:0007095
all species →		Biological Processmitotic G2 DNA damage checkpoint signalingInterproscan
GO:0030870
all species →		Cellular ComponentMre11 complexInterproscan
GO:0032508
all species →		Biological ProcessDNA duplex unwindingInterproscan

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
K10867NBN, NBS1; nibrin-DNA repair and recombination proteinsko03400deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of ENSBQFP00000030373.1 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
85.0Max TPM
17.7Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Whole coral 17 14 13.35 24.73
polyp and skeleton · 31C, 3week 6 6 19.59 23.68
polyp and skeleton · 28C, 3week 6 5 26.47 85.04
polyp and skeleton · 26C, 3week 4 3 22.61 38.59
polyp and skeleton · 28C, 24hr 2 2 21.32 26.34
polyp and skeleton · 31C, 24hr 2 1 8.59 17.19

Per sample · hover a bar for the full sample record

Show the sample table (37 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
ERR6178777 Whole coral Whole coral not recorded not recorded ERP120267 24.73
ERR6178781 Whole coral Whole coral not recorded not recorded ERP120267 21.92
ERR6178773 Whole coral Whole coral not recorded not recorded ERP120267 17.99
ERR6178776 Whole coral Whole coral not recorded not recorded ERP120267 17.96
ERR6178387 Whole coral Whole coral not recorded not recorded ERP120267 17.78
ERR6178389 Whole coral Whole coral not recorded not recorded ERP120267 16.94
ERR6178388 Whole coral Whole coral not recorded not recorded ERP120267 16.78
ERR6178774 Whole coral Whole coral not recorded not recorded ERP120267 15.04
ERR6178779 Whole coral Whole coral not recorded not recorded ERP120267 14.94
ERR6178772 Whole coral Whole coral not recorded not recorded ERP120267 13.94
ERR6178778 Whole coral Whole coral not recorded not recorded ERP120267 13.88
ERR6178783 Whole coral Whole coral not recorded not recorded ERP120267 12.61
ERR6178780 Whole coral Whole coral not recorded not recorded ERP120267 11.42
ERR6178770 Whole coral Whole coral not recorded not recorded ERP120267 11.05
ERR6178771 Whole coral Whole coral not recorded not recorded ERP120267 0.00
ERR6178775 Whole coral Whole coral not recorded not recorded ERP120267 0.00
ERR6178782 Whole coral Whole coral not recorded not recorded ERP120267 0.00
SRR12587800 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 23.68
SRR12587804 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 22.77
SRR12578066 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 21.20
SRR12578065 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 17.61
SRR12587799 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 16.51
SRR12578068 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 15.77
SRR5949849 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 85.04
SRR12587802 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 23.58
SRR12587807 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 20.42
SRR12587808 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 18.64
SRR12587803 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 11.11
SRR12578067 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 0.00
SRR12587806 polyp and skeleton · 26C, 3week polyp and skeleton not recorded 26C, 3week SRP115860 38.59
SRR12587798 polyp and skeleton · 26C, 3week polyp and skeleton not recorded 26C, 3week SRP115860 26.08
SRR12587805 polyp and skeleton · 26C, 3week polyp and skeleton not recorded 26C, 3week SRP115860 25.77
SRR12587801 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 26.34
SRR5949850 polyp and skeleton · 28C, 24hr polyp and skeleton not recorded 28C, 24hr SRP115860 16.30
SRR12578064 polyp and skeleton · 31C, 24hr polyp and skeleton not recorded 31C, 24hr SRP115860 17.19
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 correlated25ENSBQFP000000366560.914003905448957
Negatively correlated4ENSBQFP00000035499-0.727318396831083

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 ENSBQFP00000030373, 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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