Detailed information of ENSBQFP00000024889.1 in Heliopora coerulea

Genomic Location: JASJOG010000074.1:709590...727538
NR annotation: XP_028395367.1, LOW QUALITY PROTEIN: nucleosome-remodeling factor subunit BPTF-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
Q12830Nucleosome-remodeling factor subunit BPTF OS=Homo sapiens OX=9606 GN=BPTF PE=1 SV=3
Q9W0T1Nucleosome-remodeling factor subunit NURF301 OS=Drosophila melanogaster OX=7227 GN=E(bx) PE=1 SV=2
Q6BER5Nucleosome-remodeling factor subunit NURF301-like OS=Caenorhabditis elegans OX=6239 GN=nurf-1 PE=1 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0004598 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00439
all species →		BromodomainBromodomainDomainInterproscan
PF15613
all species →		WSDWilliams-Beuren syndrome DDT (WSD), D-TOX E motifFamilyInterproscan
PF00628
all species →		PHDPHD-fingerDomainInterproscan
PF02791
all species →		DDTDDT domainFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR036427
all species →		Homologous_superfamilyBromodomain-like superfamilyInterproscan
IPR019787
all species →		DomainZinc finger, PHD-fingerInterproscan
IPR001487
all species →		DomainBromodomainInterproscan
IPR001965
all species →		DomainZinc finger, PHD-typeInterproscan
IPR011011
all species →		Homologous_superfamilyZinc finger, FYVE/PHD-typeInterproscan
IPR028941
all species →		DomainWHIM2 domainInterproscan
IPR018359
all species →		Conserved_siteBromodomain, conserved siteInterproscan
IPR013083
all species →		Homologous_superfamilyZinc finger, RING/FYVE/PHD-typeInterproscan
IPR018501
all species →		DomainDDT domainInterproscan
IPR019786
all species →		Conserved_siteZinc finger, PHD-type, conserved siteInterproscan
IPR038028
all species →		FamilyNucleosome-remodeling factor subunit BPTFInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR45975
all species →		NUCLEOSOME-REMODELING FACTOR SUBUNIT BPTFInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005515
all species →		Molecular Functionprotein bindingInterproscan
GO:0000978
all species →		Molecular FunctionRNA polymerase II cis-regulatory region sequence-specific DNA bindingInterproscan
GO:0006357
all species →		Biological Processregulation of transcription by RNA polymerase IIInterproscan
GO:0016589
all species →		Cellular ComponentNURF complexInterproscan
GO:0035064
all species →		Molecular Functionmethylated histone 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
K11728BPTF, E(bx); nucleosome-remodeling factor subunit BPTF-Chromosome and associated proteinsko03036deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of ENSBQFP00000024889.1 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
34TPM > 0
6Conditions
53.2Max TPM
26.5Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Whole coral 17 16 17.51 25.20
polyp and skeleton · 31C, 3week 6 6 36.33 45.15
polyp and skeleton · 28C, 3week 6 5 29.58 52.89
polyp and skeleton · 26C, 3week 4 3 27.55 48.61
polyp and skeleton · 28C, 24hr 2 2 45.70 53.19
polyp and skeleton · 31C, 24hr 2 2 42.32 44.42

Per sample · hover a bar for the full sample record

Show the sample table (37 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
ERR6178389 Whole coral Whole coral not recorded not recorded ERP120267 25.20
ERR6178773 Whole coral Whole coral not recorded not recorded ERP120267 24.64
ERR6178779 Whole coral Whole coral not recorded not recorded ERP120267 22.94
ERR6178388 Whole coral Whole coral not recorded not recorded ERP120267 22.67
ERR6178774 Whole coral Whole coral not recorded not recorded ERP120267 21.53
ERR6178776 Whole coral Whole coral not recorded not recorded ERP120267 20.88
ERR6178387 Whole coral Whole coral not recorded not recorded ERP120267 19.62
ERR6178778 Whole coral Whole coral not recorded not recorded ERP120267 18.80
ERR6178781 Whole coral Whole coral not recorded not recorded ERP120267 18.73
ERR6178771 Whole coral Whole coral not recorded not recorded ERP120267 18.41
ERR6178782 Whole coral Whole coral not recorded not recorded ERP120267 17.80
ERR6178772 Whole coral Whole coral not recorded not recorded ERP120267 17.37
ERR6178770 Whole coral Whole coral not recorded not recorded ERP120267 14.64
ERR6178783 Whole coral Whole coral not recorded not recorded ERP120267 14.41
ERR6178777 Whole coral Whole coral not recorded not recorded ERP120267 10.28
ERR6178780 Whole coral Whole coral not recorded not recorded ERP120267 9.75
ERR6178775 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 45.15
SRR12578066 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 42.05
SRR12578065 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 39.06
SRR12587799 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 38.82
SRR12587800 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 31.43
SRR12578068 polyp and skeleton · 31C, 3week polyp and skeleton not recorded 31C, 3week SRP115860 21.48
SRR5949849 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 52.89
SRR12587802 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 45.64
SRR12587807 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 29.88
SRR12587808 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 26.27
SRR12587803 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 22.79
SRR12578067 polyp and skeleton · 28C, 3week polyp and skeleton not recorded 28C, 3week SRP115860 0.00
SRR12587801 polyp and skeleton · 26C, 3week polyp and skeleton not recorded 26C, 3week SRP115860 48.61
SRR12587805 polyp and skeleton · 26C, 3week polyp and skeleton not recorded 26C, 3week SRP115860 31.94
SRR12587798 polyp and skeleton · 26C, 3week polyp and skeleton not recorded 26C, 3week SRP115860 29.63
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 53.19
SRR12578063 polyp and skeleton · 28C, 24hr polyp and skeleton not recorded 28C, 24hr SRP115860 38.21
SRR5949848 polyp and skeleton · 31C, 24hr polyp and skeleton not recorded 31C, 24hr SRP115860 44.42
SRR12578064 polyp and skeleton · 31C, 24hr polyp and skeleton not recorded 31C, 24hr SRP115860 40.21

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 correlated20ENSBQFP000000372900.872430525531963
Negatively correlated33ENSBQFP00000003140-0.82108233319877

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 ENSBQFP00000024889, 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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