Detailed information of asel_s0237.g39.t1 in Acropora selago

Genomic Location: sc0000237_pilon:441491...456345
NR annotation: XP_029206897.2, phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit beta isoform-like [Acropora millepora]
Species Acropora selago · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q9Z1L0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit beta isoform OS=Rattus norvegicus OX=10116 GN=Pik3cb PE=2 SV=1
Q8BTI9Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit beta isoform OS=Mus musculus OX=10090 GN=Pik3cb PE=1 SV=2
P42338Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit beta isoform OS=Homo sapiens OX=9606 GN=PIK3CB PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0001304 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00794
all species →
PI3K_rbdPI3-kinase family, ras-binding domainDomainInterproscan
PF02192
all species →
PI3K_p85BPI3-kinase family, p85-binding domainFamilyInterproscan
PF00613
all species →
PI3KaPhosphoinositide 3-kinase family, accessory domain (PIK domain)RepeatInterproscan
PF00792
all species →
PI3K_C2Phosphoinositide 3-kinase C2DomainInterproscan
PF00454
all species →
PI3_PI4_kinasePhosphatidylinositol 3- and 4-kinaseFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR000341
all species →
DomainPhosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domainInterproscan
IPR015433
all species →
FamilyPhosphatidylinositol kinaseInterproscan
IPR003113
all species →
DomainPhosphatidylinositol 3-kinase, adaptor-binding domainInterproscan
IPR000403
all species →
DomainPhosphatidylinositol 3-/4-kinase, catalytic domainInterproscan
IPR035892
all species →
Homologous_superfamilyC2 domain superfamilyInterproscan
IPR011009
all species →
Homologous_superfamilyProtein kinase-like domain superfamilyInterproscan
IPR001263
all species →
DomainPhosphoinositide 3-kinase, accessory (PIK) domainInterproscan
IPR002420
all species →
DomainC2 phosphatidylinositol 3-kinase-type domainInterproscan
IPR018936
all species →
Conserved_sitePhosphatidylinositol 3/4-kinase, conserved siteInterproscan
IPR016024
all species →
Homologous_superfamilyArmadillo-type foldInterproscan
IPR029071
all species →
Homologous_superfamilyUbiquitin-like domain superfamilyInterproscan
IPR042236
all species →
Homologous_superfamilyPhosphoinositide 3-kinase, accessory (PIK) domain superfamilyInterproscan
IPR036940
all species →
Homologous_superfamilyPhosphatidylinositol 3-/4-kinase, catalytic domain superfamilyInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR10048
all species →
PHOSPHATIDYLINOSITOL KINASEInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005737
all species →
Cellular ComponentcytoplasmInterproscan
GO:0005886
all species →
Cellular Componentplasma membraneInterproscan
GO:0005942
all species →
Cellular Componentphosphatidylinositol 3-kinase complexInterproscan
GO:0014065
all species →
Biological Processobsolete phosphatidylinositol 3-kinase signalingInterproscan
GO:0016020
all species →
Cellular ComponentmembraneInterproscan
GO:0016303
all species →
Molecular Function1-phosphatidylinositol-3-kinase activityInterproscan
GO:0016477
all species →
Biological Processcell migrationInterproscan
GO:0035005
all species →
Molecular Function1-phosphatidylinositol-4-phosphate 3-kinase activityInterproscan
GO:0036092
all species →
Biological Processphosphatidylinositol-3-phosphate biosynthetic processInterproscan
GO:0046854
all species →
Biological Processphosphatidylinositol phosphate biosynthetic processInterproscan
GO:0048015
all species →
Biological Processphosphatidylinositol-mediated signalingInterproscan
GO:0052742
all species →
Molecular Functionphosphatidylinositol kinase activityInterproscan
GO:0016301
all species →
Molecular Functionkinase activityInterproscan

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
K00922PIK3CA_B_D; phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha/beta/deltaEC:2.7.1.153
Membrane traffickingko04131deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of asel_s0237.g39.t1 across 24 RNA-seq samples of Acropora selago. 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.

24Samples
22TPM > 0
1Conditions
31.1Max TPM
21.2Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
coral larvae 24 22 21.15 31.09

Per sample · hover a bar for the full sample record

Show the sample table (24 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR14308026 coral larvae coral larvae not recorded not recorded SRP315987 31.09
SRR14308015 coral larvae coral larvae not recorded not recorded SRP315987 29.20
SRR14308021 coral larvae coral larvae not recorded not recorded SRP315987 28.67
SRR14308018 coral larvae coral larvae not recorded not recorded SRP315987 27.72
SRR14308006 coral larvae coral larvae not recorded not recorded SRP315987 27.45
SRR14308024 coral larvae coral larvae not recorded not recorded SRP315987 27.08
SRR14308022 coral larvae coral larvae not recorded not recorded SRP315987 26.42
SRR14308012 coral larvae coral larvae not recorded not recorded SRP315987 25.65
SRR14308008 coral larvae coral larvae not recorded not recorded SRP315987 25.32
SRR14308027 coral larvae coral larvae not recorded not recorded SRP315987 25.20
SRR14308025 coral larvae coral larvae not recorded not recorded SRP315987 24.49
SRR14308011 coral larvae coral larvae not recorded not recorded SRP315987 24.06
SRR14308016 coral larvae coral larvae not recorded not recorded SRP315987 23.16
SRR14308014 coral larvae coral larvae not recorded not recorded SRP315987 20.96
SRR14308010 coral larvae coral larvae not recorded not recorded SRP315987 20.21
SRR14308019 coral larvae coral larvae not recorded not recorded SRP315987 19.77
SRR14308004 coral larvae coral larvae not recorded not recorded SRP315987 19.76
SRR14308007 coral larvae coral larvae not recorded not recorded SRP315987 19.63
SRR14308017 coral larvae coral larvae not recorded not recorded SRP315987 18.58
SRR14308023 coral larvae coral larvae not recorded not recorded SRP315987 16.26
SRR14308013 coral larvae coral larvae not recorded not recorded SRP315987 14.28
SRR14308020 coral larvae coral larvae not recorded not recorded SRP315987 12.74
SRR14308005 coral larvae coral larvae not recorded not recorded SRP315987 0.00
SRR14308009 coral larvae coral larvae not recorded not recorded SRP315987 0.00

Source: CnidoSite RNA-seq expression matrices (ASELA_TPM, StringTie quantification over 24 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 Acropora selago 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 correlated46asel_s0001.g48.t10.95685947898996
Negatively correlated4asel_s0162.g22.t1-0.838568874124257

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.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Acropora selago, 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.

DNA methylation (bisulphite samples)

SampleMethylation profile
Coral_Fragment_Parentopen
Larval_Pool_Offspringopen

The DNA Methylation page locates this gene by scanning the bisulphite table, which holds one row per cytosine. For the largest datasets that scan takes a while to return; it does not mean the link is broken.

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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