Detailed information of gfas1.m1.744.m1 in Galaxea fascicularis

Genomic Location: Sc0000015:574...16851
NR annotation: CAH3192828.1, unnamed protein product [Porites evermanni]
Species Galaxea fascicularis · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q15042Rab3 GTPase-activating protein catalytic subunit OS=Homo sapiens OX=9606 GN=RAB3GAP1 PE=1 SV=3
Q80UJ7Rab3 GTPase-activating protein catalytic subunit OS=Mus musculus OX=10090 GN=Rab3gap1 PE=1 SV=4
Q642R9Rab3 GTPase-activating protein catalytic subunit OS=Xenopus laevis OX=8355 GN=rab3gap1 PE=2 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0003186 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF13890
all species →		Rab3-GTPase_catRab3 GTPase-activating protein catalytic subunitFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR045700
all species →		FamilyRab3GAP catalytic subunitInterproscan
IPR026147
all species →		DomainRab3GAP catalytic subunit, conserved domainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR21422
all species →		RAB3 GTPASE-ACTIVATING PROTEIN CATALYTIC SUBUNITInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005096
all species →		Molecular FunctionGTPase activator activityInterproscan
GO:0043547
all species →		Biological Processpositive regulation of GTPase 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
K18270RAB3GAP1; Rab3 GTPase-activating protein catalytic subunit-Exosomeko04147deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of gfas1.m1.744.m1 across 22 RNA-seq samples of Galaxea fascicularis. 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.

22Samples
20TPM > 0
4Conditions
152.0Max TPM
37.0Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
coral holosome · Control 7 7 51.56 152.03
coral holosome · 30ic treatment 6 4 22.68 39.56
coral holosome · Prometryn (herbicidess) treatment 5 5 35.77 54.27
coral holosome · Prometryn (herbicidess) and 30ic treatment 4 4 34.70 50.91

Per sample · hover a bar for the full sample record

Show the sample table (22 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR27118485 coral holosome · Control coral holosome not recorded Control SRP476288 152.03
SRR27118488 coral holosome · Control coral holosome not recorded Control SRP476288 62.53
SRR27118480 coral holosome · Control coral holosome not recorded Control SRP476288 38.22
SRR27118487 coral holosome · Control coral holosome not recorded Control SRP476288 33.45
SRR27118486 coral holosome · Control coral holosome not recorded Control SRP476288 30.11
SRR27118491 coral holosome · Control coral holosome not recorded Control SRP476288 22.56
SRR27118492 coral holosome · Control coral holosome not recorded Control SRP476288 22.04
SRR27118476 coral holosome · 30ic treatment coral holosome not recorded 30ic treatment SRP476288 39.56
SRR27118478 coral holosome · 30ic treatment coral holosome not recorded 30ic treatment SRP476288 39.06
SRR27118479 coral holosome · 30ic treatment coral holosome not recorded 30ic treatment SRP476288 34.77
SRR27118466 coral holosome · 30ic treatment coral holosome not recorded 30ic treatment SRP476288 22.71
SRR27118468 coral holosome · 30ic treatment coral holosome not recorded 30ic treatment SRP476288 0.00
SRR27118477 coral holosome · 30ic treatment coral holosome not recorded 30ic treatment SRP476288 0.00
SRR27118483 coral holosome · Prometryn (herbicidess) treatment coral holosome not recorded Prometryn (herbicidess) treatment SRP476288 54.27
SRR27118482 coral holosome · Prometryn (herbicidess) treatment coral holosome not recorded Prometryn (herbicidess) treatment SRP476288 47.16
SRR27118484 coral holosome · Prometryn (herbicidess) treatment coral holosome not recorded Prometryn (herbicidess) treatment SRP476288 35.17
SRR27118481 coral holosome · Prometryn (herbicidess) treatment coral holosome not recorded Prometryn (herbicidess) treatment SRP476288 30.75
SRR27118469 coral holosome · Prometryn (herbicidess) treatment coral holosome not recorded Prometryn (herbicidess) treatment SRP476288 11.49
SRR27118489 coral holosome · Prometryn (herbicidess) and 30ic treatment coral holosome not recorded Prometryn (herbicidess) and 30ic treatment SRP476288 50.91
SRR27118472 coral holosome · Prometryn (herbicidess) and 30ic treatment coral holosome not recorded Prometryn (herbicidess) and 30ic treatment SRP476288 36.88
SRR27118490 coral holosome · Prometryn (herbicidess) and 30ic treatment coral holosome not recorded Prometryn (herbicidess) and 30ic treatment SRP476288 28.56
SRR27118475 coral holosome · Prometryn (herbicidess) and 30ic treatment coral holosome not recorded Prometryn (herbicidess) and 30ic treatment SRP476288 22.46

Source: CnidoSite RNA-seq expression matrices (GFASC_TPM, StringTie quantification over 22 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 Galaxea fascicularis 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 correlated17gfas1.m1.3366.m10.949103260006557
Negatively correlated14gfas1.m1.2354.m1-0.801512324656564

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 Galaxea fascicularis, 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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