Detailed information of XP_068688048.1 in Montipora foliosa

Genomic Location: chr14:17161564...17210330
NR annotation: XP_029214566.2, rab3 GTPase-activating protein catalytic subunit-like isoform X2 [Acropora millepora]
Species Montipora foliosa · 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
Q6NUV0Rab3 GTPase-activating protein catalytic subunit OS=Danio rerio OX=7955 GN=rab3gap1 PE=2 SV=2
 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
PF19533
all species →		Rab3-GAP_cat_CRab3 GTPase-activating protein catalytic subunit C-terminalDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR026147
all species →		DomainRab3GAP catalytic subunit, conserved domainInterproscan
IPR045698
all species →		DomainRab3GAP catalytic subunit, C-terminalInterproscan
IPR045700
all species →		FamilyRab3GAP catalytic subunitInterproscan

 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 XP_068688048.1 across 36 RNA-seq samples of Montipora foliosa. 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.

36Samples
29TPM > 0
1Conditions
24.7Max TPM
10.1Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Polyps 36 29 10.06 24.73

Per sample · hover a bar for the full sample record

Show the sample table (36 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR12786903 Polyps Polyps OA4 day0 not recorded SRP199550 24.73
SRR27940180 Polyps Polyps not recorded not recorded SRP199550 17.13
SRR12904780 Polyps Polyps not recorded not recorded SRP199550 17.04
SRR12959224 Polyps Polyps E4 day3 not recorded SRP199550 16.99
SRR12959198 Polyps Polyps E4 day15 not recorded SRP199550 15.85
SRR12710854 Polyps Polyps OA4 day9 not recorded SRP199550 15.75
SRR12959225 Polyps Polyps E4 day3 not recorded SRP199550 15.17
SRR12959199 Polyps Polyps E4 day15 not recorded SRP199550 14.88
SRR12959238 Polyps Polyps E4 day0 not recorded SRP199550 13.89
SRR12959200 Polyps Polyps E4 day15 not recorded SRP199550 13.50
SRR12786904 Polyps Polyps OA4 day0 not recorded SRP199550 13.32
SRR12710852 Polyps Polyps OA4 day9 not recorded SRP199550 13.06
SRR12786895 Polyps Polyps OA4 day0 not recorded SRP199550 12.87
SRR27940177 Polyps Polyps not recorded not recorded SRP199550 12.41
SRR12710853 Polyps Polyps OA4 day9 not recorded SRP199550 12.39
SRR12904791 Polyps Polyps not recorded not recorded SRP199550 12.21
SRR12959212 Polyps Polyps E4 day9 not recorded SRP199550 11.98
SRR12959181 Polyps Polyps E4 day0 not recorded SRP199550 11.89
SRR12959213 Polyps Polyps E4 day9 not recorded SRP199550 11.32
SRR12959237 Polyps Polyps E4 day0 not recorded SRP199550 11.17
SRR12959226 Polyps Polyps E4 day3 not recorded SRP199550 10.86
SRR27940179 Polyps Polyps not recorded not recorded SRP199550 10.45
SRR12904792 Polyps Polyps not recorded not recorded SRP199550 10.43
SRR12710866 Polyps Polyps OA4 day3 not recorded SRP199550 10.13
SRR12710865 Polyps Polyps OA4 day3 not recorded SRP199550 9.63
SRR12959186 Polyps Polyps E4 day21 not recorded SRP199550 6.93
SRR12959185 Polyps Polyps E4 day21 not recorded SRP199550 6.30
SRR12959211 Polyps Polyps E4 day9 not recorded SRP199550 5.28
SRR12959187 Polyps Polyps E4 day21 not recorded SRP199550 4.61
SRR12710845 Polyps Polyps OA4 day3 not recorded SRP199550 0.00
SRR12807380 Polyps Polyps OA4 day0 not recorded SRP199550 0.00
SRR12849112 Polyps Polyps OA4 day0 not recorded SRP199550 0.00
SRR12927879 Polyps Polyps E4 day0 not recorded SRP199550 0.00
SRR12963483 Polyps Polyps E4 day0 not recorded SRP199550 0.00
SRR9129315 Polyps Polyps not recorded not recorded SRP199550 0.00
SRR9613518 Polyps Polyps not recorded not recorded SRP199550 0.00

Source: CnidoSite RNA-seq expression matrices (MFOLI_TPM, StringTie quantification over 36 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 Montipora foliosa 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 correlated20XP_068693705.10.94885543715378
Negatively correlated3XP_068681185.1-0.460604017017016

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 Montipora foliosa, 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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