Detailed information of g8697.t1 in Acropora digitifera

Genomic Location: chr4Alt:11999143...12000808
NR annotation: XP_029204262.1, ras-related protein Rab-14-like [Acropora millepora]
Species Acropora digitifera · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
P36410Ras-related protein Rab-14 OS=Dictyostelium discoideum OX=44689 GN=rab14 PE=1 SV=2
Q05737GTP-binding protein YPTM2 OS=Zea mays OX=4577 GN=YPTM2 PE=2 SV=1
Q9FPJ4Ras-related protein RABD2b OS=Arabidopsis thaliana OX=3702 GN=RABD2B PE=1 SV=1
 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00071
all species →		RasRas familyDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR027417
all species →		Homologous_superfamilyP-loop containing nucleoside triphosphate hydrolaseInterproscan
IPR001806
all species →		FamilySmall GTPaseInterproscan
IPR050227
all species →		FamilyRas-related protein RabInterproscan
IPR005225
all species →		DomainSmall GTP-binding protein domainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR47977
all species →		RAS-RELATED PROTEIN RABInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003924
all species →		Molecular FunctionGTPase activityInterproscan
GO:0005525
all species →		Molecular FunctionGTP bindingInterproscan
GO:0005802
all species →		Cellular Componenttrans-Golgi networkInterproscan
GO:0016192
all species →		Biological Processvesicle-mediated transportInterproscan
GO:0031985
all species →		Cellular ComponentGolgi cisternaInterproscan

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
No KEGG orthology assignment for g8697.t1.

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

Expression pattern (RNA-seq)

Transcript abundance of g8697.t1 across 39 RNA-seq samples of Acropora digitifera. 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.

39Samples
39TPM > 0
1Conditions
66.7Max TPM
48.8Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Coral branch 39 39 48.83 66.70

Per sample · hover a bar for the full sample record

Show the sample table (39 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR23047219 Coral branch Coral branch adult not recorded SRP416931 66.70
SRR23047209 Coral branch Coral branch adult not recorded SRP416931 61.87
SRR23047232 Coral branch Coral branch adult not recorded SRP416931 60.56
SRR23047218 Coral branch Coral branch adult not recorded SRP416931 58.57
SRR23047237 Coral branch Coral branch adult not recorded SRP416931 58.21
SRR23047223 Coral branch Coral branch adult not recorded SRP416931 56.24
SRR23047225 Coral branch Coral branch adult not recorded SRP416931 55.83
SRR23047227 Coral branch Coral branch adult not recorded SRP416931 55.11
SRR23047214 Coral branch Coral branch adult not recorded SRP416931 54.30
SRR23047207 Coral branch Coral branch adult not recorded SRP416931 54.28
SRR23047211 Coral branch Coral branch adult not recorded SRP416931 54.20
SRR23047215 Coral branch Coral branch adult not recorded SRP416931 54.18
SRR23047224 Coral branch Coral branch adult not recorded SRP416931 52.80
SRR23047238 Coral branch Coral branch adult not recorded SRP416931 51.99
SRR23047217 Coral branch Coral branch adult not recorded SRP416931 51.52
SRR23047242 Coral branch Coral branch adult not recorded SRP416931 51.51
SRR23047239 Coral branch Coral branch adult not recorded SRP416931 51.46
SRR23047230 Coral branch Coral branch adult not recorded SRP416931 51.37
SRR23047216 Coral branch Coral branch adult not recorded SRP416931 50.57
SRR23047233 Coral branch Coral branch adult not recorded SRP416931 49.70
SRR23047228 Coral branch Coral branch adult not recorded SRP416931 49.61
SRR23047240 Coral branch Coral branch adult not recorded SRP416931 46.80
SRR23047212 Coral branch Coral branch adult not recorded SRP416931 46.56
SRR23047234 Coral branch Coral branch adult not recorded SRP416931 46.48
SRR23047206 Coral branch Coral branch adult not recorded SRP416931 45.56
SRR23047231 Coral branch Coral branch adult not recorded SRP416931 44.91
SRR23047226 Coral branch Coral branch adult not recorded SRP416931 43.92
SRR23047244 Coral branch Coral branch adult not recorded SRP416931 43.41
SRR23047210 Coral branch Coral branch adult not recorded SRP416931 42.55
SRR23047220 Coral branch Coral branch adult not recorded SRP416931 42.48
SRR23047208 Coral branch Coral branch adult not recorded SRP416931 42.12
SRR23047229 Coral branch Coral branch adult not recorded SRP416931 41.41
SRR23047213 Coral branch Coral branch adult not recorded SRP416931 41.38
SRR23047222 Coral branch Coral branch adult not recorded SRP416931 39.56
SRR23047235 Coral branch Coral branch adult not recorded SRP416931 38.76
SRR23047236 Coral branch Coral branch adult not recorded SRP416931 38.36
SRR23047221 Coral branch Coral branch adult not recorded SRP416931 36.65
SRR23047243 Coral branch Coral branch adult not recorded SRP416931 36.45
SRR23047241 Coral branch Coral branch adult not recorded SRP416931 36.34

Source: CnidoSite RNA-seq expression matrices (ADIGI_TPM, StringTie quantification over 39 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 digitifera 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 correlated1g22856.t10.738606399129884
Negatively correlated7g6273.t1-0.656019345925651

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 digitifera, 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.

Peak calls overlapping this gene

AssaySamplePeaksRegion

No called peak overlaps this gene in 1 available assay. Either the gene is not near an accessible or marked region in those samples, or it is not represented in the peak caller’s annotation.

Browse the full epigenomic landscape of this species: DNase-seq (DHS).

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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