Detailed information of g20511.t1 in Montipora capitata

Genomic Location: Sc0001200:45132...49621
NR annotation: KAJ7383965.1, Ras- protein Rab-1A [Desmophyllum pertusum]
Species Montipora capitata · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
P62822Ras-related protein Rab-1A OS=Canis lupus familiaris OX=9615 GN=RAB1A PE=1 SV=3
P62820Ras-related protein Rab-1A OS=Homo sapiens OX=9606 GN=RAB1A PE=1 SV=3
P62821Ras-related protein Rab-1A OS=Mus musculus OX=10090 GN=Rab1a PE=1 SV=3
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0000044 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00071
all species →		RasRas familyDomainInterproscan

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

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

 Gene Ontology
GO termCategoryDescriptionSource
GO:0016192
all species →		Biological Processvesicle-mediated transportInterproscan
GO:0003924
all species →		Molecular FunctionGTPase activityInterproscan
GO:0005525
all species →		Molecular FunctionGTP 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
K07874RAB1A; Ras-related protein Rab-1A-GTP-binding proteinsko04031deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g20511.t1 across 48 RNA-seq samples of Montipora capitata. 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.

48Samples
48TPM > 0
3Conditions
440.0Max TPM
283.3Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
whole organisms · ambient pH treatment 21 21 288.49 440.02
whole organisms · low pH treatment 15 15 276.44 419.35
whole organisms · extra low pH treatment pH treatment 12 12 282.69 426.29

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR11452242 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 440.02
SRR11452243 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 428.62
SRR11452237 whole organisms · ambient pH treatment whole organisms gastrula ambient pH treatment SRP254626 426.91
SRR11452246 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 409.28
SRR11452250 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 397.80
SRR11452252 whole organisms · ambient pH treatment whole organisms prawn chip ambient pH treatment SRP254626 393.46
SRR11452234 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 351.47
SRR11452254 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 296.60
SRR11452232 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 288.96
SRR11452233 whole organisms · ambient pH treatment whole organisms morula ambient pH treatment SRP254626 287.85
SRR11452259 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 278.45
SRR11452263 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 238.06
SRR11452217 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 227.63
SRR11452231 whole organisms · ambient pH treatment whole organisms blastula ambient pH treatment SRP254626 224.08
SRR11452240 whole organisms · ambient pH treatment whole organisms fertilized embryo ambient pH treatment SRP254626 220.03
SRR11452260 whole organisms · ambient pH treatment whole organisms cleavage ambient pH treatment SRP254626 214.40
SRR11452262 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 209.09
SRR11452251 whole organisms · ambient pH treatment whole organisms egg ambient pH treatment SRP254626 198.60
SRR11452230 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 188.66
SRR11452222 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 172.10
SRR11452228 whole organisms · ambient pH treatment whole organisms planulae ambient pH treatment SRP254626 166.21
SRR11452236 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 419.35
SRR11452247 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 390.18
SRR11452245 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 384.40
SRR11452238 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 365.71
SRR11452241 whole organisms · low pH treatment whole organisms gastrula low pH treatment SRP254626 349.89
SRR11452249 whole organisms · low pH treatment whole organisms prawn chip low pH treatment SRP254626 341.02
SRR11452258 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 291.65
SRR11452253 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 218.76
SRR11452216 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 216.01
SRR11452229 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 213.89
SRR11452218 whole organisms · low pH treatment whole organisms fertilized embryo low pH treatment SRP254626 211.33
SRR11452255 whole organisms · low pH treatment whole organisms cleavage low pH treatment SRP254626 194.36
SRR11452221 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 186.06
SRR11452223 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 185.15
SRR11452224 whole organisms · low pH treatment whole organisms planulae low pH treatment SRP254626 178.84
SRR11452239 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 426.29
SRR11452248 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 405.61
SRR11452244 whole organisms · extra low pH treatment pH treatment whole organisms prawn chip extra low pH treatment pH treatment SRP254626 404.05
SRR11452235 whole organisms · extra low pH treatment pH treatment whole organisms gastrula extra low pH treatment pH treatment SRP254626 391.57
SRR11452257 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 293.86
SRR11452256 whole organisms · extra low pH treatment pH treatment whole organisms cleavage extra low pH treatment pH treatment SRP254626 285.01
SRR11452220 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 243.62
SRR11452261 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 222.18
SRR11452219 whole organisms · extra low pH treatment pH treatment whole organisms fertilized embryo extra low pH treatment pH treatment SRP254626 197.79
SRR11452225 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 193.81
SRR11452227 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 172.71
SRR11452226 whole organisms · extra low pH treatment pH treatment whole organisms planulae extra low pH treatment pH treatment SRP254626 155.82

Source: CnidoSite RNA-seq expression matrices (MCAPI_TPM, StringTie quantification over 48 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 capitata 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 correlated19g15745.t10.947966475935788
Negatively correlated16g3545.t1-0.925855802333449

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 capitata, 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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