Detailed information of XP_068756404.1 in Montipora capricornis

Genomic Location: chr6:71193968...71202056
NR annotation: CAH3018334.1, unnamed protein product [Porites evermanni]
Species Montipora capricornis · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q5ZI57Trafficking protein particle complex subunit 3 OS=Gallus gallus OX=9031 GN=TRAPPC3 PE=2 SV=1
O55013Trafficking protein particle complex subunit 3 OS=Mus musculus OX=10090 GN=Trappc3 PE=1 SV=1
Q5U1Z2Trafficking protein particle complex subunit 3 OS=Rattus norvegicus OX=10116 GN=Trappc3 PE=2 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0008022 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF04051
all species →		TRAPPTransport protein particle (TRAPP) componentFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR007194
all species →		FamilyTransport protein particle (TRAPP) componentInterproscan
IPR024096
all species →		Homologous_superfamilyNO signalling/Golgi transport ligand-binding domain superfamilyInterproscan
IPR016721
all species →		FamilyBet3 familyInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR13048
all species →		TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 3Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0030008
all species →		Cellular ComponentTRAPP complexInterproscan
GO:0048193
all species →		Biological ProcessGolgi vesicle transportInterproscan
GO:0005829
all species →		Cellular ComponentcytosolInterproscan
GO:0006888
all species →		Biological Processendoplasmic reticulum to Golgi vesicle-mediated transportInterproscan
GO:0006891
all species →		Biological Processintra-Golgi vesicle-mediated transportInterproscan
GO:0033106
all species →		Cellular Componentcis-Golgi network membraneInterproscan

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
K20302TRAPPC3, BET3; trafficking protein particle complex subunit 3-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 XP_068756404.1 across 36 RNA-seq samples of Montipora capricornis. 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
200.4Max TPM
97.4Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Polyps 36 29 97.43 200.35

Per sample · hover a bar for the full sample record

Show the sample table (36 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR12959230 Polyps Polyps E3 day3 not recorded SRP199550 200.35
SRR12959203 Polyps Polyps E3 day15 not recorded SRP199550 143.37
SRR12959201 Polyps Polyps E3 day15 not recorded SRP199550 138.43
SRR12959202 Polyps Polyps E3 day15 not recorded SRP199550 136.92
SRR27940192 Polyps Polyps not recorded not recorded SRP199550 133.34
SRR12710855 Polyps Polyps OA3 day9 not recorded SRP199550 130.02
SRR27940191 Polyps Polyps not recorded not recorded SRP199550 126.38
SRR12904783 Polyps Polyps not recorded not recorded SRP199550 125.98
SRR12904781 Polyps Polyps not recorded not recorded SRP199550 125.30
SRR12904782 Polyps Polyps not recorded not recorded SRP199550 124.92
SRR12786898 Polyps Polyps OA3 day0 not recorded SRP199550 122.70
SRR12959216 Polyps Polyps E3 day9 not recorded SRP199550 121.91
SRR12959188 Polyps Polyps E3 day21 not recorded SRP199550 119.66
SRR12959229 Polyps Polyps E3 day3 not recorded SRP199550 119.64
SRR27940193 Polyps Polyps not recorded not recorded SRP199550 118.58
SRR12959189 Polyps Polyps E3 day21 not recorded SRP199550 118.32
SRR12959184 Polyps Polyps E3 day0 not recorded SRP199550 117.16
SRR12959215 Polyps Polyps E3 day9 not recorded SRP199550 117.10
SRR12710858 Polyps Polyps OA3 day9 not recorded SRP199550 116.71
SRR12710857 Polyps Polyps OA3 day9 not recorded SRP199550 115.18
SRR12786897 Polyps Polyps OA3 day0 not recorded SRP199550 113.86
SRR12786896 Polyps Polyps OA3 day0 not recorded SRP199550 113.13
SRR12959214 Polyps Polyps E3 day9 not recorded SRP199550 108.69
SRR12959190 Polyps Polyps E3 day21 not recorded SRP199550 106.62
SRR12959182 Polyps Polyps E3 day0 not recorded SRP199550 105.14
SRR12959183 Polyps Polyps E3 day0 not recorded SRP199550 104.65
SRR12710847 Polyps Polyps OA3 day3 not recorded SRP199550 99.02
SRR12710848 Polyps Polyps OA3 day3 not recorded SRP199550 96.59
SRR12710846 Polyps Polyps OA3 day3 not recorded SRP199550 87.81
SRR12807381 Polyps Polyps OA3 day0 not recorded SRP199550 0.00
SRR12849113 Polyps Polyps OA3 day0 not recorded SRP199550 0.00
SRR12927880 Polyps Polyps E3 day0 not recorded SRP199550 0.00
SRR12959227 Polyps Polyps E3 day3 not recorded SRP199550 0.00
SRR12963484 Polyps Polyps E3 day0 not recorded SRP199550 0.00
SRR9129316 Polyps Polyps not recorded not recorded SRP199550 0.00
SRR9613519 Polyps Polyps not recorded not recorded SRP199550 0.00

Source: CnidoSite RNA-seq expression matrices (MCAPR_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 capricornis 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 correlated25XP_068727014.10.964177080088951
Negatively correlated23XP_068724527.1-0.573195754141647

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 capricornis, 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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