Detailed information of BRAKERTYJP00000020733.1 in Cladopsammia gracilis

Genomic Location: JAJGOT010000112.1:167171...167854
NR annotation: no NCBI-NR hit recorded
Species Cladopsammia gracilis · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0000369 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF13520
all species →		AA_permease_2Amino acid permeaseFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR002293
all species →		FamilyAmino acid/polyamine transporter IInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR43243
all species →		INNER MEMBRANE TRANSPORTER YGJI-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0000064
all species →		Molecular FunctionL-ornithine transmembrane transporter activityInterproscan
GO:0005886
all species →		Cellular Componentplasma membraneInterproscan
GO:0006865
all species →		Biological Processamino acid transportInterproscan
GO:0015171
all species →		Molecular Functionamino acid transmembrane transporter activityInterproscan
GO:0015181
all species →		Molecular FunctionL-arginine transmembrane transporter activityInterproscan
GO:0015189
all species →		Molecular FunctionL-lysine transmembrane transporter activityInterproscan
GO:0097638
all species →		Biological ProcessL-arginine import across plasma membraneInterproscan
GO:1903352
all species →		Biological ProcessL-ornithine transmembrane transportInterproscan
GO:0016020
all species →		Cellular ComponentmembraneInterproscan
GO:0022857
all species →		Molecular Functiontransmembrane transporter activityInterproscan
GO:0055085
all species →		Biological Processtransmembrane transportInterproscan

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 BRAKERTYJP00000020733.1.

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

Co-expression network

Genes whose expression across the transcriptome samples of Cladopsammia gracilis 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.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Cladopsammia gracilis, 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.no expression matrix–
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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