Gene detail

Detailed information of ENSPYFP00000025833.1 in Pteroeides griseum

Genomic Location: chr4:3720451...3753016
NR annotation: no NCBI-NR hit recorded
Species Pteroeides griseum · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

ENSPYFT00000027360

ATGGATGATAAAGAAAAGCCTCATCGTGTTGCAGACTATTTTGTGGTTGTTGGCCTTGGTCAAAGCCCAAAACGAGTTGACTCAGATTATACTGCTAGAGTTGATCCAATCACTGACATCACAGTAATTTTCAAAGGAAAAGGGGAAAGTCCACCTGATGGATTTACTTGTATTGAGACTACACCAGGTGGTTACACTGCTGATCTTAATGCTGGATCTCTAAGAAGTGAATCTTGTTTTCTCTGCTACCGACGAGGAAGAGATAAACCACCAATTGTTGACATTGGTGTTTTGTACGAAGGAAAGGAAAGACTGAAATCAGGATGTGACATTTTAGATACCACACCAAATGGCCATTCAGCAAACATTAGTGATAGTAGTGGCAGTAGAATTTTCATCACATTTCGTCGATCTTCTGCAAAACTTTCTCATTCATCATTGGCAGTAACTGCTATTAATGTCATAATAACAAGCAAGaATGAAAAAACTCCTCATGCATTCTGTTtgataaataaaaatttaaacaaaGGCATGTTATTTTTTGTCACAGAAATTCTCAGTAGGTATCCACAGAAAGATGATGCTGGTTTTCCTCTCCCTGAACAAGTTCCATTATTTTGTTTGCCAATGGGAGTTATTGTTGAATGTTGGCCTCGCAAGTCACCTCACCCATTACCCATTTTCTCCACCTTTGTCCTTACAAATGCCATTGGACAGAAGATTTATGGTGCTGCTGTGACCTTTTTTGAGGAACTTCCAGCTAACCAAGTGACCCAAAAATTGGGAGAATTAAGACAAATTGTTCATACAAACAAATGTATTTGTCTTATGTCTCATTGGCCATTCTTTGAAGCATTCAAAAAGTTTCTTTCATCTTTGTATCGAATCTCTGTTTCTACCCAACCTATACCTTTGGAAAGGTATATTTCTCATTTCATTTTGAATGTGCCATTTCCTTCTCCACAAACACCCAGGATTCTTGTACAGATGAATTTATATGAACCTTTTGAAATTTGTCAGCCTTACTCAACATCTTTACCTGTCAGTGGTGCTTCGTTTTCTGCTTTGCTTCGTTGGCTTGGTCCTGAGAACTCTATTAAATTATTCTATTATGCTTTGACTGAACATAAACTACTCATTCATTCACTCCGTGCTGCTCTGCTTACCAGTGTATCTGAAGCTCTTATCAGTattatttttccTTTCAGTTGGCAATGTCCTTTCATTCCCCTTTGTCCAGTTGCTCTTTCTGGTGTACTTCATGCTCCTTGTCCTTTTATTGTTGGTATTGATTCTCGTTACTTTGAGCTGTGTGACCCTCCAGATGATGTCATTTTCATTGATTTAGACACAAACATGATTTCTCCGTATGTATCTAAAGAGcttaatatcttgtttatttttgcATTGGTTGAGTCTCATGGACCACTCAATATCGAGATAGCAATCCAGGAagcttttctaaaatttaacataTACCTAGTTTTCAAAGAGTTGAATGTTAACCATCTTTTTTTGGTACAGTTGTTCAGCCGGTTTATTGAACAGAGATCTTTTGTTTCATCGCAAGATTCGTGCCTGGAGTTTTTTGACGAGTGTCTAGAAAAGGTAAACAGCGTCACTAGgcgagttgaattgtcttgccgtTTTTTCCAGAGCCAACTGTTTTTATGTTTTAGTTATCCAACATTCCCAACCCTCAACGATCAACTATTTATAACGGAAAAATCAGAGCCAGTTCCCGCTTTGAATTCAAGTCCTGTTACCCCGTTTGGCAAGCGTACTTCCAAGGAACGCCATCAGTCAGTACAGATTTGTTTCTTTTTTAGTTGCCTTTTGGCTTACTGCTATAGTGTTTGGTTTATTCACCTCCCTGCTTATGTTAGAGCACATCATAATAAATCCAAGGCACTTCTTAACGCCTATGAGATTCTTTGCAAGATGCAGAAAGAGAAAGTAAAACAACCTGATGAAGTCTGTTATCGTATCCTCATGCAACTTTGTGGTCAGTACGATCACCCTGCTTTAGCTGTAAAGGCCTTGTCCGAGATGAAAAAGAATGGCGTAGAGCCAAAAGTAGTTACTTATGGTTATTATATGAAGGCTGTATTTGAAGGAAAATGGGCATCTACCTCAACCAGCTTTCACAGATGGCGACGCATATTTCATGTTATTTCAGCAGTGAACTACTTAATGAAAGTTGGTTCCAGAAAGAAACTAACAGAAGTCAAGACCTATCACTTCTCCGACTCATCGAACGCAGCGTTTAGCCCGGGAAATGAAGCGATTTCAGATGACAGTGGAATTGCTGATGAACCTGGGCTTCACAATACAGTACTAGGACAAGGACGAGGGAACTATTTTGGGAAAGTAAATCTTGAGCGATCTTATAGTACGAACTCAGACTTCAGTGATTCTTCTCAATGTCAACTGATTATTAACACGATTGATGACAGTGATAGCAACATAGAAGGATACCAGAATACAACATCTGGAATTGACGATATTGATTGGCGAAGTCATTGTGGTATGGTGCCacgagatattttgtttgaaGCATTACTTTGCAGTTGTAACCAATGTAAAAGTTGTGAGAAGTTTATGTATGATGAGGAGATCATGACTGGATGGACATCCGATGATTCTAACCTAAATACCAGGTATTCCACTAACACACCAGGACATATCACAGATTATCGTAACTGTTATTCAAGAGATGGAAGTAACTTTTCTTCAACTCCTTCAAGCTACAACAGCAGCGAGTTTTTATCAATAGCTCCAGATAATACCCCTCCGAAACCTTCACTAATGATACCACCATCAAATAAAGAAACAGCCAAGCGAGCTGTTAATACTACACAGGACCAAAGTTTAGCACGTTCCTTTTCACCGCCCGGTGTTTCGCTCCCTGTGAACATACGGACCAATAGAAAACAACGTCATGCATCCAGTGCACCGTCCAGTGCAACTAATAGTCCTGGGGGTAGTCTCGTAGCCAGTCCTAGACCGCGAGATCGTTTGGGAATAACACGCTCAAACAGTATACCTGGTATTGGCAGTCAGAGTAcaATGCCTGAAGAACGAGTTTCTATATGTGTGAATTATGTTAGTCCTTTGGTGCTGCGAAAAGAACTGGAAAACCTTTTAGAAAACGAAGGTGTGGGTGCCTTAGAATCTCCAAATATCATAAATGAAAAGCAAGTGATATTTTGGAACATGatttGGTATTTTCGACGACTGAATTTACCAACCCATTTAACTGACCATATTTATACCAATTATTCTGAGGATGACCAATATGATCGTGTCAAgGTGATTGTATCGACGTCCTGGGATTTAGACCGTCTCCCAGAATGTGATCATATCCCTCTTTATGTTTTGTGGAACGTTCCTGGTACGAGAAATATTGTATACTTTGTGGTGCAATCTGTCGTGGCTCACATTAAAACAAATGATATCGCAACACCATTTGGATTTCTTTTTGAAGAACGGAACAGGCAAAAACTGATCAATCCGAATACTCAATGGAGTATCTATAGAGAAATGCTCTTTTTATGTATAATGGCTTGTGGTAGCGATAATATTGATATAGATGCTTTTGATCAAAAGTACAGAGCCACATATCGTACATTACAGAAAGAATGTACTTATTCATTGACCAATGAAGATCATCCTCCACAGAAAAGATCAATGTGTTGTCGTCGAATGTTTAAACCACCGACTTTACAACCTAGACTACCACCAAGTCGTTACTTTCTCAGCCAAGGATTGATTTAG

Transcript

ENSPYFT00000027360

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003075 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02141 all species →	DENN	DENN (AEX-3) domain	Family	Interproscan
PF03456 all species →	uDENN	uDENN domain	Domain	Interproscan
PF17177 all species →	PPR_long	Pentacotripeptide-repeat region of PRORP	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR043153 all species →	Homologous_superfamily	DENN domain, C-terminal lobe	Interproscan
IPR001194 all species →	Domain	cDENN domain	Interproscan
IPR037516 all species →	Domain	Tripartite DENN domain	Interproscan
IPR005113 all species →	Domain	uDENN domain	Interproscan
IPR023341 all species →	Domain	MABP domain	Interproscan
IPR011990 all species →	Homologous_superfamily	Tetratricopeptide-like helical domain superfamily	Interproscan
IPR051696 all species →	Family	DENN Domain-Containing GEFs	Interproscan
IPR002885 all species →	Repeat	Pentatricopeptide repeat	Interproscan
IPR033443 all species →	Domain	Pentacotripeptide-repeat region of PRORP	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12296 all species →	DENN DOMAIN-CONTAINING PROTEIN 4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005515 all species →	Molecular Function	protein binding	Interproscan
GO:0031410 all species →	Cellular Component	cytoplasmic vesicle	Interproscan
GO:0032483 all species →	Biological Process	regulation of Rab protein signal transduction	Interproscan

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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K20163	DENND4; DENN domain-containing protein 4	-	Membrane trafficking	ko04131	deepkoala

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 Pteroeides griseum 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 Pteroeides griseum, 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.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search 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 found	open →
Expression heatmap	Draw 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 / orthogroup	Look 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 analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →