Detailed information of ENSAPQP00000007439.1 in Leptogorgia sarmentosa

Genomic Location: chr14:6220303...6242010
NR annotation: CAB3981060.1, WD repeat and FYVE domain-containing 3 isoform X3 [Paramuricea clavata]
Species Leptogorgia sarmentosa · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q6VNB8WD repeat and FYVE domain-containing protein 3 OS=Mus musculus OX=10090 GN=Wdfy3 PE=1 SV=1
Q8IZQ1WD repeat and FYVE domain-containing protein 3 OS=Homo sapiens OX=9606 GN=WDFY3 PE=1 SV=2
E9Q2M9WD repeat- and FYVE domain-containing protein 4 OS=Mus musculus OX=10090 GN=Wdfy4 PE=1 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0002329 (this species only) · gene tree & orthology
Ubiquitin familyUBD|Other|Beta-prp · all ubiquitin genes in this species
Ubiquitin familyE3|E3 adaptor Cullin RING|DWD · all ubiquitin genes in this species

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF15787
all species →
DUF4704Neurobeachin/BDCP, DUF4704 alpha solenoid regionRepeatInterproscan
PF01363
all species →
FYVEFYVE zinc fingerDomainInterproscan
PF20426
all species →
NBCH_WD40Neurobeachin beta propeller domainRepeatInterproscan
PF14844
all species →
PH_BEACHPH domain associated with Beige/BEACHDomainInterproscan
PF02138
all species →
BeachBeige/BEACH domainFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR031570
all species →
DomainNeurobeachin/BDCP, DUF4704Interproscan
IPR016024
all species →
Homologous_superfamilyArmadillo-type foldInterproscan
IPR051944
all species →
FamilyBEACH domain-containing proteinInterproscan
IPR023362
all species →
DomainPH-BEACH domainInterproscan
IPR000306
all species →
DomainFYVE zinc fingerInterproscan
IPR011993
all species →
Homologous_superfamilyPH-like domain superfamilyInterproscan
IPR000409
all species →
DomainBEACH domainInterproscan
IPR046851
all species →
DomainNeurobeachin, beta-propeller domainInterproscan
IPR036372
all species →
Homologous_superfamilyBEACH domain superfamilyInterproscan
IPR013083
all species →
Homologous_superfamilyZinc finger, RING/FYVE/PHD-typeInterproscan
IPR015943
all species →
Homologous_superfamilyWD40/YVTN repeat-like-containing domain superfamilyInterproscan
IPR036322
all species →
Homologous_superfamilyWD40-repeat-containing domain superfamilyInterproscan
IPR011011
all species →
Homologous_superfamilyZinc finger, FYVE/PHD-typeInterproscan
IPR019775
all species →
Conserved_siteWD40 repeat, conserved siteInterproscan
IPR001680
all species →
RepeatWD40 repeatInterproscan
IPR017455
all species →
DomainZinc finger, FYVE-relatedInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR46108
all species →
BLUE CHEESEInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0046872
all species →
Molecular Functionmetal ion bindingInterproscan
GO:0005515
all species →
Molecular Functionprotein 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
K22262WDFY3, ALFY; WD repeat and FYVE domain-containing protein 3-Membrane traffickingko04131deepkoala

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 Leptogorgia sarmentosa 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 Leptogorgia sarmentosa, 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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