Gene detail

Detailed information of evm.model.HiC_scaffold_20.84 in Chrysaora quinquecirrha

Genomic Location: HiC_scaffold_20:951039...965785
NR annotation: XP_032220069.1, vacuolar protein sorting-associated protein 52 homolog [Nematostella vectensis]
Species Chrysaora quinquecirrha · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

evm.model.HiC_scaffold_20.84

ATGGCGACAGAACCTGGAGCTGTGCTTGAAGATTCAAGTTACGATAATATTGACAATTCTCTGGAAAATCAGCCGCAAAAAGATgatttaagTCAGCTTGGATTAGAGCTTGATGACCTTGACATAACGTCACAAGATGATTATATTTTAGATGAATTAGATGTATTTATCCAGAAGAATCTGAAAGATGAGTTGGTCCAGCAAGCTCTTGCAAAGGGTACAGATCTGAGACAGTATTCAAAAGAGATTGAAAATGAGCTACGTTCTGTTGAAAGACTTTCAATTCAGGACTACATCAAGGAAAGCAAAAGCATTGCAAGTTTacacaaacaaataaaaaattgtgATGGAATTTTATCGacaatggaAAACATGCTAAGCAGTTTTCAGACAGATCTTCAGAGTATAAGTTCAGAAATTCAGACATTACAAGAACAATCGCTGTCAATGaatgtgaaattgaagaatAGACAGGCAATACGCGGTGAACTAAGTCAATTTATCGATGAAATGCTTGTTGGCGACACAATGATTCAGCACTATATGTTGCATCGCATAAAATTGCTTGCATTTCTGTGTTGCATCAAGTTTGGAATGGTTGCATCAGCTATGGCGTGTAATGATGTCAAAGATGTCCTCGATAAACTCAAAACTAAGGCCGTTCAGAAGCTTCGAGAATTCATTTTGCAACGAATTTACCAATGTAGAAAACCAATGTCGAATTATCAAATACCACAGAATGCATTGCTCAAAAATAGATATTTTTATGAATTTCTTCTGGCTCATCACAGACAAGTGGCACGTGAGATTCGAGATGAATATGTCGACACAAtgagcaaaatttatttttcatatttcagaGGATATATTAGCAAGTTAATGAAATTACAGTTTGAAGAGGTCGCGGACAAAGATGATTTAATGGGACTTGAAGACAGTGCAAAGAGGGGGTTCTTTTCTTCGAAGCAACCACTCAAGAATCGCTCTACCATCTTCAGTCTTGGTAACCGTGGCAACGTTTTGACATCCGAACTGGAAGAGCCAATCATTGTTCCACACGCTGCACAGAAATCAGAAAAAAGGTATTCATTCGAGGCCTTATTCAGAAGCCAGCACTTCGCTTTGTTAGACAACTGCTGTCGTGAATATCTATTTCTCAGTGATTTCTTCATGGTTACTGGTAATCAGGCAAAAGATTTATTCATTGCTGTAATGGGAAAAGTCGTCACATTATTTGGGAAACATATGGAAAGCTATGTGCCAAGTTGTTACGACGCCATTGCCATTTTTCTGTGTATTCATATTATTCATCGATACAAAATCATCATGCTGAAAAGAGAAGTGCCTGCTTTAGAAAAGTATTGGAACACATTACTAGATCTTTTGTGGCCTCGTTTTCAGCATATCATTGAGTTGAATTCTCAAAGTATTCGTGACACAGATCCACAGAAACTTGGGTCGATTGATGTCCGTCCGCATTATATAACAAGAAGGTATGCTGAATTTTCTGCTGCTATCAACAGCCTAAATGAAAGTTTTCCTGACGATCGAgTTTCTAAATCCTTGGGATTGCTCCAGAATGAAGTAGAAAACTTTATTCTTCGTCGAGCTGCAGAATTCGTGAATCGAAAAGATCAACTTGTTTTTCTGATCAACAATTACGACATGATGTTACAAGTACTTGCTgAAAGAACCGCAGAGGACTCGAAGGAAACAGAGAGTTTTCAGCAGTTATTGAATGGAAGGACTCAGGAATATGTTGAAGagGTCTTGTCGCCTTACTTTGGAGGAATGATATCATTTGTGAAGGAAACAGAACCAATGCTTGAACGAGGCTCTTCGCTGCCTCGTATGGACGAATATAAGATTGAGCAGTTGGTCAGAGGTTTTGCCGCTGATTGGAAGCAGGCGATAGAAACTATTAACCAGGATGTGATGCGTTCTTTCTCTAATTTCAAAACTGGAACAAACATTCTTCAGGTAATGTTATTTCCTCAGCTCAGACCACTTAAAGAAAACACTTAA

Transcript

evm.model.HiC_scaffold_20.84

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q8N1B4	Vacuolar protein sorting-associated protein 52 homolog OS=Homo sapiens OX=9606 GN=VPS52 PE=1 SV=1
Q8C754	Vacuolar protein sorting-associated protein 52 homolog OS=Mus musculus OX=10090 GN=Vps52 PE=1 SV=1
O55166	Vacuolar protein sorting-associated protein 52 homolog OS=Rattus norvegicus OX=10116 GN=Vps52 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003181 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04129 all species →	Vps52_CC	Vps52/Sac2 family, coiled-coil	Repeat	Interproscan
PF20655 all species →	Vps52_C	Vps52, C-terminal	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR007258 all species →	Family	Vps52	Interproscan
IPR048319 all species →	Domain	Vps52, coiled-coil domain	Interproscan
IPR048361 all species →	Domain	Vps52, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR14190 all species →	SUPPRESSOR OF ACTIN MUTATIONS 2/VACUOLAR PROTEIN SORTING 52	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000938 all species →	Cellular Component	GARP complex	Interproscan
GO:0006896 all species →	Biological Process	Golgi to vacuole transport	Interproscan
GO:0007041 all species →	Biological Process	lysosomal transport	Interproscan
GO:0019905 all species →	Molecular Function	syntaxin binding	Interproscan
GO:0032456 all species →	Biological Process	endocytic recycling	Interproscan
GO:0042147 all species →	Biological Process	retrograde transport, endosome to Golgi	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
K20298	VPS52; vacuolar protein sorting-associated protein 52	-	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 Chrysaora quinquecirrha 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 Chrysaora quinquecirrha, 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 →