Gene detail

Detailed information of BRAKERMNPP00000011594.1 in Nemopilema nomurai

Genomic Location: scaffold11:1622605...1641407
NR annotation: XP_020624905.1, transitional endoplasmic reticulum ATPase [Orbicella faveolata]
Species Nemopilema nomurai · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERMNPT00000011594

ATGGATTCAGGCGAGGCAAAGGAAGAGTGCAcaacaaatgaagaagaagcagacccgaatgaaaagaaatcaccACAACTTAAATGGCCACCAGTTAActgtaaagaaaaaattGAGATTATTGAGcaattatttttcagaaaagagcATTGTGCACTCCCCGAGGTGGAAGACATTGCATTGCCGCCTCCGCATGTTTTGCGTGTGATTTTCATTTACGGAAGGTCTCACTGTAGTTTGAGTATATCAGAAGAGAAGCTAAAGGAATtcgaaaatttgaaaaaatcacCATACTTCTTTTTGGATGTTCTCTATCTCCACGAAATTCCTTCTCCAGATAACAAAGCTGAGGAGATTTATGACTTCTTCTGCAATCTAGACAAGGAGGAAAAGGGATACATATTGGAAGTCTCAGGCAGTGCCAAAATTCTGTTTGAGACATTCGCAAAGCTGATCTCCCATCCTTTGCAGAGGTCACCTCAAAACGAAGCTTCCTATGATCTGATTCCATCACCAGCTGAAGAAGTCGTCGGAAACGTATTggATGAACTGGCAACTGCCATTCTCAAGCAGAAAGCTAAGCCAAACAGATTGATGGTCGAAGAGGCAGTGAATGATGACAATTCTGTTGTAACCATGTCACAGGCAAAAATGGATGAACTGCAACTTTTTCGGGGTGACACAGTCCTTCTCAAAGGAAAACGACGAAAGGAGACTGTTTGCATCGCTTTATCAGATGAAACttgttcaaatgaaaaaataaggATAAACAGAGTTGTCAGGCAGAACCTGAGAGTTAGACTTGGTGACATTGTAAGCATACAAGCTTGTCCTGATGTGAAGTATGGTAAAAGAATTTATGTTCTACCCATTGATGACACAGTGGAAGGACTAACCGGGAGCTTGTTCGATGTTTATTTGAAGCCATATTTCTTAGAAGCTTACAGACCAGTGTGTAAAGGTGATATATTCTTGATCAGAGGGGGCATGAGAGCTGTGGAGTTCAAAGTAGTAGAGACAGACCCAGCACCATACTGCATTGTGGCACCAGACACTGTAATACACTGTGAAGGAGAGCCAATTAAGCGAGAGGATGAAGAAGAAGCTCTGAATGAAGTTGGCTATGATGATGTTGGTGGTTGTAGAAAACAGCTTGCTCAGATAAAAGAGATGGTGGAACTTCCTTTGAGACACCCTCAGCTATTCAAAGCTCTTGGAATCAAGcctccCAGAGGTATTCTTCTCTATGGACCACCAGGAACTGGAAAGACTTTGATAGCTAGGGCTGTGGCAAATGAAACTggtgctttcttttttctcatAAATGGACCTGAGATTATGAGCAAGTTGGCTGGCGAATCAGAAAGTAATCTCAGAAAAGCATTTGAGGAAGCTGAGAAAAATTCTCCTGCAATCATATTTATTGATGAAATTGATGCCATTGCCccaaaaagagaaaagACTCATGGTGAAGTGGAGAGAAGAATTGTTTCACAGTTGCTTACTCTTATGGATGGATTGAAACAGAGATCACATGTCATTGTTATGGCAGCCACCAACAGACCAAACAGTATAGATGCTGCTCTTAGGAGATTTGGTCGTTTTGATCGGGAAGTTGACATTGGTATACCAGATGCAACAGGCCGTTTGGAGATCCTGCAGATCCATACCAAAAATATGAGGCTTGATGATGAAGTTGATTTAGAACAAGTAGCTGCCGAAACACATGGTTATGTTGGCTCAGACATGGCCTCTTTGTGTTCAGAAGCAGCTCTTCAACAGATTAGAGAAAAGATGGACCTCATTGATTTAGAAGATGATACAATTGATGCTGAAGTTCTCAATTCACTAGCAGTAACAATGGACAACTTTAGGTTTGCAATGGGCTCAACCAATCCTTCTGCTCTGCGAGAAACAGTTGTGGAAGTTCCAACAGTAAGTTGGCAAGACATTGGAGggcttgaaaatgtcaaaaggGAGTTGCAAGAGCTGGTGCAGTACCCAGTTGAACATCCAGAAAAGTTCCTCAAGTTTGGAATGACTCCTTCAAAGGGTGTCTTGTTTTACGGCCCACCAGGTTGTGGTAAAACTCTTTTAGCTAAAGCCATTGCTAATGAATGTCAAGCCAATTTCATCTCAATCAAAGGCCCAGAGCTGCTCACAATGTGGTTTGGTGAATCAGAAGCTAATGTTAGAGATGTATTTGACAAGGCTCGTATGGCTGCACCTTGTGTGCTGTTCTTTGATGAATTGGATTCAATTGCCAAGTCACGTGGTGGAAATGCTGGAGATGGTGGTGGTGCCTCTGATCGTGTCATTAACCAGATTCTCACAGAAATGGATGGTATGGGACCAAAAAAGAATGTCTTCATCATTGGTGCTACAAACAGACCAGATATCATTGACCCTGCAATATTGAGGCCTGGGCGTCTTGATCAGCTCATTTACATCCCCCTTCCAGATGAACCTTCCAGACTGTCTATTTTGAATGCATCACTCAGAAAGTCTCCTGTTGCCAAGGATGTTGATCTGGTCTACCTGTCCAAGGTCACACATGGCTTTAGTGGAGCAGATTTGACAGAAATTTGTCAAAGGgCATGCAAACTTGCAATCAGAGAGAGCATAGAGTCTGACATacgaaaagagaaagaaagggAGGGAAACCAAGAAGCAAATATGGAttttgaagatgatgaagatgctGTGCCAGAAATCCGAAGAGATCATTTTGAGGAAGCAATGAGATTTGCCCGAAGATCAGTTAGTGATAATGACATCCGAAGATATGAGATGTTTGCACAAACTCTTCAGCAGAGCAGGGGACTGGGCGGTGGCTTTAGATTCCCTGGCCAACAACAAGGTGGAAGTGGGGGTTCACAGGGCACTGGTGGCAACCAGGGTGCGGGTGCAGATGGGAGCGGCCTTTACAACAACGATGAAGATGACCTGTACGGCTAA

Transcript

BRAKERMNPT00000011594

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q6GL04	Transitional endoplasmic reticulum ATPase OS=Xenopus tropicalis OX=8364 GN=vcp PE=2 SV=1
P55072	Transitional endoplasmic reticulum ATPase OS=Homo sapiens OX=9606 GN=VCP PE=1 SV=4
Q01853	Transitional endoplasmic reticulum ATPase OS=Mus musculus OX=10090 GN=Vcp PE=1 SV=4

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000716 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF17862 all species →	AAA_lid_3	AAA+ lid domain	Domain	Interproscan
PF02359 all species →	CDC48_N	Cell division protein 48 (CDC48), N-terminal domain	Domain	Interproscan
PF09336 all species →	Vps4_C	Vps4 C terminal oligomerisation domain	Domain	Interproscan
PF02933 all species →	CDC48_2	Cell division protein 48 (CDC48), domain 2	Domain	Interproscan
PF00004 all species →	AAA	ATPase family associated with various cellular activities (AAA)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR041569 all species →	Domain	AAA ATPase, AAA+ lid domain	Interproscan
IPR003338 all species →	Domain	CDC48, N-terminal subdomain	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR015415 all species →	Domain	Spastin/Vps4, C-terminal	Interproscan
IPR004201 all species →	Domain	CDC48, domain 2	Interproscan
IPR029067 all species →	Homologous_superfamily	CDC48 domain 2-like superfamily	Interproscan
IPR003593 all species →	Domain	AAA+ ATPase domain	Interproscan
IPR005938 all species →	Family	AAA ATPase, CDC48 family	Interproscan
IPR009010 all species →	Homologous_superfamily	Aspartate decarboxylase-like domain superfamily	Interproscan
IPR003960 all species →	Conserved_site	ATPase, AAA-type, conserved site	Interproscan
IPR050168 all species →	Family	AAA ATPase domain-containing protein	Interproscan
IPR003959 all species →	Domain	ATPase, AAA-type, core	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR23077 all species →	AAA-FAMILY ATPASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016887 all species →	Molecular Function	ATP hydrolysis activity	Interproscan
GO:0016787 all species →	Molecular Function	hydrolase activity	Interproscan
GO:0005524 all species →	Molecular Function	ATP binding	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0030433 all species →	Biological Process	obsolete ubiquitin-dependent ERAD pathway	Interproscan
GO:0030970 all species →	Biological Process	retrograde protein transport, ER to cytosol	Interproscan
GO:0031593 all species →	Molecular Function	polyubiquitin modification-dependent protein binding	Interproscan
GO:0034098 all species →	Cellular Component	VCP-NPL4-UFD1 AAA ATPase complex	Interproscan
GO:0051228 all species →	Biological Process	mitotic spindle disassembly	Interproscan
GO:0071712 all species →	Biological Process	obsolete ER-associated misfolded protein catabolic process	Interproscan
GO:0097352 all species →	Biological Process	autophagosome maturation	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

No KEGG orthology assignment for BRAKERMNPP00000011594.1.

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 Nemopilema nomurai 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 Nemopilema nomurai, 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 →