Gene detail

Detailed information of BRAKERMNPP00000007880.1 in Nemopilema nomurai

Genomic Location: scaffold18:1952873...1958621
NR annotation: XP_048586295.1, presenilin-1 isoform X3 [Nematostella vectensis]
Species Nemopilema nomurai · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
O12977	Presenilin-2 OS=Xenopus laevis OX=8355 GN=psen2 PE=2 SV=1
Q61144	Presenilin-2 OS=Mus musculus OX=10090 GN=Psen2 PE=1 SV=3
Q90ZE4	Presenilin-2 OS=Danio rerio OX=7955 GN=psen2 PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006883 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01080 all species →	Presenilin	Presenilin	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001108 all species →	Family	Peptidase A22A, presenilin	Interproscan
IPR006639 all species →	Family	Presenilin/signal peptide peptidase	Interproscan
IPR042524 all species →	Homologous_superfamily	Presenilin, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10202 all species →	PRESENILIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0016485 all species →	Biological Process	protein processing	Interproscan
GO:0042500 all species →	Molecular Function	aspartic endopeptidase activity, intramembrane cleaving	Interproscan
GO:0004175 all species →	Molecular Function	endopeptidase activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005743 all species →	Cellular Component	mitochondrial inner membrane	Interproscan
GO:0005765 all species →	Cellular Component	lysosomal membrane	Interproscan
GO:0005887 all species →	Cellular Component	plasma membrane	Interproscan
GO:0005938 all species →	Cellular Component	cell cortex	Interproscan
GO:0006509 all species →	Biological Process	membrane protein ectodomain proteolysis	Interproscan
GO:0006816 all species →	Biological Process	calcium ion transport	Interproscan
GO:0007220 all species →	Biological Process	Notch receptor processing	Interproscan
GO:0009986 all species →	Cellular Component	cell surface	Interproscan
GO:0016324 all species →	Cellular Component	apical plasma membrane	Interproscan
GO:0030018 all species →	Cellular Component	Z disc	Interproscan
GO:0030426 all species →	Cellular Component	growth cone	Interproscan
GO:0031594 all species →	Cellular Component	neuromuscular junction	Interproscan
GO:0035253 all species →	Cellular Component	ciliary rootlet	Interproscan
GO:0042987 all species →	Biological Process	amyloid precursor protein catabolic process	Interproscan
GO:0043025 all species →	Cellular Component	neuronal cell body	Interproscan
GO:0043066 all species →	Biological Process	negative regulation of apoptotic process	Interproscan
GO:0043198 all species →	Cellular Component	dendritic shaft	Interproscan
GO:0045121 all species →	Cellular Component	membrane raft	Interproscan
GO:0048471 all species →	Cellular Component	perinuclear region of cytoplasm	Interproscan
GO:0050435 all species →	Biological Process	amyloid-beta metabolic process	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
K04505	PSEN1, PS1; presenilin 1	EC:3.4.23.-	Peptidases and inhibitors	ko01002	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 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 →