Gene detail

Detailed information of PcrG021923.mRNA1 in Podabacia crustacea

Genomic Location: scaffold_42:249845...273265
NR annotation: no NCBI-NR hit recorded
Species Podabacia crustacea · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

PcrG021923.mRNA1

ATGGCGCCGGTTGCCGAGCAGAAGAAAGAGAAAGAGACAACTACAGACAAGAAAGAAGAGTCAATATCTAAAGATGACACTAAAAAGGAAGAAGAACCTGAACTGAGCGAAGAGGACAGGCAATTGCAAGAGGAGTTGACAATGCTCGTAGAAAGATTATCGGAGTCTAATGTATCACTACACAAGCCTGCACTGGAAGCCTTGAGATCACAAATCAGAGCCAGTACGAGTTCAATGACGTCAGTTCCAAAACCTCTTAAATTCCTCAGACCACACTTTGCAACACTGAAAGAGATTTATGACAAGTGGGGAGATGGTGAAAGCAAGAGATTCTTGGCAGACATTATCTCAGTTCTCGGCATGACAATCAGCGAGGGACGTGAGTGTCTGAAGTTCAGGATGCTGGGGTCCAAAGAGGAGCTAGAATCTTGGGGGCATGAATATGTCAGACACTTGGCAGAGGAAATTCGCGGAGAGTACAGTGACAGATCAGATAAAAGTGAAGGAGTAGATGACCTAGTGGCCCTTGCCAAAGAAATTTTACCATATAACATGCAGCACAATGCAGAAACTGAAGCTTGTGATTTACTGATGGAGATTGAACGTTTGGAGTTACTGGAACAATACGTTGACAAAAACAGCTTTCAGAGAGTGTGTCTTTATCTTACAAGCTGTGTGAGTTATGTTCCTGAACCAGAAGACAGCACATTGTTAAAAACTGCGCTGAACATTTTTAGAAAGTTTGACCATCAGCCAGAAGCCATGAAGCTTGCAATTCAGTTGAATGATATTGATCTCATCAAGGACATATTTATTTCTTGCACTGGAAGTGAAGAGAAAAAATTAATTCAGAAACAGATGGCTTTTATGCTGGCCAGACAGCAGATCTATCTTGAGCTTGATGAAAACATGGATGAATATGATGAGCTGGTAGAAATCATGTCCAATGCACATCTCAACAACAACTTCCTTAGTCTTGCAAGAGAGTTGGATATCATGGAGCCTAAAGTTCCTGAAGATATTTATAAAACACATCTTGAGAACAAAGGAGTTTCCAGTGGTGTTGCTTTGGATTCTGCAAGACAAAATTTAGCTTCTTCATTTGTAAATTCTTTTGTTAATGCCGCATTTGGTTCTGATAAGCTGTTAACAGAGGATGGTAATAAATGGATTTACAAAAACAAGGAACATGGTATGATGAGCACAACAGCCTCACTTGGGCTCATTTTGTTGTGGGATGTCGACGCTGGACTTACTCAGATTGATAAATATTTATATTCTACAGAAGACTACATCAAGGCTGGAGCCTTGTTGGCTTGTGGCATTGTCAATTCTGGGGTGAAGAATGAATGTGACCCAGCCCTTGCTTTGCTGTCAGATTATGTTCTACATAACAACAATATCATGAGACTTGGGTCTGTAGTGGGGCTTGGCCTTGCTTATGCTGGTTCTAACAGACAAGATGTGTTATCTCTAATTCTTCCTGTTCTGGGTGACCCAAAGTCAAACTTGGAGGTGATTGGAATGGCAAGCATTGCCTGTGGTTTGGTTGCCATAGGAACATGTAATGGAGAAGTGACGTCAACTATACTTCAAACAATGATGGAACGCTCTGAGACAGAGGTCAAGGAAACACATGCTCGTAACTTAGCTTTAGGGCTTGGCTTGACATTCTTAGGAAAGCAAGAAGCAGCGGAAGCCACTCTTGAGGCCTTGAAAGTTGTTCCAGAACCTCTTGGAAAGTGGGCTTCTATCTTAGTTGAAATCTGTGCATATGCTGGGACTGGAAATGTCCTAAAAATTCAAGAAATGCTGCACATCTGTAGCGAACACTTTGAACAGAAGGATGATGaagaaaaagacaaagattctaaagacaaagataaagacaaggacaaagacaaGAAAGAAGCTGAGAAGTCAAGTGACGGCAGTCACCAGGGGATCGCTGTACTGGGGATCGCTTTAGTTGCCATGGGTGAGGAGATTGGTTGCCAGATGGCACTCAGGACATGCAATCATTTGCTGCAGTATGGTGAACCAGTGATACGCCGTGCAGTCCCTCTAGCTCTTGCTATCCTATCAGCCTCTAATCCTCAATTGAGTATAATCGACACTCTTAGCAAGCTGTCACATGACAACGACGCCGAGGTGTCACACAACTCCATCTTTGCCATGGGGATTGTCGGTGCAGGTACAAACAATGCTAGATTAGGAGGAATGCTTCGACAACTGGCCATGTACTACCACAAGGATGCAAACAACTTGTTTATGGTGCGACTTGCTCAGGGATTAGTTCACCTTGGTAAAGGCACACTAACGCTTGGTCCTTATCACTGCGATCGTTCACTCATGATGCCTGTGGCAGTGGGTGGTCTGTTATCTGTTCTTGTCTCATTCTTGGATGTAAAGAATGTAATTCTTGGTAAATCACATTATGTCCTCTTTAATCTGGTGTCTGCTATGCAACCCAGAATGTTAGTCACGTTTGACACAGATCTGCGCCCTTTGCCTGTCTCTGTAAGAGTTGGCCAGGCAGTTGATGTTGTGGGTCAAGCAGGAAAGCCAAAGACAATAACAGGATTTCAGACCCACACTACACCAGTGTTGCTTGCATATGGAGAAAGAGCAGAGCTTGCAACAGAGGAATATATTTCTCTTGCACCAATAATGGAGGGTTTCGTTATCTTGAAAAAGAACCCAGAATATGAAAAGCAAGAGAGTTGA

Transcript

PcrG021923.mRNA1

Protein

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0005285 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF17781 all species →	RPN1_RPN2_N	RPN1 N-terminal domain	Domain	Interproscan
PF18051 all species →	RPN1_C	26S proteasome non-ATPase regulatory subunit RPN1 C-terminal	Domain	Interproscan
PF01851 all species →	PC_rep	Proteasome/cyclosome repeat	Repeat	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR016643 all species →	Family	26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit	Interproscan
IPR040892 all species →	Domain	RPN1, N-terminal	Interproscan
IPR041433 all species →	Domain	26S proteasome non-ATPase regulatory subunit RPN1, C-terminal	Interproscan
IPR011989 all species →	Homologous_superfamily	Armadillo-like helical	Interproscan
IPR016024 all species →	Homologous_superfamily	Armadillo-type fold	Interproscan
IPR002015 all species →	Repeat	Proteasome/cyclosome repeat	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10943 all species →	26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000502 all species →	Cellular Component	proteasome complex	Interproscan
GO:0030234 all species →	Molecular Function	enzyme regulator activity	Interproscan
GO:0042176 all species →	Biological Process	regulation of protein catabolic process	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0008540 all species →	Cellular Component	proteasome regulatory particle, base subcomplex	Interproscan
GO:0034515 all species →	Cellular Component	proteasome storage granule	Interproscan
GO:0043161 all species →	Biological Process	proteasome-mediated ubiquitin-dependent protein catabolic 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
K03028	PSMD2, RPN1; 26S proteasome regulatory subunit N1	-	Proteasome	ko03051	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 Podabacia crustacea 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 Podabacia crustacea, 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 →