Detailed information of evm.model.HiC_scaffold_23.448 in Chrysaora quinquecirrha

Genomic Location: HiC_scaffold_23:5887763...5893526
NR annotation: XP_019635170.1, PREDICTED: proteasome subunit beta type-3 [Branchiostoma belcheri]
Species Chrysaora quinquecirrha · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
O73817Proteasome subunit beta type-3 OS=Oncorhynchus mykiss OX=8022 GN=psmb3 PE=2 SV=1
Q9R1P1Proteasome subunit beta type-3 OS=Mus musculus OX=10090 GN=Psmb3 PE=1 SV=1
P40112Proteasome subunit beta type-3 OS=Rattus norvegicus OX=10116 GN=Psmb3 PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0009082 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF15753
all species →
BLOC1S3Biogenesis of lysosome-related organelles complex 1 subunit 3FamilyInterproscan
PF00227
all species →
ProteasomeProteasome subunitDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR017245
all species →
FamilyBLOC-1 complex, subunit 3Interproscan
IPR029055
all species →
Homologous_superfamilyNucleophile aminohydrolases, N-terminalInterproscan
IPR023333
all species →
FamilyProteasome B-type subunitInterproscan
IPR001353
all species →
FamilyProteasome, subunit alpha/betaInterproscan
IPR033811
all species →
FamilyProteasome beta 3 subunitInterproscan
IPR016050
all species →
Conserved_siteProteasome beta-type subunit, conserved siteInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR32194
all species →
METALLOPROTEASE TLDDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005839
all species →
Cellular Componentproteasome core complexInterproscan
GO:0051603
all species →
Biological Processproteolysis involved in protein catabolic processInterproscan
GO:0019774
all species →
Cellular Componentproteasome core complex, beta-subunit complexInterproscan
GO:0043161
all species →
Biological Processproteasome-mediated ubiquitin-dependent protein catabolic processInterproscan

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 evm.model.HiC_scaffold_23.448.

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.

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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