Detailed information of evm.model.HiC_scaffold_26.896 in Chrysaora quinquecirrha

Genomic Location: HiC_scaffold_26:10078188...10098811
NR annotation: XP_047130028.1, ribosome biogenesis protein bop1-B [Hydra vulgaris]
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
Q7T0W1Ribosome biogenesis protein bop1-A OS=Xenopus laevis OX=8355 GN=bop1-a PE=2 SV=1
Q7ZXX9Ribosome biogenesis protein bop1-B OS=Xenopus laevis OX=8355 GN=bop1-b PE=2 SV=1
A4IHS2Ribosome biogenesis protein bop1 OS=Xenopus tropicalis OX=8364 GN=bop1 PE=2 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0005021 (this species only) · gene tree & orthology
Ubiquitin familyUBD|Other|Beta-prp · all ubiquitin genes in this species
Ubiquitin familyE3|E3 adaptor Cullin RING|CDC20 · all ubiquitin genes in this species
Ubiquitin familyE3|E3 adaptor Cullin RING|DWD · all ubiquitin genes in this species

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00400
all species →
WD40WD domain, G-beta repeatRepeatInterproscan
PF08145
all species →
BOP1NTBOP1NT (NUC169) domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR012953
all species →
DomainBOP1, N-terminal domainInterproscan
IPR001680
all species →
RepeatWD40 repeatInterproscan
IPR015943
all species →
Homologous_superfamilyWD40/YVTN repeat-like-containing domain superfamilyInterproscan
IPR028598
all species →
FamilyWD repeat BOP1/Erb1Interproscan
IPR019775
all species →
Conserved_siteWD40 repeat, conserved siteInterproscan
IPR036322
all species →
Homologous_superfamilyWD40-repeat-containing domain superfamilyInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR17605
all species →
RIBOSOME BIOGENESIS PROTEIN BOP1 BLOCK OF PROLIFERATION 1 PROTEINInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0006364
all species →
Biological ProcessrRNA processingInterproscan
GO:0005515
all species →
Molecular Functionprotein bindingInterproscan
GO:0000463
all species →
Biological Processmaturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)Interproscan
GO:0030687
all species →
Cellular Componentpreribosome, large subunit precursorInterproscan
GO:0042254
all species →
Biological Processribosome biogenesisInterproscan
GO:0043021
all species →
Molecular Functionribonucleoprotein complex bindingInterproscan
GO:0070545
all species →
Cellular ComponentPeBoW complexInterproscan

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
KOEnzymeEnzyme IDPathwayMap IDSource
K14824ERB1, BOP1; ribosome biogenesis protein ERB1-Ribosome biogenesisko03009deepkoala

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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