Detailed information of evm.model.HiC_scaffold_17.98 in Chrysaora quinquecirrha

Genomic Location: HiC_scaffold_17:1110672...1125815
NR annotation: XP_047132622.1, speedy protein A isoform X5 [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
Q5MJ70Speedy protein A OS=Homo sapiens OX=9606 GN=SPDYA PE=1 SV=2
Q8R496Speedy protein A OS=Rattus norvegicus OX=10116 GN=Spdya PE=2 SV=1
Q5IBH7Speedy protein A OS=Mus musculus OX=10090 GN=Spdya PE=1 SV=2
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0007759 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF01138
all species →		RNase_PH3' exoribonuclease family, domain 1DomainInterproscan
PF11357
all species →		Spy1Cell cycle regulatory proteinFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR012340
all species →		Homologous_superfamilyNucleic acid-binding, OB-foldInterproscan
IPR001247
all species →		DomainExoribonuclease, phosphorolytic domain 1Interproscan
IPR052316
all species →		FamilySpeedy/Ringo cell cycle regulatorInterproscan
IPR036345
all species →		Homologous_superfamilyExoribonuclease, PH domain 2 superfamilyInterproscan
IPR020984
all species →		FamilyCell cycle regulatory protein SpeedyInterproscan
IPR020568
all species →		Homologous_superfamilyRibosomal protein uS5 domain 2-type superfamilyInterproscan
IPR027408
all species →		Homologous_superfamilyPNPase/RNase PH domain superfamilyInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR31545
all species →		SEEDY PROTEIN A/C FAMILY MEMBERInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0019901
all species →		Molecular Functionprotein kinase bindingInterproscan
GO:0045737
all species →		Biological Processpositive regulation of cyclin-dependent protein serine/threonine kinase activityInterproscan

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_17.98.

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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