Detailed information of evm.model.HiC_scaffold_16.482 in Chrysaora quinquecirrha

Genomic Location: HiC_scaffold_16:5962849...5966929
NR annotation: CAB3981084.1, Transposon Tf2-9 poly [Paramuricea clavata]
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)
No Swiss-Prot hit above the reporting threshold for this gene.
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0000003 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF14893
all species →
PNMAPNMAFamilyInterproscan
PF17919
all species →
RT_RNaseH_2RNase H-like domain found in reverse transcriptaseDomainInterproscan
PF17921
all species →
Integrase_H2C2Integrase zinc binding domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR001584
all species →
DomainIntegrase, catalytic coreInterproscan
IPR001969
all species →
Active_siteAspartic peptidase, active siteInterproscan
IPR048270
all species →
DomainParaneoplastic antigen Ma-like, C-terminal domainInterproscan
IPR043128
all species →
Homologous_superfamilyReverse transcriptase/Diguanylate cyclase domainInterproscan
IPR041577
all species →
DomainReverse transcriptase/retrotransposon-derived protein, RNase H-like domainInterproscan
IPR012337
all species →
Homologous_superfamilyRibonuclease H-like superfamilyInterproscan
IPR036397
all species →
Homologous_superfamilyRibonuclease H superfamilyInterproscan
IPR041588
all species →
DomainIntegrase zinc-binding domainInterproscan
IPR043502
all species →
Homologous_superfamilyDNA/RNA polymerase superfamilyInterproscan
IPR050951
all species →
FamilyRetrovirus-related Pol polyproteinInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR37984
all species →
PROTEIN CBG26694Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0015074
all species →
Biological ProcessDNA integrationInterproscan
GO:0004190
all species →
Molecular Functionaspartic-type endopeptidase activityInterproscan
GO:0006508
all species →
Biological ProcessproteolysisInterproscan
GO:0003676
all species →
Molecular Functionnucleic acid bindingInterproscan

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_16.482.

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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