Detailed information of evm.model.HiC_scaffold_154.22 in Chrysaora quinquecirrha

Genomic Location: HiC_scaffold_154:174678...207621
NR annotation: XP_047139268.1, 5'-3' exoribonuclease 1 isoform X2 [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
Q8IZH25'-3' exoribonuclease 1 OS=Homo sapiens OX=9606 GN=XRN1 PE=1 SV=1
P977895'-3' exoribonuclease 1 OS=Mus musculus OX=10090 GN=Xrn1 PE=1 SV=1
P403835'-3' exoribonuclease 1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=exo2 PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0001137 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF18334
all species →
XRN1_D2_D3Exoribonuclease Xrn1 D2/D3 domainDomainInterproscan
PF18332
all species →
XRN1_D1Exoribonuclease Xrn1 D1 domainDomainInterproscan
PF17846
all species →
XRN_MXrn1 helical domainDomainInterproscan
PF03159
all species →
XRN_NXRN 5'-3' exonuclease N-terminusFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR041106
all species →
DomainExoribonuclease Xrn1, D2/D3 domainInterproscan
IPR027073
all species →
Family5'-3' exoribonucleaseInterproscan
IPR040992
all species →
Domain5'-3' exoribonuclease 1, D1 domainInterproscan
IPR041412
all species →
DomainXrn1, helical domainInterproscan
IPR004859
all species →
DomainXrn1, N-terminalInterproscan
IPR047007
all species →
Homologous_superfamily5'-3' exoribonuclease 1, D1 domain superfamilyInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR12341
all species →
5'->3' EXORIBONUCLEASEInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003676
all species →
Molecular Functionnucleic acid bindingInterproscan
GO:0004527
all species →
Molecular Functionexonuclease 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
KOEnzymeEnzyme IDPathwayMap IDSource
K12618XRN1, SEP1, KEM1; 5'-3' exoribonuclease 1EC:3.1.13.-
Chromosome and associated proteinsko03036deepkoala

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 →
TOP