Detailed information of scaffold5.g135.t1 in Morbakka virulenta

Genomic Location: scaffold5:5013963...5056918
NR annotation: MCG8035099.1, hypothetical protein [Candidatus Thiodiazotropha taylori]
Species Morbakka virulenta · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q5FVA9mRNA export factor OS=Xenopus tropicalis OX=8364 GN=rae1 PE=2 SV=1
Q8C570mRNA export factor OS=Mus musculus OX=10090 GN=Rae1 PE=1 SV=1
A5GFN6mRNA export factor OS=Sus scrofa OX=9823 GN=RAE1 PE=3 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0002151 (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 activity RING|PHD · all ubiquitin genes in this species
Ubiquitin familyE3|E3 adaptor Cullin RING|DWD · all ubiquitin genes in this species

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF03372
all species →
Exo_endo_phosEndonuclease/Exonuclease/phosphatase familyDomainInterproscan
PF00628
all species →
PHDPHD-fingerDomainInterproscan
PF00078
all species →
RVT_1Reverse transcriptase (RNA-dependent DNA polymerase)DomainInterproscan
PF00400
all species →
WD40WD domain, G-beta repeatRepeatInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR001680
all species →
RepeatWD40 repeatInterproscan
IPR036691
all species →
Homologous_superfamilyEndonuclease/exonuclease/phosphatase superfamilyInterproscan
IPR043502
all species →
Homologous_superfamilyDNA/RNA polymerase superfamilyInterproscan
IPR005135
all species →
DomainEndonuclease/exonuclease/phosphataseInterproscan
IPR019787
all species →
DomainZinc finger, PHD-fingerInterproscan
IPR000477
all species →
DomainReverse transcriptase domainInterproscan
IPR019775
all species →
Conserved_siteWD40 repeat, conserved siteInterproscan
IPR011011
all species →
Homologous_superfamilyZinc finger, FYVE/PHD-typeInterproscan
IPR015943
all species →
Homologous_superfamilyWD40/YVTN repeat-like-containing domain superfamilyInterproscan
IPR036322
all species →
Homologous_superfamilyWD40-repeat-containing domain superfamilyInterproscan
IPR013083
all species →
Homologous_superfamilyZinc finger, RING/FYVE/PHD-typeInterproscan
IPR019786
all species →
Conserved_siteZinc finger, PHD-type, conserved siteInterproscan
IPR001965
all species →
DomainZinc finger, PHD-typeInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR10971
all species →
MRNA EXPORT FACTOR AND BUB3Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005515
all species →
Molecular Functionprotein bindingInterproscan
GO:0003824
all species →
Molecular Functioncatalytic activityInterproscan
GO:0000972
all species →
Biological Processtranscription-dependent tethering of RNA polymerase II gene DNA at nuclear peripheryInterproscan
GO:0003723
all species →
Molecular FunctionRNA bindingInterproscan
GO:0005643
all species →
Cellular Componentnuclear poreInterproscan
GO:0006405
all species →
Biological ProcessRNA export from nucleusInterproscan
GO:0043130
all species →
Molecular Functionubiquitin 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 scaffold5.g135.t1.

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 Morbakka virulenta 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 Morbakka virulenta, 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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