Detailed information of HOLI03250.G1014 in Hydra oligactis

Genomic Location: HOLI03250:24049...24321
NR annotation: WP_234641920.1, Fe-S cluster assembly scaffold IscU [Delftia tsuruhatensis]
Species Hydra oligactis · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
P0ACD6Iron-sulfur cluster assembly scaffold protein IscU OS=Escherichia coli O157:H7 OX=83334 GN=iscU PE=1 SV=1
P0ACD5Iron-sulfur cluster assembly scaffold protein IscU OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) OX=199310 GN=iscU PE=3 SV=1
P0ACD4Iron-sulfur cluster assembly scaffold protein IscU OS=Escherichia coli (strain K12) OX=83333 GN=iscU PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0007628 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF01592
all species →		NifU_NNifU-like N terminal domainFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR002871
all species →		DomainNIF system FeS cluster assembly, NifU, N-terminalInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR10093
all species →		IRON-SULFUR CLUSTER ASSEMBLY ENZYME NIFU HOMOLOGInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005506
all species →		Molecular Functioniron ion bindingInterproscan
GO:0016226
all species →		Biological Processiron-sulfur cluster assemblyInterproscan
GO:0051536
all species →		Molecular Functioniron-sulfur cluster bindingInterproscan
GO:0005737
all species →		Cellular ComponentcytoplasmInterproscan
GO:0006879
all species →		Biological Processintracellular iron ion homeostasisInterproscan
GO:0008198
all species →		Molecular Functionferrous iron bindingInterproscan
GO:0051537
all species →		Molecular Function2 iron, 2 sulfur cluster 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 HOLI03250.G1014.

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 Hydra oligactis 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 Hydra oligactis, 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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