Gene detail

Detailed information of HOLI00001.G52398 in Hydra oligactis

Genomic Location: HOLI00001:4306414...4307010
NR annotation: HCN45479.1, RNA polymerase subunit sigma [Pseudomonas sp.]
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 accession	Description
P23484	Ferric citrate uptake sigma factor FecI OS=Escherichia coli (strain K12) OX=83333 GN=fecI PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0012201 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08281 all species →	Sigma70_r4_2	Sigma-70, region 4	Domain	Interproscan
PF04542 all species →	Sigma70_r2	Sigma-70 region 2	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013249 all species →	Domain	RNA polymerase sigma factor 70, region 4 type 2	Interproscan
IPR039425 all species →	Family	RNA polymerase sigma-70 like	Interproscan
IPR013325 all species →	Homologous_superfamily	RNA polymerase sigma factor, region 2	Interproscan
IPR014284 all species →	Domain	RNA polymerase sigma-70 like domain	Interproscan
IPR007627 all species →	Domain	RNA polymerase sigma-70 region 2	Interproscan
IPR036388 all species →	Homologous_superfamily	Winged helix-like DNA-binding domain superfamily	Interproscan
IPR013324 all species →	Homologous_superfamily	RNA polymerase sigma factor, region 3/4-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR43133 all species →	RNA POLYMERASE ECF-TYPE SIGMA FACTO	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0003700 all species →	Molecular Function	DNA-binding transcription factor activity	Interproscan
GO:0006352 all species →	Biological Process	DNA-templated transcription initiation	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan
GO:0016987 all species →	Molecular Function	sigma factor activity	Interproscan

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 HOLI00001.G52398.

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.

Analysis	What it does	Status
Primer design	Design PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.	template found	open →
BLAST	Search 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 found	open →
Expression heatmap	Draw 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 / orthogroup	Look 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 analysis	Start a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.		open →