Detailed information of HOLI00001.G53812 in Hydra oligactis

Genomic Location: HOLI00001:6131828...6132136
NR annotation: WP_273909110.1, MULTISPECIES: ribosome-associated translation inhibitor RaiA [unclassified Pseudomonas]
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
P0A147Ribosome hibernation promoting factor OS=Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440) OX=160488 GN=hpf PE=3 SV=1
P0A148Ribosome hibernation promoting factor OS=Pseudomonas putida OX=303 GN=hpf PE=3 SV=1
P17160Ribosome hibernation promoting factor OS=Azotobacter vinelandii OX=354 GN=hpf PE=3 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0030401 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF02482
all species →		Ribosomal_S30AESigma 54 modulation protein / S30EA ribosomal proteinFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR036567
all species →		Homologous_superfamilyRibosome hibernation promotion factor-likeInterproscan
IPR050574
all species →		FamilyHPF/YfiA ribosome-associatedInterproscan
IPR003489
all species →		FamilyRibosome hibernation promoting factor/RaiAInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR33231
all species →		30S RIBOSOMAL PROTEINInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0022627
all species →		Cellular Componentcytosolic small ribosomal subunitInterproscan
GO:0043024
all species →		Molecular Functionribosomal small subunit bindingInterproscan
GO:0045900
all species →		Biological Processnegative regulation of translational elongationInterproscan
GO:0044238
all species →		Biological Processprimary metabolic processInterproscan

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
K05808hpf; ribosome hibernation promoting factor-Ribosome biogenesisko03009deepkoala

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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