Gene detail

Detailed information of HOLI00001.G50889 in Hydra oligactis

Genomic Location: HOLI00001:2387634...2389838
NR annotation: WP_262155158.1, MULTISPECIES: OsmC domain/YcaO domain-containing protein [unclassified Pseudomonas]
Species Hydra oligactis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

HOLI00001.g50889.t1

ATGGAAATCAAGGTCAACTTTCTCGACAACCTTCGACTTGAAGCCAAGTTCGATGACTTCACGGTGGTGGCGGATCAGCCGATCCGCTACAAGGGCGATGGCTCGGCACCCGGTCCGTTCGACTACTTCCTGGCGTCGTCGGCCTTGTGTGCGGCGTACTTCGTGAAGCTGTACTGCCAGACCCGGGACATCCCGACCGAGAACATCCGCCTGTCGCAGAACAACATTGTCGACCCGGAAAACCGCTATCAGCAGATCTTCAAGATCCAGGTCGAGTTGCCCGCCGACATTTCCGCCAAGGACCGCCAGGGCATCCTGCGTTCGATCGATCGCTGCACGGTGAAGAAGGTGGTGCAGGCCGGGCCGGAGTTCGTCATCGAAGAAGTGGAAAACCTCGATGCCGATGCCCAGGCCCTGTTGATGCCGGGCCTGGACGCGGGCACCAGCACCAGCATCCTGGGCAAGGACCTGCCGCTGGAGCAGACCATCGCCAACATGTCGGGGATCCTCGCGGGCCTGGGCATGAAGATCGAAATCGCCTCGTGGCGCAACATCGTGCCGAATGTCTGGTCGCTGCACGTTCGCGACGCGCAGTCGCCGATGTGCTTCACCAACGGCAAGGGCGCCACCAAGGAAGGCGCGCTGGCCTCGGCCCTCGGCGAGTTCATCGAGCGCTTGAACTGCAACTTCTTCTACAACGACCAGTTCTGGGGCGAAGACATCGCCAACGCGGCGTTCGTGCATTACCCCAACGAGCGTTGGTTCAAGCCCGGCCGCAAGGACGCGCTGCCGGCGGAAATCCTCGACGAGTACTGCCTGGGCATCTACAACCCCGATGGCGAGCTGCGCGGCTCGCACCTGTACGACACCAACTCCGGCAATGTCGAGCGCGGCATCTGCTCGTTGCCGTTCGTGCGCCAGTCCGATGGTGAAACGGTGTACTTCCCGTCCAACCTCATTGAAAACCTCTACCTCAGCAACGGCATGAGCGCCGGCAACACCCTGGCCGAAGCGCAGGTGCAGTGCCTGTCGGAGATTTTCGAGCGGGCGGTGAAGCGGCAGATCCTCGAAGGCGAACTGGCGTTGCCGGATGTGCCCGAGGATGTGCTGGCCAAGTACCCGGCCATCGTTGCCAGCATCCAGGGCCTGGAAGAGCAGGGCTTCCCGGTGCTGGTCAAGGATGCGTCGCTGGGCGGTGAATTCCCGGTGATGTGCGTGACCCTGATGAACCCGCGCACCGGTGGCGTGTTCGCTTCGTTCGGCGCGCACCCGAGCTTCGAGGTCGCGCTGGAGCGCAGCCTTACCGAACTGCTCCAGGGCCGCAGCTTCGAGGGTCTCAACGACCTGCCGCAGCCGACGTTCGAAAGCCATGCACTGATGGAACCGAACAACTTCGTCGAACACTTCATCGATTCCAGCGGTGTGGTGTCGTGGCGTTTCTTCAGCGCCAAGGCCGACTTCGAATTCGTCGAATGGGATTTCTCCGGCGCCGGGGAAAACTCCAACGCCGAAGAAGCCGCGACCCTGTTCGGCATCCTCGAAGACATGGGCAAGGAGGTGTACATGGCCGTCTACGACGACCTCGGCGCCACTGCCTGCCGCATCCTGGTGCCGGACTATTCGGAGATCTACCCGGTCGACGACCTGATCTGGGACAACACCAACAAGGCGCTGTTCTTCCGCGAAGACATCCTCAACCTGCACCGCCTCGACGACGACGCCCTCGACGCACTGCTGGAGCGCCTGCTGGAGTCCGAGCTGGACGAGTACACCGAGATCAAGACGCTGATCGGCGTCGAGTTCGACGACAACACCGTCTGGGGCCAGTTGACCATTCTCGAGCTGAAGATCCTGATCCAGGTCGCGCTGAAGAAGTTCGACGACGCCAAGGAACTGGTGGAGATGTTCCTGCAGTACAACGACAACACCGTCGAACGCGGCCTGTTCTACCAGGCGCTGAACGTGGTGTTGGAAGTGCAGTTGGACAACGAGCTTGCCCTGGAGCACTACGAGCACAACTTCCGCCGCATGTTCGGCAACGAGCGGATGGACGCGGTGATCGGCTCGGTGCAGGGCAGCGTGCGCTTCCATGGCCTGACCCCGACCAGCCTGAAGCTCGAAGGCCTCGATCGCCACCAGCGCCTGGTCGACAGCTACAAGAAACTGCATGCAGCGCGGGCGAGGGCGGCAGGCCTGAGCCTGTAA

Transcript

HOLI00001.g50889.t1

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P75838	Ribosomal protein S12 methylthiotransferase accessory factor YcaO OS=Escherichia coli (strain K12) OX=83333 GN=ycaO PE=1 SV=2
P44144	Uncharacterized protein HI_1265 OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) OX=71421 GN=HI_1265 PE=4 SV=2

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF18381 all species →	YcaO_C	YcaO cyclodehydratase C-terminal domain	Repeat	Interproscan
PF02566 all species →	OsmC	OsmC-like protein	Family	Interproscan
PF02624 all species →	YcaO	YcaO cyclodehydratase, ATP-ad Mg2+-binding	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR041080 all species →	Domain	YcaO cyclodehydratase, C-terminal	Interproscan
IPR052903 all species →	Family	Ribosomal protein S12 methylthiotransferase accessory	Interproscan
IPR003776 all species →	Domain	YcaO-like domain	Interproscan
IPR003718 all species →	Family	OsmC/Ohr family	Interproscan
IPR036102 all species →	Homologous_superfamily	OsmC/Ohr superfamily	Interproscan
IPR015946 all species →	Homologous_superfamily	K homology domain-like, alpha/beta	Interproscan
IPR019938 all species →	Family	YcaO domain protein	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR39624 all species →	PROTEIN INVOLVED IN RIMO-MEDIATED BETA-METHYLTHIOLATION OF RIBOSOMAL PROTEIN S12 YCAO	Interproscan

Gene Ontology

No Gene Ontology signature was recorded for HOLI00001.G50889 in Hydra oligactis.

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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K09136	ycaO; ribosomal protein S12 methylthiotransferase accessory factor	-	Ribosome biogenesis	ko03009	deepkoala

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 →