Gene detail

Detailed information of HOLI00001.G51685 in Hydra oligactis

Genomic Location: HOLI00001:3436634...3439798
NR annotation: WP_262154398.1, MULTISPECIES: CusA/CzcA family heavy metal efflux RND transporter [unclassified Pseudomonas]
Species Hydra oligactis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

HOLI00001.g51685.t1

ATGTTCGAACGCATCATTCAATTCGCCATCGAGCAGCGCCTGATCGTGCTGCTCGGTGTGCTGCTGATGGCCGGGCTGGGTTTGGCCAGCTATCAGAAACTGCCGATCGACGCGGTACCGGACATCACCAACGTCCAGGTGCAGATCAACACCTCGGCGGACGGCTTTTCGCCACTGGAAACCGAGCAGCGCATCACCTTCGCCATCGAGACCGCCATGGCCGGCCTGCCGGGCCTGGAGCAGACCCGCTCGCTGTCGCGTTCGGGGTTGTCGCAGGTGACGGTGATCTTCGAAGACGGCACTGACCTGTTCTTCGCCCGGCAACTGGTCAACGAGCGCCTGCAACTGGCCCGTGGCCAACTGCCCGAGGGTGTCGAGACGGCCATGGGACCGATCTCCACCGGCCTCGGCGAGATCTTCCTGTGGACCGTGGAAGCCGAGGAGGGGGCGCGCAAGGCCGATGGCAGCCCCTACACGCCGACCGACCTGCGCGAGATCCAGGACTGGATCATCAAGCCGCAGTTGCGCAACGTGCGTGGCGTGGCCGAGATCAACAGCATCGGCGGTTTCGCCAAGGAGTATCAGATCGCGCCCGACCTCAAGCGTCTGGCGGCCTACAAGCTGACCCTGAACGATCTGCTCACCGCGCTGGAGCGCAACAACGCCAACGTCGGTGCCGGCTACATCGAGCGCCAGGGCGAGCAATTGCTGATCCGTGCGCCGGGGCAACTGGGCGGCATCGACGATATCGCCAACATCGTTCTGGCCAATGTCGATGGCACGCCGATCCGCGTGCGCTCGGTGGCCGAGGTCGGGATCGGTCGCGAGCTGCGCAGCGGCGCGGCCACTGAAAACGGTCGTGAAGTGGTGCTGGGCACGGTGTTCATGCTGATCGGCGAAAACAGCCGCAGCGTGTCCCAGGCGGTGGCGGCAAAACTCGCGCAGATCAACAAGACCCTGCCCGAAGGGGTCAAGGCGGTGACTGTCTATGACCGCACCGATCTGGTCGACAAAGCCATCGCCACGGTGAAGAAAAACCTGGTGGAAGGCGCGGTGCTGGTGATCGCGGTGCTGTTCCTGTTTCTCGGCAACATCCGCGCGGCGCTGATCACCGCGATGGTGATTCCGCTGTCGATGCTGTTCACCTTCACCGGGATGTTCAGCAACAAGGTCAGCGCCAACCTGATGAGCCTCGGCGCGCTGGACTTCGGCATCATCGTCGACGGCGCGGTGGTGATCGTCGAAAACGCGATTCGCCGCCTGGCCCACGCGCAGCAGCACCACGGTCGCCTGCTGACCCGCGCCGAGCGCCTGCGCGAAGTCTTCGCCGCCGCCCGCGAAGCACGCCGGCCGCTGATCTACGGCCAGTTGATCATCATGGTGGTGTACCTGCCGATCTTCGCCCTGAGCGGTGTCGAGGGGCGGATGTTCCACCCGATGGCCTTTACCGTGGTCATCGCCTTGCTCGGTGCCATGCTGTTGTCGGTGACCTTCGTTCCCGCAGCGATTGCGCTGTTCGTCACCGGCAAGGTCAAGGAAGAAGAAAACGCCCTGATGCGCGGTGCCAAGCGTGGCTACGCGCCGCTGCTGCGCTGGGTCATGGGCCGACGCACGCTGGCGTTCAGCCTGGCGGCGGCGACGGTGGTGTTGTCCGGGCTGCTGGCCGCGCGCATGGGCAGCGAGTTCGTGCCGAGCCTGAGCGAAGGCGACTTTGCCCTGCAAGCCTTGCGCGTACCGGGCACCAGCCTGAGCCAGTCGGTGCAGATGCAGCAGCAACTGGAAAAGAGCGTGATCGAGCAGGTGCCGGAAGTCGAACGGGTGTTCGCCCGCACCGGCACCGCCGAGATCGCCGCCGACCCGATGCCGCCGAACATCTCCGACAGCTACGTGATGCTCAAGCCGAAGGCGCAATGGCCGGATCCGGGCAAGACCCGCGAGCAGTTGATCGCCGATATCCAGCGCGCCGCCGCACGGGTGCCGGGCAGCAACTACGAGCTGTCGCAGCCGATCCAGTTGCGCTTCAACGAGCTGATTTCGGGGGTGCGCAGTGATGTCGCGGTGAAGCTGTTCGGCGATGACATGGCCGTGCTCAATCGCACCGCCGCGCAGATCGCCAGCGCCTTGCAAGGCGTCCCCGGAGCTTCGGAAGTGAAGGTGGAGCAGACCAGCGGCTTGCCGGTGCTGACCATCGATATCGACCGTGAACGGGCCGCGCGCTATGGGCTCAACGTCGGTGACGTGCAGGACAGCATCGCCGTGGCAGTGGGCGGGCGCAAGGCGGGGACGCTGTACGAGGGCGACCGGCGCTTCGATCTGGTGGTGCGTCTGCCGGACGAACTGCGCACCGACATCCAGGGCATCTCGCGGATGCTGATCCCGGTGCCGGCCAGCGGTGGCAGTCAGCAGATCGGCTTCATCAGCCTTGCCGACGTGGCGCGGGTGGAACTGGTGCAAGGCCCCAACCAGATCAGCCGCGAGAACGGCAAGCGCCTGGTGGTGGTCAGCGCCAACGTGCGCGGGCGTGATATCGGCTCGTTCGTCGCCGAAGCGCAGGAGCGCATCGACGCCGAAGTGAAGATCCCGGCCGGTTACTGGGCCAACTGGGGTGGTCAGTTCGAGCAGTTGCAGTCGGCGGCGCAGCGTCTGCAGGTGGTGGTGCCGGTGGCGCTGCTGCTGGTCTTCGCGCTGCTGTTCATGATGTTCAACAACCTCAAGGACGGTCTGCTGGTGTTCACCGGCATTCCCTTCGCCCTCACCGGCGGGGTGGTGGCGTTGTGGTTGCGGGATATTCCCCTGTCGATTTCCGCCGGGGTCGGCTTCATCGCCCTGTCGGGTGTGGCGGTGCTCAACGGGCTGGTGATGATCGCCTTCATTCGCAGCCTGCGCGAGCAGGGTCTGCCGTTGCGCCAGGCCATCGACGAAGGGGCGCTGACGCGCTTGCGGCCGGTGCTGATGACGGCGCTGGTGGCGTCGCTGGGCTTTATCCCGATGGCCCTGGCCACCGGCACCGGCGCCGAAGTGCAGCGACCGCTGGCGACCGTGGTGATTGGCGGGATTCTCTCGTCCACCGCGCTGACCTTGCTGGTGTTGCCGGCGCTGTACTACCGCGCTCACCGCAAGGATGAAGAGGCCGAGGCCACGCAACTGCAGGAGGCCGATGCCTGA

Transcript

HOLI00001.g51685.t1

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P94177	Cation efflux system protein CzcA OS=Alcaligenes sp. (strain CT14) OX=68998 GN=czcA PE=3 SV=1
P13511	Cobalt-zinc-cadmium resistance protein CzcA OS=Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34) OX=266264 GN=czcA PE=1 SV=3
Q48815	Protein HelA OS=Legionella pneumophila OX=446 GN=helA PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0012446 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF00873 all species →	ACR_tran	AcrB/AcrD/AcrF family	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027463 all species →	Homologous_superfamily	Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains	Interproscan
IPR001036 all species →	Family	Acriflavin resistance protein	Interproscan
IPR004763 all species →	Family	Cation efflux system CusA-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR32063 all species →	-	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016020 all species →	Cellular Component	membrane	Interproscan
GO:0022857 all species →	Molecular Function	transmembrane transporter activity	Interproscan
GO:0055085 all species →	Biological Process	transmembrane transport	Interproscan
GO:0005886 all species →	Cellular Component	plasma membrane	Interproscan
GO:0042910 all species →	Molecular Function	xenobiotic transmembrane transporter activity	Interproscan
GO:0006812 all species →	Biological Process	monoatomic cation transport	Interproscan
GO:0008324 all species →	Molecular Function	monoatomic cation transmembrane transporter 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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K15726	czcA, cusA, cnrA; heavy metal efflux system protein	-	Transporters	ko02000	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 →