Gene detail

Detailed information of HOLI00001.G53772 in Hydra oligactis

Genomic Location: HOLI00001:6084321...6087148
NR annotation: RMQ68457.1, Glycine betaine/carnitine/choline ABC transporter [Pseudomonas viridiflava]
Species Hydra oligactis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

HOLI00001.g53772.t1

ATGCGCACGCTTCTTATCGCCCCAATGATGCTGGCCGCCTGCGTGGCCAACGCCGCCGACTCGGTGAAGATCTACAACTGGTCGAGCTACATCGCCCCGGACACCCTGGCCAGCTTCCAGCAGGCCAGCGGTATCGTGCCCACCTACGACGTGTTCGACAGCAACGAAACCCTCGACGGCAAGCTGATGACCGGCAACTCCGGCTATGACGTGGTGTTTCCGTCCAACCACTTCATGGCCCGGCAGATCCAGGGCAAGGCCCTGAAGCGCCTGGACAAGAGCCAGTTGCCCAACTGGAAGAACCTCAACCCGGTGCTGCTCAAGGCGCTGGAGGTGAACGACCCGGGCAACCAGTACGGTTTCCCGTACCTGTGGGGCAGCACCGGCATCGGCTACAACATCGACAAGGTCAAGGCAGTACTCGGCGACAACGCCCCGGTGGACTCCTGGGATCTGATCTTCAAGCCCGAGTACATCGGCAAACTCAAGAGCTGCGGCGTCGCGGTGCTGGATAACGGCCCCGAACTGCTGCCGATCGCCCTGCATTACCTGGGCCTGCCGCACCACAGCCAGAACCCGGCCGACTACGAGAAAGCCAAGGAGTTGCTGATGAAGGTGCGGCCATACATCAGCTACTTCCACTCGTCGAAGTACACCGGCGACCTGGCCAATGGCGACGTGTGCGTGGTGGTGGGGTTCTCGGGCGACGTGTTGCAGGCGAAAAACCGCGCCATCGAGGCGAACAACGGCGTCAAGGTGGGCTATTCGATTCCGAAGGAAGGTGCGCCGATGTGGTTCGACATGGTTGCCATGCCGGCCGATGCGCCGGATGAGAAGGCCGGCTATGCGTACATGAATTACCTGCTGCAACCGGAGGTGATGGCCAACATCAGCAACCATGTGCAGTACGCCAACGGCAACCTCAAGGCAGACGCCCTGGTCGACCCGCAACTGAAGGCCAACAACATGATCTATCCGGGCGATGAGGTGATGGGCAAGCTGTATGCCCTGGAGGCGATGCCGGCAAAGATCGACCGGCTCAGGAACGCGGATCTGGACCAGCGTGAAGGCGGGCAACTGACCCTCGTGATGCTCGCGGGTGGCGCGGAATTTCACGTCCGGCCAGCGCTCTTCCATCAGCGCCAGGTTGACCCGGGTCGGCGCCAGGTAGGTCAGGTGACCGCCGCCATCCACCGCCAGGTTTTCAACCGCCTTGACCTTGAATTCCTCGAGCTTCTTCTTGTCGTCGCAACTGATCCAGCGCGCCGACCAGACGGTGATCGGCTCGTAGGCACATTCGACCTTGTATTCCTCTTTCAGGCGGCTGGCGACCACATCGAACTGCAGCACACCGACGGCGCCGAGGATGATGTCGTTGCTGCGCTCGGGGAAGAACACCTGGGTCGCGCCTTCTTCGGCCAGTTGCTGCAGGCCCTGACGCAGTTGCTTGGACTTGAGCGGGTCTTTCAGGCGCACGCGGCGGAACAGTTCCGGGGCGAAGTGCGGGATACCGGTGAAGCCCAGGCTCTCGCCTTCGGTGAAGGTATCGCCGATCTGGATCGTGCCGTGGTTGTGCAGACCGATGATGTCGCCGGCGAAGGCTTCTTCCAGTTGCTCACGCTCGGACGAGAAGAACGTCAGTGCGTCGCCGATGCGCAGGTCTTTGCCGGTACGCACGTGACGCATTTTCATGCCTTTCTCGTACTTGCCCGAGCAGATGCGCATGAAGGCGATACGGTCGCGGTGCTTGGGGTCCATGTTCGCCTGGATCTTGAACACGAAGCCGCTGAATTTCTCTTCCACCGGTTCCACGGTGCGTTCGTGGGCAACCCGTGGCAGCGGGCGTGGCGCCCAGTCGACGACCGCGTCGAGGACGTGGTCGACACCGAAGTTGCCCAGCGCGGTACCGAAGAACACCGGGGTCAACTGGCCGTTGATGAACTCGTCCTGGTTGAACTCGTGGCAGGCGCCCTGCACCAGTTCCAGTTGTTCGAGGAAGCGCTCGTACTCGTCGCCCAGGTGCTCGCGGGCTTCGTCGGAGTCGAGTTTCTCGATGATCTTCACCTCGGTGCGCTCGTGGCCGTGGCCCGGGGTGTAGACGATGATGTAGTCACCGGCGAGGTGATAGACACCCTTGAAGTCCCGGTAGCAGCCGATCGGCCAGGTGATCGGCGCAGCCTTGATCTTCAGAACCGCTTCGATTTCGTCGAGCAGTTCGATCGGGTCGCGGATATCGCGGTCGAGTTTGTTGATGAAGCTGACGATGGGCGTGTCGCGCAGGCGGCAGACATCCATCAGGGCGATGGTCCGCGGCTCGACGCCTTTACCGCCGTCGAGCACCATCAACGCCGAGTCCACGGCGGTCAGGGTGCGGTAGGTATCTTCCGAGAAGTCTTCGTGACCGGGGGTGTCGAGCAGGTTGATCATGTGCTCGCGGTAGGGGAACTGCATCACCGAGGTGGTGATCGAGATACCCCGTTGCTTCTCCATTTCCATCCAGTCGGAGGTGGCATGGCGGTCGGACTTGCGCGATTTCACCGTACCGGCGATGGCAATGGCCTTGCCCATCAGCAGCAGCTTCTCGGTGATGGTGGTCTTACCGGCGTCGGGGTGGGAAATGATTGCGAAAGTGCGGCGCTTCGCGACTTCGGCGGCCTGGTTGGTCATGGGAAATCGCCTGACTGGGGATTGAAAAAAGGGGCGGTATCATACCTGAAGTCGGGCTGA

Transcript

HOLI00001.g53772.t1

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q9I6J0	Spermidine-binding periplasmic protein SpuE OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=spuE PE=1 SV=1
Q02UB7	Putrescine-binding periplasmic protein SpuD OS=Pseudomonas aeruginosa (strain UCBPP-PA14) OX=208963 GN=spuD PE=1 SV=1
Q9I6J1	Putrescine-binding periplasmic protein SpuD OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=spuD PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0019863 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13416 all species →	SBP_bac_8	Bacterial extracellular solute-binding protein	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR006059 all species →	Family	Bacterial-type extracellular solute-binding protein	Interproscan
IPR001188 all species →	Family	Spermidine/putrescine-binding periplasmic protein	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR30222 all species →	SPERMIDINE/PUTRESCINE-BINDING PERIPLASMIC PROTEIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0015846 all species →	Biological Process	polyamine transport	Interproscan
GO:0019808 all species →	Molecular Function	polyamine binding	Interproscan
GO:0042597 all species →	Cellular Component	periplasmic space	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.G53772.

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 →