Gene detail

Detailed information of HOLI00001.G52559 in Hydra oligactis

Genomic Location: HOLI00001:4528055...4532566
NR annotation: WP_110970347.1, glutamate synthase large subunit [Pseudomonas huaxiensis]
Species Hydra oligactis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

HOLI00001.g52559.t1

ATGGTAAGTGGTTGTATTAAAAAGAGATTTGCCTTTGTGAGAGGCGAACCTGGTGAGAATGTGTCTATGAAAACAGGTCTGTACCATCCCGAAGAATTCAAAGATAACTGTGGTTTTGGCCTGATTGCCCACATGACGGGCGAACCCAGCCACCACCTTTTGCAAACGGCTATCGAAGCCCTGACCTGCATGACCCACCGCGGTGGGATCAACGCCGACGGCAAGACCGGCGACGGTTGCGGCCTGCTGATGCAAAAGCCCGATCTGTTCCTGCGCGCAGTCGCCAAGGAGCATTTCGGTAGCGAACTGCCGAAGCAGTACGCGGTGGGCATGGTGTTCTTCAACCAGAACGACGCCAAGGCCGAAGCCGCCCGCGAAAACATGAACCGCGAGATCCTCGCTGCCGGCCTGCAACTGGTCGGCTGGCGCAAAGTGCCGATCGACACCAGCGTTCTGGGTCGCCTGGCGCTGGAGCGTCTGCCGCAGATCGAGCAAGTGTTCATCGGTGCCGAAGGCCTGAGCGATCAGGAATTCGCCATCAAGCTGTTCAGTGCCCGTCGCCGTTCCTCGGTTGCCAACGCCGAAGACACCGACCACTACATCTGCAGCTTTTCGCACAAGACCATCATCTATAAAGGCCTGATGATGCCGGCGGACCTCACCGCCTTCTATCCGGACCTGAGCGACGAGCGTCTGCAAACCGCGATCTGCGTGTTCCACCAGCGCTTCTCCACCAACACCCTGCCGAAATGGCCGCTTGCCCAGCCATTCCGCTTCCTTGCCCACAACGGCGAAATCAACACCATCACCGGTAACCGCAACTGGGCCCAGGCCCGTCGCACCAAGTTCGAGAACGAACTGATCCCGGATCTGGAAGAGCTCGGCCCGCTGGTCAACCGCGTGGGTTCCGACTCGTCCTCGATGGACAACATGCTCGAACTGATGGTCACCGGCGGCATCGACCTGTTCCGTGGCGTGCGGATGATCATTCCGCCAGCGTGGCAGAACGTCGAGACCATGGACGCCGACCTGCGCGCCTTCTACGAATACAACTCCATGCACATGGAGCCGTGGGACGGCCCTGCCGGCGTGGTCATGACCGAAGGTCGCCACGCGGTCTGCCTGCTCGACCGCAACGGCCTGCGCCCGGCGCGCTGGGTCACCACCAAGAACGGCTACATCACCCTGGCGTCGGAAATCGGCGTGTGGGACTACAAGCCTGAAGACGTCATCGCCAAGGGCCGTGTCGGCCCGGGCCAGATCTTCGCCGTGGACACCGAGACCGGTCAGATCCTCGACACCGACGCCATCGACAACCGCCTCAAGTCGCGCCATCCGTACAAGCGCTGGCTGCGCCAGAATGCCCTGCGCATCCAGGCCGACCTGAGCGACGACCAGGGCGCTGCGAGCTACGACACCGACCAGCTCAAGCAATACATGAAGATGTTCCAGGTCACCTTCGAAGAGCGTGACCAGGTGCTGCGTCCGCTCGGCGAACAAGGCCAGGAAGCGGTCGGCTCGATGGGCGACGACACGCCGATGGCGATCCTGTCGCAGCGCGTGCGTTCGACCTACGACTACTTCCGCCAGCAGTTCGCGCAGGTCACCAACCCGCCGATCGACCCGCTGCGCGAAGCCATCGTCATGTCGCTGGAGATCTGCCTCGGTGCCGAGCGCAACATCTTCCAGGAATCGCCCGAGCACGCTTCGCGGGTGATCCTCAGCTCGCCGGTGATCTCGCCGGCCAAGTGGCGCTCGCTGATGAACCTCGAACGCCCTGGCTTCGAGCGTCATCTGATCGACCTCAACTATGAAGAAAGCCTGGGTCTGGAAGCCGCGGTGCGCAGCATCGCCGACCAGGCCGAAGAAGCCGTGCGCAGCGGCAAGACCCAACTGGTCCTGAGCGACCGGCATATCGCTCCGGGCAAGCTGCCGGTGCATGCCTCGCTGGCAGTCGGTGCCGTGCACCACCGCCTGACCGAAAAAGGCCTGCGCTGCGACAGCAACATCCTGGTCGAGACCGCTACCGCCCGCGACCCGCATCACTTCGCCGTGCTGCTCGGTTTCGGTGCTTCCGCCGTCTACCCGTACCTCGCCTACGAAGTGCTGGCCGACCTGATCCGCACCGGCGAAGTGCTGGGCGATCTGGACGAAGTCTTCAAGTACTACCGTAAAGGCATCTCCAAGGGCCTGCTGAAGATCCTGTCGAAGATGGGCATCTCCACCATTGGCTCGTACCGCGGCGCGCAACTGTTCGAAGCGGTTGGCCTGTCCGAGGAAGTGGTCAACCTGAGCTTCCGTGGCGTTCCGAGCCGCCTGAAAGGCGCGCGCTTCGTCGACATCGAGAACGAGCAGAAGCTGCTCGCTGCCGAAGCCTGGAGCCCGCGCAAGCCGATCCAGCAAGGTGGCCTGCTGAAGTTCGTCCACGGTGGCGAGTACCACGCCTACAACCCGGATGTGGTCAACACCCTGCAAGCCGCCGTGCAACAGGGCGACTACGAGAAGTTCAAGGAATACACCGCACTGGTGGACAACCGTCCGGTGTCGATGATCCGCGACCTGCTCAAGGTCAAGACCGCCGAGCAGCCGCTGGACCTCGGCGAAGTCGAGCCACTGCAGGCGATCCTGCAGCGCTTCGACTCCGCCGGTATCTCCCTCGGCGCGCTGTCTCCGGAAGCCCACGAAGCACTGGCCGAGGCGATGAACCGTCTGGGCGCGCGCTCCAACTCCGGTGAGGGCGGCGAAGACCCGGCCCGCTACGGCACCATCCGCAGCTCGAAAATCAAGCAAGTGGCCACCGGTCGTTTCGGTGTCACCCCCGAGTACCTGGTCAACGCCGAAGTGCTGCAGATCAAGGTCGCCCAGGGCGCCAAGCCGGGCGAGGGCGGTCAACTGCCGGGCGGCAAGGTCAACGGTCTGATCGCCAAACTGCGTTACGCAGTACCGGGCGTGACCCTGATCTCGCCACCGCCGCACCACGACATCTACTCGATCGAAGACCTGTCGCAACTGATCTTCGACCTCAAGCAGGTCAACCCGCAGGCGCTGGTATCGGTCAAGCTGGTGGCGGAAGCCGGTGTCGGCACCATCGCCGCCGGCGTGGCCAAGGCCTATGCCGACCTCATCACCATTTCCGGTTATGACGGTGGCACCGGCGCTTCGCCGCTGACCTCGATCAAATACGCCGGCGCCCCGTGGGAACTGGGCCTGGCCGAGACCCACCAGACCCTGCGCGGCAACGATTTGCGCGGCAAGGTCCGGGTGCAGACCGACGGCGGCCTGAAAACCGGCCTCGACGTGATCAAGGCGGCCATCCTCGGCGCCGAAAGCTTCGGCTTCGGCACTGCGCCGATGATCGCCCTGGGCTGCAAATACCTGCGCATCTGCCACCTGAACAACTGCGCCACCGGCGTAGCGACCCAGAACGACAAGCTGCGCAAGGACCACTACATCGGTACCGTCGACATGGTGGTGAACTTCTTCACCTACATTGCCGAAGAAACCCGTGAGTGGCTGGCTCGTCTGGGCGTGCGCAGCCTCGGCGACCTGATCGGTCGTACCGACCTGCTGGAAATGCTCCCGGGCGAAACCGAGAAACAGAAACACCTCGACCTCAGCCCGCTGCTGGGCAGCCCGCATGTACCGGCCGACAAGCCGCAGTTCTGCGAAGTTGACCGCAACCCGCCGTTCGACAAGGGCGTGCTTGCCGAGAAGATGGTGCAAATGGCCCTGCCGGCCATTCGCGACCTGAGTGGCGGCGAGTTCGAACTGGATATCTGCAACTGCGACCGTTCCATCGGCGCGCGGATTTCCGGCGAGATCGCCCGTCTGCATGGCAACCAGGGCATGGCCAAGGCGCCAGTCACCTTCCGCTTCAAGGGTACCGCTGGTCAGAGCTTCGGCGTGTGGAACGCCGGTGGCCTGAACATGCGCCTGGAAGGTGACGCCAACGACTACGTCGGCAAGGGCATGACCGGCGGCAAGCTGGTCATCGTGCCGCCAGCCGGCAGCCCGTTCGCCACGCAGGACAGCGCCATCGTCGGCAACACCTGCCTGTACGGCGCCACTGGCGGCAAGCTGTTCGCCGCCGGTACCGCGGGCGAGCGTTTCGCGGTGCGCAACTCGGGTGCCCACACTATCGTTGAAGGAACTGGCGATCACTGCTGCGAATACATGACCGGTGGTTTTGTCTGCGTTCTGGGCAAGACCGGCTACAACTTCGGCTCCGGCATGACAGGCGGCTTCGCCTACGTGCTGGATATGGACAACAGCTTCGTGGACAAACTGAACCACGAACTGGTGGAGATCCAGCGCATCACCGGCGAGTCGATGGAGGCTTATCGCAGCCACCTGAGCCGTGTGCTGGCCGAGTATGTCGAAGAGACCGGCAGCGAATGGGGCCGTGAGCTCTGGGAAAACCTGGACGACTATGCGCGTCGCTTCTGGCTGGTCAAGCCAAAGGCGGCGAGCCTGAAGAACCTGCTGTCCAGCACCCGGGCCAACCCGCAATAA

Transcript

HOLI00001.g52559.t1

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
E1V8I1	Glutamate synthase [NADPH] large chain OS=Halomonas elongata (strain ATCC 33173 / DSM 2581 / NBRC 15536 / NCIMB 2198 / 1H9) OX=768066 GN=gltB PE=1 SV=1
P09831	Glutamate synthase [NADPH] large chain OS=Escherichia coli (strain K12) OX=83333 GN=gltB PE=1 SV=3
Q9ZNZ7	Ferredoxin-dependent glutamate synthase 1, chloroplastic/mitochondrial OS=Arabidopsis thaliana OX=3702 GN=GLU1 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002087 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04898 all species →	Glu_syn_central	Glutamate synthase central domain	Domain	Interproscan
PF00310 all species →	GATase_2	Glutamine amidotransferases class-II	Domain	Interproscan
PF01645 all species →	Glu_synthase	Conserved region in glutamate synthase	Domain	Interproscan
PF01493 all species →	GXGXG	GXGXG motif	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR013785 all species →	Homologous_superfamily	Aldolase-type TIM barrel	Interproscan
IPR036485 all species →	Homologous_superfamily	Glutamate synthase, alpha subunit, C-terminal domain superfamily	Interproscan
IPR029055 all species →	Homologous_superfamily	Nucleophile aminohydrolases, N-terminal	Interproscan
IPR006982 all species →	Domain	Glutamate synthase, central-N	Interproscan
IPR050711 all species →	Family	Electron transfer and nitrogen metabolism enzyme	Interproscan
IPR017932 all species →	Domain	Glutamine amidotransferase type 2 domain	Interproscan
IPR002932 all species →	Domain	Glutamate synthase domain	Interproscan
IPR002489 all species →	Domain	Glutamate synthase, alpha subunit, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11938 all species →	FAD NADPH DEHYDROGENASE/OXIDOREDUCTASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016491 all species →	Molecular Function	oxidoreductase activity	Interproscan
GO:0006807 all species →	Biological Process	obsolete nitrogen compound metabolic process	Interproscan
GO:0015930 all species →	Molecular Function	glutamate synthase activity	Interproscan
GO:0006537 all species →	Biological Process	glutamate biosynthetic process	Interproscan
GO:0019676 all species →	Biological Process	ammonia assimilation cycle	Interproscan
GO:0016638 all species →	Molecular Function	oxidoreductase activity, acting on the CH-NH2 group of donors	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
K00265	gltB; glutamate synthase (NADPH) large chain	EC:1.4.1.13	Peptidases and inhibitors	ko01002	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 →