Gene detail

Detailed information of XP_001630169.2 in Nematostella vectensis

Genomic Location: NC_064045.1:4936020...4942603
NR annotation: XP_001630169.2, glutamate dehydrogenase [Nematostella vectensis]
Species Nematostella vectensis · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
P94598	Glutamate dehydrogenase OS=Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50) OX=226186 GN=gdhA PE=3 SV=2
P95544	NAD(P)-specific glutamate dehydrogenase OS=Xylanibacter ruminicola OX=839 GN=gdhA PE=1 SV=1
P43793	NADP-specific glutamate dehydrogenase OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) OX=71421 GN=gdhA PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0002528 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02812 all species →	ELFV_dehydrog_N	Glu/Leu/Phe/Val dehydrogenase, dimerisation domain	Domain	Interproscan
PF00208 all species →	ELFV_dehydrog	Glutamate/Leucine/Phenylalanine/Valine dehydrogenase	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR033524 all species →	Active_site	Leu/Phe/Val dehydrogenases active site	Interproscan
IPR050724 all species →	Family	Glutamate/Leucine/Phenylalanine/Valine dehydrogenases	Interproscan
IPR033922 all species →	Domain	NAD(P) binding domain of glutamate dehydrogenase	Interproscan
IPR006095 all species →	Family	Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase	Interproscan
IPR006097 all species →	Domain	Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase, dimerisation domain	Interproscan
IPR036291 all species →	Homologous_superfamily	NAD(P)-binding domain superfamily	Interproscan
IPR046346 all species →	Homologous_superfamily	Aminoacid dehydrogenase-like, N-terminal domain superfamily	Interproscan
IPR006096 all species →	Domain	Glutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase, C-terminal	Interproscan
IPR014362 all species →	Family	Glutamate dehydrogenase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR43571 all species →	NADP-SPECIFIC GLUTAMATE DEHYDROGENASE 1-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004354 all species →	Molecular Function	glutamate dehydrogenase (NADP+) activity	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0006537 all species →	Biological Process	glutamate biosynthetic process	Interproscan
GO:0016639 all species →	Molecular Function	oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor	Interproscan
GO:0006520 all species →	Biological Process	amino acid metabolic process	Interproscan
GO:0016491 all species →	Molecular Function	oxidoreductase 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
K00262	E1.4.1.4, gdhA; glutamate dehydrogenase (NADP+)	EC:1.4.1.4	Arginine biosynthesis	ko00220	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of XP_001630169.2 across 48 RNA-seq samples of Nematostella vectensis. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

48Samples

48TPM > 0

16Conditions

265.8Max TPM

158.0Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole 6 week old aboral regenerate · regenerate 96hpa	3	3	107.31	118.15
whole 6 week old aboral regenerate · regenerate 144hpa	3	3	91.09	101.22
whole 6 week old aboral regenerate · regenerate 0hpa	3	3	200.68	250.47
whole 6 week old aboral regenerate · regenerate 2hpa	3	3	181.84	196.92
whole 6 week old aboral regenerate · regenerate uncut	3	3	148.27	169.04
whole 6 week old aboral regenerate · regenerate 4hpa	3	3	172.34	200.88
whole 6 week old aboral regenerate · regenerate 120hpa	3	3	111.40	126.21
whole 6 week old aboral regenerate · regenerate 36hpa	3	3	154.95	179.89
whole 6 week old aboral regenerate · regenerate 24hpa	3	3	172.35	211.73
whole 6 week old aboral regenerate · regenerate 20hpa	3	3	191.84	254.76
whole 6 week old aboral regenerate · regenerate 16hpa	3	3	190.73	211.91
whole 6 week old aboral regenerate · regenerate 72hpa	3	3	129.09	153.37
whole 6 week old aboral regenerate · regenerate 60hpa	3	3	121.39	133.57
whole 6 week old aboral regenerate · regenerate 48hpa	3	3	139.16	157.15
whole 6 week old aboral regenerate · regenerate 8hpa	3	3	209.17	229.79
whole 6 week old aboral regenerate · regenerate 12hpa	3	3	207.17	265.77

Per sample · hover a bar for the full sample record

Show the sample table (48 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR6320836	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	118.15
SRR6320863	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	109.21
SRR6320837	whole 6 week old aboral regenerate · regenerate 96hpa	whole 6 week old aboral regenerate	six weeks	regenerate 96hpa	SRP125570	94.57
SRR6320847	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	101.22
SRR6320838	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	100.85
SRR6320841	whole 6 week old aboral regenerate · regenerate 144hpa	whole 6 week old aboral regenerate	six weeks	regenerate 144hpa	SRP125570	71.20
SRR6320840	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	250.47
SRR6320839	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	189.49
SRR6320846	whole 6 week old aboral regenerate · regenerate 0hpa	whole 6 week old aboral regenerate	six weeks	regenerate 0hpa	SRP125570	162.07
SRR6320842	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	196.92
SRR6320848	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	196.42
SRR6320861	whole 6 week old aboral regenerate · regenerate 2hpa	whole 6 week old aboral regenerate	six weeks	regenerate 2hpa	SRP125570	152.19
SRR6320845	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	169.04
SRR6320843	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	142.73
SRR6320844	whole 6 week old aboral regenerate · regenerate uncut	whole 6 week old aboral regenerate	six weeks	regenerate uncut	SRP125570	133.03
SRR6320873	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	200.88
SRR6320872	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	160.10
SRR6320849	whole 6 week old aboral regenerate · regenerate 4hpa	whole 6 week old aboral regenerate	six weeks	regenerate 4hpa	SRP125570	156.02
SRR6320850	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	126.21
SRR6320882	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	107.38
SRR6320883	whole 6 week old aboral regenerate · regenerate 120hpa	whole 6 week old aboral regenerate	six weeks	regenerate 120hpa	SRP125570	100.60
SRR6320851	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	179.89
SRR6320855	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	149.12
SRR6320852	whole 6 week old aboral regenerate · regenerate 36hpa	whole 6 week old aboral regenerate	six weeks	regenerate 36hpa	SRP125570	135.85
SRR6320856	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	211.73
SRR6320853	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	157.17
SRR6320854	whole 6 week old aboral regenerate · regenerate 24hpa	whole 6 week old aboral regenerate	six weeks	regenerate 24hpa	SRP125570	148.14
SRR6320859	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	254.76
SRR6320860	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	170.30
SRR6320857	whole 6 week old aboral regenerate · regenerate 20hpa	whole 6 week old aboral regenerate	six weeks	regenerate 20hpa	SRP125570	150.46
SRR6320858	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	211.91
SRR6320881	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	201.67
SRR6320880	whole 6 week old aboral regenerate · regenerate 16hpa	whole 6 week old aboral regenerate	six weeks	regenerate 16hpa	SRP125570	158.62
SRR6320862	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	153.37
SRR6320864	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	128.27
SRR6320865	whole 6 week old aboral regenerate · regenerate 72hpa	whole 6 week old aboral regenerate	six weeks	regenerate 72hpa	SRP125570	105.62
SRR6320867	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	133.57
SRR6320869	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	116.98
SRR6320866	whole 6 week old aboral regenerate · regenerate 60hpa	whole 6 week old aboral regenerate	six weeks	regenerate 60hpa	SRP125570	113.61
SRR6320868	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	157.15
SRR6320871	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	134.51
SRR6320870	whole 6 week old aboral regenerate · regenerate 48hpa	whole 6 week old aboral regenerate	six weeks	regenerate 48hpa	SRP125570	125.81
SRR6320876	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	229.79
SRR6320875	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	225.64
SRR6320874	whole 6 week old aboral regenerate · regenerate 8hpa	whole 6 week old aboral regenerate	six weeks	regenerate 8hpa	SRP125570	172.09
SRR6320878	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	265.77
SRR6320879	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	195.93
SRR6320877	whole 6 week old aboral regenerate · regenerate 12hpa	whole 6 week old aboral regenerate	six weeks	regenerate 12hpa	SRP125570	159.82

Source: CnidoSite RNA-seq expression matrices (NVECT_TPM, StringTie quantification over 48 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.

Proteomic evidence

Peptides from this gene's protein product were identified in 1 re-processed proteomic dataset at a false discovery rate of q ≤ 0.01 (Comet + Percolator).

1Unique peptides

1PSMs

14.2%Max coverage

0.0001Best q-value

1Datasets

Dataset	Species	Tissue / condition	Peptides	PSMs	Coverage	Best q
PXD033068	Nematostella vectensis	Embryos	1	1	14.2%	0.0000678288	peptides
K.VFSNDEDITDIQASIEGPTGTPYEGGIFK.I q=0.0000678288

Search parameters for this evidence: Comet 2026.01, precursor 10 ppm, fragment 0.02 Da, fixed C+57.021464, variable M+15.9949, PSM-level q ≤ 0.01 against . · all proteins for Nematostella vectensis

Co-expression network

Genes whose expression across the transcriptome samples of Nematostella vectensis 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.

Direction	Partners	Most correlated partner	PCC
Positively correlated	13	XP_001622874.2	0.881087299526505
Negatively correlated	107	XP_048583054.1	-0.7670610720725

Open this gene in Network Analysis → The network opens with the gene already entered and both directions selected. There you can add up to 9 more genes, switch between the positive and negative network, and export the edge list.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Nematostella vectensis, 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.

Dataset	Tissue / stage	Cells	Cell types	This gene	Marker of
NVECT_2month	2 month animal · Adult tissues/organs	1,614	23	not in this dataset	–
NVECT_bodywall	body wall with mesenteries · 6-8 weeks adults	11,742	13	in viewer open ↗	Gastrodermis (2.843, 0.835%) Muscle (1.607, 0.684%)
NVECT_embryo	embryos · 8, 10 and 12 h after fertilisation (deposit labels 8h/10h/12h)	9,711	17	not in this dataset	–
NVECT_gastrula	Blastula-gastrula intermediate · Developmental stages	49,166	27	not in this dataset	–
NVECT_gastruloid	dissociated and reaggregated embryos · 4-48 hpa	36,550	8	not in this dataset	–
NVECT_neoplasm	neoplasm · Adult tissues/organs	2,532	16	in viewer open ↗	Cluster 10 (1.53, 0.57%)
NVECT_nervous	Gastrula Cells · nervous system	16,590	27	unmapped	–
NVECT_notch48h	embryos treated 24-48 hpf (DMSO vs LY411575) · 48 hpf	19,044	7	not in this dataset	–
NVECT_tentacle	tentacle · Adult tissues/organs	7,977	19	not in this dataset	–

Opening a dataset shows the UMAP with this gene coloured and the violin plot of its expression per cell type. A gene is in viewer when the dataset ships a per-cell expression vector for it; marker only means it is in the dataset’s ranked marker table but no vector was exported, so the atlas cannot draw it; not in this dataset means the dataset’s own gene-ID table does not list it, so no expression claim can be made for that dataset. unmapped is deliberately weaker still: the dataset has no gene-ID table on CnidoSite yet, so nothing is claimed in either direction. Where markers are listed, the numbers are log2 fold change and the percentage of cells of that type in which the gene was detected.

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.

Peak calls overlapping this gene

Assay	Sample	Peaks	Region
ChIP-seq	H3K27ac_Ncol3_negative	1	Promoter (<=1kb) 1
	H3K27ac_Ncol3_positive	1	Promoter (<=1kb) 1
	H3K27ac_Nep3_negative	1	Promoter (<=1kb) 1
	H3K27ac_Nep3_positive	1	Promoter (<=1kb) 1
	H3K36me3_planulae_4days	3	Exon 1 · Promoter (2-3kb) 1 · Promoter (1-2kb) 1
	H3K36me3_polyps	4	Exon 1 · Promoter (<=1kb) 1 · Promoter (1-2kb) 1 · Promoter (2-3kb) 1
	H3K4me1_gastrulae_24h	1	Promoter (<=1kb) 1
	H3K4me1_neuronal_ELAV_cells	1	Promoter (<=1kb) 1
	H3K4me1_planulae_4days	2	Promoter (<=1kb) 2
	H3K4me2_neuronal_ELAV_cells	1	Promoter (<=1kb) 1
	late_gastrula	1	Promoter (<=1kb) 1
	late_planula_4d	3	Exon 2 · Promoter (2-3kb) 1

Browse the full epigenomic landscape of this species: ChIP-seq · ATAC-seq.

DNA methylation (bisulphite samples)

Sample	Methylation profile
Whole_adults	open

The DNA Methylation page locates this gene by scanning the bisulphite table, which holds one row per cytosine. For the largest datasets that scan takes a while to return; it does not mean the link is broken.

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.	ready	open →
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 →