Detailed information of g27402.t1 in Acropora digitifera

Genomic Location: chr13Alt:4768614...4771803
NR annotation: XP_029189734.2, LOW QUALITY PROTEIN: NADP-specific glutamate dehydrogenase-like [Acropora millepora]
Species Acropora digitifera · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
P94598Glutamate 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
P95544NAD(P)-specific glutamate dehydrogenase OS=Xylanibacter ruminicola OX=839 GN=gdhA PE=1 SV=1
P43793NADP-specific glutamate dehydrogenase OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) OX=71421 GN=gdhA PE=3 SV=1
 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF02812
all species →		ELFV_dehydrog_NGlu/Leu/Phe/Val dehydrogenase, dimerisation domainDomainInterproscan
PF00208
all species →		ELFV_dehydrogGlutamate/Leucine/Phenylalanine/Valine dehydrogenaseDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR006096
all species →		DomainGlutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase, C-terminalInterproscan
IPR033922
all species →		DomainNAD(P) binding domain of glutamate dehydrogenaseInterproscan
IPR033524
all species →		Active_siteLeu/Phe/Val dehydrogenases active siteInterproscan
IPR006097
all species →		DomainGlutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenase, dimerisation domainInterproscan
IPR036291
all species →		Homologous_superfamilyNAD(P)-binding domain superfamilyInterproscan
IPR050724
all species →		FamilyGlutamate/Leucine/Phenylalanine/Valine dehydrogenasesInterproscan
IPR046346
all species →		Homologous_superfamilyAminoacid dehydrogenase-like, N-terminal domain superfamilyInterproscan
IPR014362
all species →		FamilyGlutamate dehydrogenaseInterproscan
IPR006095
all species →		FamilyGlutamate/phenylalanine/leucine/valine/L-tryptophan dehydrogenaseInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR43571
all species →		NADP-SPECIFIC GLUTAMATE DEHYDROGENASE 1-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0006520
all species →		Biological Processamino acid metabolic processInterproscan
GO:0016491
all species →		Molecular Functionoxidoreductase activityInterproscan
GO:0016639
all species →		Molecular Functionoxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptorInterproscan
GO:0004354
all species →		Molecular Functionglutamate dehydrogenase (NADP+) activityInterproscan
GO:0005829
all species →		Cellular ComponentcytosolInterproscan
GO:0006537
all species →		Biological Processglutamate biosynthetic processInterproscan

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
KOEnzymeEnzyme IDPathwayMap IDSource
K00262E1.4.1.4, gdhA; glutamate dehydrogenase (NADP+)EC:1.4.1.4
Arginine biosynthesisko00220deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g27402.t1 across 39 RNA-seq samples of Acropora digitifera. 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.

39Samples
39TPM > 0
1Conditions
358.4Max TPM
95.1Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Coral branch 39 39 95.07 358.43

Per sample · hover a bar for the full sample record

Show the sample table (39 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR23047217 Coral branch Coral branch adult not recorded SRP416931 358.43
SRR23047227 Coral branch Coral branch adult not recorded SRP416931 283.12
SRR23047214 Coral branch Coral branch adult not recorded SRP416931 253.78
SRR23047242 Coral branch Coral branch adult not recorded SRP416931 191.26
SRR23047213 Coral branch Coral branch adult not recorded SRP416931 170.71
SRR23047228 Coral branch Coral branch adult not recorded SRP416931 163.88
SRR23047216 Coral branch Coral branch adult not recorded SRP416931 163.57
SRR23047224 Coral branch Coral branch adult not recorded SRP416931 158.89
SRR23047212 Coral branch Coral branch adult not recorded SRP416931 155.32
SRR23047240 Coral branch Coral branch adult not recorded SRP416931 139.09
SRR23047215 Coral branch Coral branch adult not recorded SRP416931 132.56
SRR23047238 Coral branch Coral branch adult not recorded SRP416931 130.63
SRR23047223 Coral branch Coral branch adult not recorded SRP416931 124.41
SRR23047239 Coral branch Coral branch adult not recorded SRP416931 103.62
SRR23047233 Coral branch Coral branch adult not recorded SRP416931 97.54
SRR23047230 Coral branch Coral branch adult not recorded SRP416931 94.69
SRR23047229 Coral branch Coral branch adult not recorded SRP416931 85.83
SRR23047206 Coral branch Coral branch adult not recorded SRP416931 79.71
SRR23047225 Coral branch Coral branch adult not recorded SRP416931 75.37
SRR23047241 Coral branch Coral branch adult not recorded SRP416931 73.67
SRR23047231 Coral branch Coral branch adult not recorded SRP416931 73.02
SRR23047235 Coral branch Coral branch adult not recorded SRP416931 71.89
SRR23047218 Coral branch Coral branch adult not recorded SRP416931 71.28
SRR23047234 Coral branch Coral branch adult not recorded SRP416931 68.58
SRR23047237 Coral branch Coral branch adult not recorded SRP416931 64.31
SRR23047226 Coral branch Coral branch adult not recorded SRP416931 49.90
SRR23047209 Coral branch Coral branch adult not recorded SRP416931 48.10
SRR23047232 Coral branch Coral branch adult not recorded SRP416931 44.20
SRR23047211 Coral branch Coral branch adult not recorded SRP416931 40.39
SRR23047236 Coral branch Coral branch adult not recorded SRP416931 35.32
SRR23047219 Coral branch Coral branch adult not recorded SRP416931 32.47
SRR23047208 Coral branch Coral branch adult not recorded SRP416931 29.97
SRR23047210 Coral branch Coral branch adult not recorded SRP416931 10.68
SRR23047222 Coral branch Coral branch adult not recorded SRP416931 10.18
SRR23047244 Coral branch Coral branch adult not recorded SRP416931 7.68
SRR23047221 Coral branch Coral branch adult not recorded SRP416931 5.78
SRR23047243 Coral branch Coral branch adult not recorded SRP416931 3.96
SRR23047207 Coral branch Coral branch adult not recorded SRP416931 2.51
SRR23047220 Coral branch Coral branch adult not recorded SRP416931 1.35

Source: CnidoSite RNA-seq expression matrices (ADIGI_TPM, StringTie quantification over 39 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.

Co-expression network

Genes whose expression across the transcriptome samples of Acropora digitifera 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.

DirectionPartnersMost correlated partnerPCC
Positively correlated36g29083.t10.965184117565763
Negatively correlated4g26575.t1-0.729644491200338

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 Acropora digitifera, 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.

Peak calls overlapping this gene

AssaySamplePeaksRegion

No called peak overlaps this gene in 1 available assay. Either the gene is not near an accessible or marked region in those samples, or it is not represented in the peak caller’s annotation.

Browse the full epigenomic landscape of this species: DNase-seq (DHS).

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.

AnalysisWhat it doesStatus
Primer designDesign PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.template foundopen →
BLASTSearch 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 foundopen →
Expression heatmapDraw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.readyopen →
Gene family / orthogroupLook 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 analysisStart a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.open →
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