Detailed information of g2361.t1 in Acropora digitifera

Genomic Location: chr1Alt:37165928...37175268
NR annotation: XP_029185651.2, nucleoside diphosphate kinase 7-like isoform X1 [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
Q9Y5B8Nucleoside diphosphate kinase homolog 7 OS=Homo sapiens OX=9606 GN=NME7 PE=1 SV=1
Q9QXL8Nucleoside diphosphate kinase homolog 7 OS=Mus musculus OX=10090 GN=Nme7 PE=1 SV=2
Q9QXL7Nucleoside diphosphate kinase homolog 7 OS=Rattus norvegicus OX=10116 GN=Nme7 PE=1 SV=2
 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00334
all species →		NDKNucleoside diphosphate kinaseDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR036850
all species →		Homologous_superfamilyNucleoside diphosphate kinase-like domain superfamilyInterproscan
IPR006602
all species →		DomainDM10 domainInterproscan
IPR037993
all species →		DomainNDPK7, second NDPk domainInterproscan
IPR034907
all species →		DomainNucleoside diphosphate kinase-like domainInterproscan
IPR011410
all species →		FamilyNucleoside diphosphate kinase 7Interproscan
IPR001564
all species →		FamilyNucleoside diphosphate kinaseInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR43109
all species →		NUCLEOSIDE DIPHOSPHATE KINASE 7Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0004550
all species →		Molecular Functionnucleoside diphosphate kinase activityInterproscan
GO:0005524
all species →		Molecular FunctionATP bindingInterproscan
GO:0005813
all species →		Cellular ComponentcentrosomeInterproscan
GO:0006183
all species →		Biological ProcessGTP biosynthetic processInterproscan
GO:0006228
all species →		Biological ProcessUTP biosynthetic processInterproscan
GO:0006241
all species →		Biological ProcessCTP 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
K00940ndk, NME; nucleoside-diphosphate kinaseEC:2.7.4.6
Membrane traffickingko04131deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g2361.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
62.0Max TPM
38.2Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Coral branch 39 39 38.17 62.03

Per sample · hover a bar for the full sample record

Show the sample table (39 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR23047226 Coral branch Coral branch adult not recorded SRP416931 62.03
SRR23047237 Coral branch Coral branch adult not recorded SRP416931 61.76
SRR23047221 Coral branch Coral branch adult not recorded SRP416931 49.74
SRR23047207 Coral branch Coral branch adult not recorded SRP416931 48.45
SRR23047213 Coral branch Coral branch adult not recorded SRP416931 47.73
SRR23047223 Coral branch Coral branch adult not recorded SRP416931 45.84
SRR23047219 Coral branch Coral branch adult not recorded SRP416931 45.79
SRR23047216 Coral branch Coral branch adult not recorded SRP416931 44.53
SRR23047211 Coral branch Coral branch adult not recorded SRP416931 42.98
SRR23047242 Coral branch Coral branch adult not recorded SRP416931 40.55
SRR23047239 Coral branch Coral branch adult not recorded SRP416931 39.01
SRR23047240 Coral branch Coral branch adult not recorded SRP416931 38.92
SRR23047243 Coral branch Coral branch adult not recorded SRP416931 38.72
SRR23047220 Coral branch Coral branch adult not recorded SRP416931 38.46
SRR23047233 Coral branch Coral branch adult not recorded SRP416931 38.36
SRR23047210 Coral branch Coral branch adult not recorded SRP416931 38.30
SRR23047236 Coral branch Coral branch adult not recorded SRP416931 38.13
SRR23047206 Coral branch Coral branch adult not recorded SRP416931 37.57
SRR23047209 Coral branch Coral branch adult not recorded SRP416931 37.34
SRR23047222 Coral branch Coral branch adult not recorded SRP416931 37.12
SRR23047229 Coral branch Coral branch adult not recorded SRP416931 36.79
SRR23047217 Coral branch Coral branch adult not recorded SRP416931 35.99
SRR23047218 Coral branch Coral branch adult not recorded SRP416931 35.98
SRR23047224 Coral branch Coral branch adult not recorded SRP416931 35.94
SRR23047214 Coral branch Coral branch adult not recorded SRP416931 35.67
SRR23047232 Coral branch Coral branch adult not recorded SRP416931 35.37
SRR23047234 Coral branch Coral branch adult not recorded SRP416931 34.10
SRR23047230 Coral branch Coral branch adult not recorded SRP416931 33.54
SRR23047212 Coral branch Coral branch adult not recorded SRP416931 33.48
SRR23047215 Coral branch Coral branch adult not recorded SRP416931 32.88
SRR23047235 Coral branch Coral branch adult not recorded SRP416931 32.26
SRR23047238 Coral branch Coral branch adult not recorded SRP416931 30.97
SRR23047244 Coral branch Coral branch adult not recorded SRP416931 30.84
SRR23047227 Coral branch Coral branch adult not recorded SRP416931 30.47
SRR23047225 Coral branch Coral branch adult not recorded SRP416931 29.51
SRR23047231 Coral branch Coral branch adult not recorded SRP416931 29.51
SRR23047241 Coral branch Coral branch adult not recorded SRP416931 28.67
SRR23047228 Coral branch Coral branch adult not recorded SRP416931 28.27
SRR23047208 Coral branch Coral branch adult not recorded SRP416931 27.07

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 correlated3g16854.t10.776521618764369
Negatively correlated12g24452.t1-0.675815009186247

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
DNase-seq (DHS)WholeAnimal2Distal Intergenic 1 · Promoter (<=1kb) 1

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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