Detailed information of g19085.t1 in Acropora digitifera

Genomic Location: chr9Alt:2132712...2137035
NR annotation: XP_029195501.1, density-regulated protein homolog isoform X2 [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
Q9VX98Density-regulated protein homolog OS=Drosophila melanogaster OX=7227 GN=DENR PE=1 SV=3
Q9CQJ6Density-regulated protein OS=Mus musculus OX=10090 GN=Denr PE=1 SV=1
Q2HJ47Density-regulated protein OS=Bos taurus OX=9913 GN=DENR PE=2 SV=1
 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF01253
all species →		SUI1Translation initiation factor SUI1DomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR050318
all species →		FamilyDENR/SUI1 Translation Initiation FactorInterproscan
IPR046447
all species →		DomainDENR, C-terminal domainInterproscan
IPR036877
all species →		Homologous_superfamilySUI1 domain superfamilyInterproscan
IPR001950
all species →		DomainSUI1 domainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR12789
all species →		DENSITY-REGULATED PROTEIN HOMOLOGInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0001731
all species →		Biological Processformation of translation preinitiation complexInterproscan
GO:0002188
all species →		Biological Processtranslation reinitiationInterproscan
GO:0003729
all species →		Molecular FunctionmRNA bindingInterproscan
GO:0003743
all species →		Molecular Functiontranslation initiation factor activityInterproscan
GO:0006413
all species →		Biological Processtranslational initiationInterproscan

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
K24272DENR, TMA22; density-regulated protein-Messenger RNA biogenesisko03019deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of g19085.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
53.7Max TPM
33.7Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Coral branch 39 39 33.68 53.74

Per sample · hover a bar for the full sample record

Show the sample table (39 samples)
SRA runConditionTissueDevelopmental stage TreatmentStudyTPM
SRR23047231 Coral branch Coral branch adult not recorded SRP416931 53.74
SRR23047212 Coral branch Coral branch adult not recorded SRP416931 50.71
SRR23047229 Coral branch Coral branch adult not recorded SRP416931 48.87
SRR23047213 Coral branch Coral branch adult not recorded SRP416931 48.06
SRR23047228 Coral branch Coral branch adult not recorded SRP416931 45.21
SRR23047211 Coral branch Coral branch adult not recorded SRP416931 42.01
SRR23047233 Coral branch Coral branch adult not recorded SRP416931 41.24
SRR23047241 Coral branch Coral branch adult not recorded SRP416931 40.59
SRR23047225 Coral branch Coral branch adult not recorded SRP416931 39.84
SRR23047214 Coral branch Coral branch adult not recorded SRP416931 39.61
SRR23047206 Coral branch Coral branch adult not recorded SRP416931 38.46
SRR23047226 Coral branch Coral branch adult not recorded SRP416931 37.01
SRR23047224 Coral branch Coral branch adult not recorded SRP416931 35.81
SRR23047230 Coral branch Coral branch adult not recorded SRP416931 35.23
SRR23047209 Coral branch Coral branch adult not recorded SRP416931 34.82
SRR23047218 Coral branch Coral branch adult not recorded SRP416931 34.09
SRR23047239 Coral branch Coral branch adult not recorded SRP416931 34.02
SRR23047207 Coral branch Coral branch adult not recorded SRP416931 33.95
SRR23047215 Coral branch Coral branch adult not recorded SRP416931 33.86
SRR23047223 Coral branch Coral branch adult not recorded SRP416931 33.86
SRR23047242 Coral branch Coral branch adult not recorded SRP416931 32.49
SRR23047236 Coral branch Coral branch adult not recorded SRP416931 32.39
SRR23047216 Coral branch Coral branch adult not recorded SRP416931 32.36
SRR23047235 Coral branch Coral branch adult not recorded SRP416931 32.22
SRR23047237 Coral branch Coral branch adult not recorded SRP416931 31.54
SRR23047219 Coral branch Coral branch adult not recorded SRP416931 30.74
SRR23047238 Coral branch Coral branch adult not recorded SRP416931 30.45
SRR23047244 Coral branch Coral branch adult not recorded SRP416931 30.13
SRR23047240 Coral branch Coral branch adult not recorded SRP416931 29.68
SRR23047227 Coral branch Coral branch adult not recorded SRP416931 28.35
SRR23047234 Coral branch Coral branch adult not recorded SRP416931 26.70
SRR23047222 Coral branch Coral branch adult not recorded SRP416931 26.50
SRR23047217 Coral branch Coral branch adult not recorded SRP416931 26.08
SRR23047210 Coral branch Coral branch adult not recorded SRP416931 25.62
SRR23047232 Coral branch Coral branch adult not recorded SRP416931 20.30
SRR23047221 Coral branch Coral branch adult not recorded SRP416931 20.11
SRR23047208 Coral branch Coral branch adult not recorded SRP416931 19.77
SRR23047220 Coral branch Coral branch adult not recorded SRP416931 19.59
SRR23047243 Coral branch Coral branch adult not recorded SRP416931 17.40

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 correlated12g295.t10.785443061789395
Negatively correlated19g16692.t1-0.738014519293608

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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