Detailed information of g4650.t1 in Acropora digitifera

Genomic Location: chr2Alt:30427065...30457216
NR annotation: XP_044162892.1, C-myc promoter-binding protein-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
Q7Z401C-myc promoter-binding protein OS=Homo sapiens OX=9606 GN=DENND4A PE=1 SV=2
Q5VZ89DENN domain-containing protein 4C OS=Homo sapiens OX=9606 GN=DENND4C PE=1 SV=3
A6H8H2DENN domain-containing protein 4C OS=Mus musculus OX=10090 GN=Dennd4c PE=1 SV=1
 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF03455
all species →		dDENNdDENN domainDomainInterproscan
PF13041
all species →		PPR_2PPR repeat family RepeatInterproscan
PF02141
all species →		DENNDENN (AEX-3) domainFamilyInterproscan
PF10240
all species →		DUF2464Multivesicular body subunit 12FamilyInterproscan
PF03456
all species →		uDENNuDENN domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR005112
all species →		DomaindDENN domainInterproscan
IPR043153
all species →		Homologous_superfamilyDENN domain, C-terminal lobeInterproscan
IPR011990
all species →		Homologous_superfamilyTetratricopeptide-like helical domain superfamilyInterproscan
IPR002885
all species →		RepeatPentatricopeptide repeatInterproscan
IPR023341
all species →		DomainMABP domainInterproscan
IPR037516
all species →		DomainTripartite DENN domainInterproscan
IPR051696
all species →		FamilyDENN Domain-Containing GEFsInterproscan
IPR001194
all species →		DomaincDENN domainInterproscan
IPR005113
all species →		DomainuDENN domainInterproscan
IPR018798
all species →		FamilyMultivesicular body subunit 12Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR12296
all species →		DENN DOMAIN-CONTAINING PROTEIN 4Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005515
all species →		Molecular Functionprotein bindingInterproscan
GO:0031410
all species →		Cellular Componentcytoplasmic vesicleInterproscan
GO:0032483
all species →		Biological Processregulation of Rab protein signal transductionInterproscan
GO:0000813
all species →		Cellular ComponentESCRT I complexInterproscan

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
K20163DENND4; DENN domain-containing protein 4-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 g4650.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
150.1Max TPM
77.3Mean TPM

By condition

ConditionSamplesTPM > 0 Mean TPMMax TPMMean, relative to max
Coral branch 39 39 77.26 150.11

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 150.11
SRR23047223 Coral branch Coral branch adult not recorded SRP416931 136.89
SRR23047242 Coral branch Coral branch adult not recorded SRP416931 121.25
SRR23047213 Coral branch Coral branch adult not recorded SRP416931 118.10
SRR23047229 Coral branch Coral branch adult not recorded SRP416931 118.05
SRR23047233 Coral branch Coral branch adult not recorded SRP416931 115.97
SRR23047239 Coral branch Coral branch adult not recorded SRP416931 109.38
SRR23047216 Coral branch Coral branch adult not recorded SRP416931 107.43
SRR23047241 Coral branch Coral branch adult not recorded SRP416931 91.95
SRR23047234 Coral branch Coral branch adult not recorded SRP416931 84.10
SRR23047231 Coral branch Coral branch adult not recorded SRP416931 82.26
SRR23047222 Coral branch Coral branch adult not recorded SRP416931 80.93
SRR23047227 Coral branch Coral branch adult not recorded SRP416931 80.69
SRR23047225 Coral branch Coral branch adult not recorded SRP416931 79.60
SRR23047206 Coral branch Coral branch adult not recorded SRP416931 78.26
SRR23047215 Coral branch Coral branch adult not recorded SRP416931 77.91
SRR23047228 Coral branch Coral branch adult not recorded SRP416931 73.64
SRR23047217 Coral branch Coral branch adult not recorded SRP416931 72.20
SRR23047238 Coral branch Coral branch adult not recorded SRP416931 70.18
SRR23047221 Coral branch Coral branch adult not recorded SRP416931 68.85
SRR23047224 Coral branch Coral branch adult not recorded SRP416931 68.63
SRR23047220 Coral branch Coral branch adult not recorded SRP416931 67.24
SRR23047214 Coral branch Coral branch adult not recorded SRP416931 66.08
SRR23047212 Coral branch Coral branch adult not recorded SRP416931 65.78
SRR23047207 Coral branch Coral branch adult not recorded SRP416931 65.18
SRR23047243 Coral branch Coral branch adult not recorded SRP416931 61.86
SRR23047210 Coral branch Coral branch adult not recorded SRP416931 60.17
SRR23047232 Coral branch Coral branch adult not recorded SRP416931 59.86
SRR23047209 Coral branch Coral branch adult not recorded SRP416931 59.70
SRR23047240 Coral branch Coral branch adult not recorded SRP416931 59.11
SRR23047230 Coral branch Coral branch adult not recorded SRP416931 59.06
SRR23047211 Coral branch Coral branch adult not recorded SRP416931 57.94
SRR23047219 Coral branch Coral branch adult not recorded SRP416931 56.01
SRR23047208 Coral branch Coral branch adult not recorded SRP416931 53.45
SRR23047237 Coral branch Coral branch adult not recorded SRP416931 52.66
SRR23047235 Coral branch Coral branch adult not recorded SRP416931 49.95
SRR23047236 Coral branch Coral branch adult not recorded SRP416931 45.65
SRR23047244 Coral branch Coral branch adult not recorded SRP416931 44.11
SRR23047218 Coral branch Coral branch adult not recorded SRP416931 42.79

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 correlated32g27857.t10.911510799118696
Negatively correlated36g9859.t1-0.897839594129856

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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