Gene detail

Detailed information of eanc_s032.g0076.t1 in Fimbriaphyllia ancora

Genomic Location: s032:1054016...1062048
NR annotation: XP_029192463.2, probable E3 ubiquitin-protein ligase DTX2 isoform X1 [Acropora millepora]
Species Fimbriaphyllia ancora · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

eanc_s032.g0076.t1

ATAGCAGTGGATAGCCTCGTACTAAAGTATGTATATGATATGAAGTACTATATGATGGCTTGACATGAAGTACTTCCCAAGATTAATCTTTGTTTTCATTTTCTGGTGGTATTCCTTGCTTTTGTTGTGTTTTTCTCCCTCTCTTGGGATGGCTTCTGCTTCCCAGACAAGCAATGTAGTCGTTTGGCTATGGGAGGAGAGACCAAATCTCTGGATTCCTTACGAAGCAGACGCTGGTCGATACTTAGAAAAACACTTCTTGAAGTTGAAACGAGGCACTTCCAAGAAGACGTCCTCCACAATCTATTTGGGAAAATGTTCCCCAGCTCTGATCTGTTACGAAGTTGATTTTGTGAACATGGAACAGATAAAAATTGGCACAGGGGCGTTAAGGAAGATCAAGAGGAAGATCTACCCAAGCCATTCGGTTCCGGGACACGAACTAAGATGGGAGTGGCACAATGATATTACATGGGTTGCTTATGATATTCCTACATCAGAATGCATTGAACGTGAATACAGTACTAAGAGCCAAGATATAGATTTATCCCAGACACCACTTGCAATTCCAAATGTTTTGGATTTTGGTAGCATGACACAGATTAATAGACATACAGGTTATACAAGAAAAGTGCAAAGGTTAACTGGCCAGTCATATCCTTTGGAAAGCCATGGATTAAGTGTTGCAGGGAAATCACCAAGTACAGGTGCAAATGCTACAGGTACTTCCAATGGTTACGCATTTCCAAGTCACAGTAAAACTTTACAAATTGGAGTTTTAGGGAAAATGGGAAAGAGCCTGTTaagcaaaggaaagaaaacagagagccagcaaagaaaagaaaagaGAGTCAAAGTGGAACATTCTGGAGCTGCAGGGGCCTGTGCAAGTGATCCCCTTTCTGAATTCTGCAATGACTTGCAAACAGCCCCTGATGAGGACTGTGCCATTTGTTTTGAAAAACTGTGCAGTATCTCCTCATTCGATGATGAATCCGAAATCAATGGAGCAGCTCACTCTCCCAGCATCAAACAGCTAAATCAATGCAAGCATGCATTTCATGCTTCTTGCCTGCAAGCAATGTATAACAGTGGAACCAAGGATGGAAGCTTGCAGTGCCCTACTTGTAAAGCCATCCATGGTGTTAAACAAGGCAATCAACCAAGAGATGGTGTTATGGATATACATCATTGTCACAGAAGCCTTCCAGGCCATCCTGACTGTGGGATGATCACAATAACCTATGACTTCAGAGGAGGGGTGCAAGGACCAGAACATCCAAACCCAGGGAAAACATACAGTGCAAGAGGTTTCCCAAGAACATGCTACCTGCCTGCTAATAAAAAGGGAAAGAAGGTGTTAAAACTGCTTAAAGAAGCTTGGCAGCGAAGGTTAGTTTTTACGATTGGTACATCATCCACAACTGGTGAACAAGACACAGTGGTTTGGAACGAGATCCACCATAAAACAGAAGCATTTTCAAACCATATGGGGCACGGTTTTCCTGACCCTAACTACCTAGACAATGTTCTTGCTGAGCTGGCTGCACAGGGTGTCCAAGGTGAAGAAGAAAGTGACAACCAGGAGAAAACAGTTTAAAGATGGACACACTGAGTGCATGAATCACTTCACATCTTTGAAGCCTAGTGTAAACTTTGCTATACTTTGTTAACAAGAAATGAGAAGGCTTGATTTCTGGCAGTCTCTCAAATCAGTGTTGCCAGTAAGACAATGTCCTGACCTTGTGTGAGTAGATAATGCTCGTGTTGAGCTAGCTGCATAGGGAGTCCAAGATAATGTTTAACGAAAGTGACAGTCAGAAATAGAAGCCTCAGGTAACTGAGAAAACTATTCAGATGAGGTGACTGTATGAATCACCTACTCTTTTGGAAGCGTAGAGGAAACTTTGCTGTTCTTTGTTACCAACAAATGCAAAGACTTGATTTATAGCAGTCTCAAAGCAATGTTAGTTCTTTCATGATCACTGGTCAGGAGTACTAAAAGTTATAAAATTTTGAAAATCCTCAAACTGAAATGCAATATCATCAGCAGTGGTACAAACGTTTGAAAAGCCAATTTGAAAAGCAGAACTTTGGTATTTCATGTACATACTCAAAACCAATCTTGAACTCCATCACTACATTTGCTGTTAATAAACTGACACTGGGGTC

Transcript

eanc_s032.g0076.t1

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q86UW9	Probable E3 ubiquitin-protein ligase DTX2 OS=Homo sapiens OX=9606 GN=DTX2 PE=1 SV=3
Q9Y2E6	E3 ubiquitin-protein ligase DTX4 OS=Homo sapiens OX=9606 GN=DTX4 PE=1 SV=2
Q6PDK8	E3 ubiquitin-protein ligase DTX4 OS=Mus musculus OX=10090 GN=Dtx4 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000854 (this species only) · gene tree & orthology
Ubiquitin family	E3\|E3 activity RING\|RING · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02825 all species →	WWE	WWE domain	Family	Interproscan
PF00097 all species →	zf-C3HC4	Zinc finger, C3HC4 type (RING finger)	Domain	Interproscan
PF18102 all species →	DTC	Deltex C-terminal domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR018123 all species →	Domain	WWE domain, subgroup	Interproscan
IPR004170 all species →	Domain	WWE domain	Interproscan
IPR037197 all species →	Homologous_superfamily	WWE domain superfamily	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR039399 all species →	Homologous_superfamily	Deltex, C-terminal domain superfamily	Interproscan
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR018957 all species →	Domain	Zinc finger, C3HC4 RING-type	Interproscan
IPR039398 all species →	Family	Deltex family	Interproscan
IPR039396 all species →	Domain	Deltex, C-terminal	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12622 all species →	DELTEX-RELATED	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0046872 all species →	Molecular Function	metal ion binding	Interproscan
GO:0005654 all species →	Cellular Component	nucleoplasm	Interproscan
GO:0007219 all species →	Biological Process	Notch signaling pathway	Interproscan
GO:0016567 all species →	Biological Process	protein ubiquitination	Interproscan
GO:0061630 all species →	Molecular Function	ubiquitin protein ligase 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
K06058	DTX; deltex	EC:2.3.2.27	Ubiquitin system	ko04121	deepkoala

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

Expression pattern (RNA-seq)

Transcript abundance of eanc_s032.g0076.t1 across 18 RNA-seq samples of Fimbriaphyllia ancora. 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.

18Samples

13TPM > 0

4Conditions

83.5Max TPM

31.6Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
ovaries	11	6	17.14	43.08
testes	5	5	63.36	83.46
Tentacles	1	1	37.64	37.64
Mouth and pharynx	1	1	25.06	25.06

Per sample · hover a bar for the full sample record

Show the sample table (18 samples)

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
DRR235381	ovaries	ovaries	oocytes with 'U'-like germinal vesicles\, >276 um in diameter and GVBD	not recorded	DRP006537	43.08
DRR235377	ovaries	ovaries	oocytes with accumulation of yolk and other components\, 126-200 um in diameter	not recorded	DRP006537	38.02
DRR235383	ovaries	ovaries	oocytes with 'U'-like germinal vesicles\, >276 um in diameter and GVBD	not recorded	DRP006537	31.52
DRR235378	ovaries	ovaries	oocytes with accumulation of yolk and other components\, 201-275 um in diameter	not recorded	DRP006537	26.15
DRR235382	ovaries	ovaries	oocytes with 'U'-like germinal vesicles\, >276 um in diameter and GVBD	not recorded	DRP006537	25.06
DRR235376	ovaries	ovaries	oocytes with accumulation of yolk and other components\, 126-200 um in diameter	not recorded	DRP006537	24.70
DRR235372	ovaries	ovaries	oocytes with cytoplasmic polarization\, <125 um in diameter	not recorded	DRP006537	0.00
DRR235374	ovaries	ovaries	oocytes with cytoplasmic polarization\, <125 um in diameter	not recorded	DRP006537	0.00
DRR235375	ovaries	ovaries	oocytes with accumulation of yolk and other components\, 126-200 um in diameter	not recorded	DRP006537	0.00
DRR235379	ovaries	ovaries	oocytes with accumulation of yolk and other components\, 201-275 um in diameter	not recorded	DRP006537	0.00
DRR235380	ovaries	ovaries	oocytes with accumulation of yolk and other components\, 201-275 um in diameter	not recorded	DRP006537	0.00
DRR235387	testes	testes	spermatogonia and primary spermatocytes	not recorded	DRP006537	83.46
DRR235386	testes	testes	spermatogonia	not recorded	DRP006537	74.97
DRR235389	testes	testes	spermatogonia and primary spermatocytes	not recorded	DRP006537	68.08
DRR235385	testes	testes	spermatogonia	not recorded	DRP006537	54.20
DRR235384	testes	testes	spermatogonia	not recorded	DRP006537	36.10
DRR397929	Tentacles	Tentacles	not recorded	not recorded	DRP011835	37.64
DRR397944	Mouth and pharynx	Mouth and pharynx	not recorded	not recorded	DRP011835	25.06

Source: CnidoSite RNA-seq expression matrices (FANCO_TPM, StringTie quantification over 18 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 Fimbriaphyllia ancora 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	20	eanc_s003.g0388.t1	0.892382787138026
Negatively correlated	7	eanc_s001.g0051.t1	-0.711495775656671

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 Fimbriaphyllia ancora, 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.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

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 →