Gene detail

Detailed information of ENSDLIP00000017394.1 in Diadumene lineata

Genomic Location: chr2:5252333...5263422
NR annotation: XP_020902194.1, E3 ubiquitin-protein ligase CHFR [Exaiptasia diaphana]
Species Diadumene lineata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

ENSDLIT00000019071

ACTTGAACGCACattccaaaaacaaacaaaatggcggcagaCGATCCTTGGTGTCAACTGgtttatacccacgaatgccgTGATCCTGTACTAATTACTAAAGATATTTACACTTTTGGTAGAGTTCCAGATTGTGATGGTTGTTTTTCTGGTTGTAAGTTTATGTCAGGGAATCATTGTTATATTATGAGAGATCAAGAAGGGCATGTTTGGCTTCATGACACAAGCACCAATGGTACTTTAGTCAATGGCAAGAAAATTAAGTCACAGTCAGTAAAGCTCTGTGACAAAGATGAAATCAAGCTTGTCCATCGCAAGGATAGCAATATCATTGGATTTGTGTATCGTGACCTCAAGACTAAAAACCAGGAGGAAATTTCACTAGATAACACAGAGGAATATATAGAAGCTGATGATGATACTCAAAAGCTTCCAGACACACAAGAAGCTGAAGATGACACTGCAAGTGAAAGTatccaaagaaaaagaacccATTGTGAGACCTCGAGCATTGACGATGTAGAAAATCCTGAAGCCAAAAGACAGCATGTTGACGGTAGTGAAACCACACCACAGCTGACAAAGAACAACTCATTGATTGCTGAAAACCTACTGTGTAACATTTGCCAGgATATCTTCCATGATTGTGTGAGTTTGCAGCCTTGTATGCACAGCTATTGTGCATCATGTTACTCTCAGTGGATGCAAAGATCACGTGAATGTCCTAGTtgCCGACTAAAAGTGTCACGAATAAATAGGAATCATTTGGTAAATAATTTGGTGGAAGCATTTCTTAATGAAAATCCAGGTAGAAAGAGGTCACAAGACGAaattgatgaaatgaataagaAGAACAAAATTACAAGTGACAtgCTCAAACCAGccaaaaaaagaagaatatTAGATATATTTACTCATGACAGTAGTGGTTCCTCTGATGACAGTATGTCTGATACCAGTGGATCTGATAACAGCTTTAtagatgacgatgatgatgacgatagtgATGGACCAATGTTTAGTCCATTTGCAGGTGGTACAATACCGACAAGTGTAGCAGGATTGTTTGGATTCCTAACACACAGTCTCTCAAACACCAGAACTCCAGTTCAAATATGCAGACAGTGTCCATCAGattcatcatcttcatccaATACACCGCCCACAGTTACAGGATGTGATGGCACTAATAGAGTAGATTGTACCAACCTTCTCTCTGGAAATAGTAATACTACAAGTAGCAACCCTCCCTCAGGATCAAATAGTAATACTACAAGTATCAACCCTCCCTCAGGATCAAATAGTAATACTACAAGTATCAACCCTCCCTCAGGATCAAATAGTAATACTACAAGTATCAACCCTCCCTCAGGATCAAATAGAAATGCTACAAGTACCAACCCTCCCTCAGGATCAAATAGTAATACTACAAGTATCAACCCTCCCTCAGGATCAAATAGTAATACTACAAGTATCAACCCTCCCTTAGGAACGAATAGTAATGCTACAACAGATGGTGCCACCCCTCCCCCATATGTTTGTCCACCAAATGGTTCACATATCCTATGTCTATGCTGTATGAGATATATGCCAGACAGACGGACACATTGCCATGATGCTGTCCCTAACCAGACTTGTAAGTATTAGTAATTATGATTAAAAGAGTGCAACTTTAGTAATTCTAAATTATAGTGCAGTCTAACTAtcttgtttgaaaaaattgttttcactAGAAATCACTTGAAAATGCTTTCTATAACTAAAGAAGGTGAAAAGAAGGCCAAATTGAAGAATTTTAGGTTCACTGAGTTGAaactttttgattttttaaaatttggtgattttgagcaaattctggatttttgcccctacccgggtaatcaaaaatggccaaattttttgataaaaatagcACTGAAATGCCATTAAAATGGTTCAGCTAATTCATAGATTTTTTATGGCTTTTTGGTTTATGgtgtatatttttatcattccTAGGTTGTGTTTGTAACCGTGCATTCTGTCATGTTTACTGGGGTTGCCATGGTTGTCGTGATGGATGTCTCAAAGAGTTTAAAG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q5RF77	E3 ubiquitin-protein ligase CHFR OS=Pongo abelii OX=9601 GN=CHFR PE=2 SV=1
Q6P256	E3 ubiquitin-protein ligase CHFR OS=Xenopus tropicalis OX=8364 GN=chfr PE=2 SV=1
Q5FWP4	E3 ubiquitin-protein ligase CHFR OS=Xenopus laevis OX=8355 GN=chfr PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004876 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13923 all species →	zf-C3HC4_2	Zinc finger, C3HC4 type (RING finger)	Domain	Interproscan
PF00498 all species →	FHA	FHA domain	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR052256 all species →	Family	E3 ubiquitin-protein ligase CHFR	Interproscan
IPR000253 all species →	Domain	Forkhead-associated (FHA) domain	Interproscan
IPR008984 all species →	Homologous_superfamily	SMAD/FHA domain superfamily	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR017907 all species →	Conserved_site	Zinc finger, RING-type, conserved site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR16079 all species →	UBIQUITIN LIGASE PROTEIN CHFR	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0004842 all species →	Molecular Function	ubiquitin-protein transferase activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0006511 all species →	Biological Process	ubiquitin-dependent protein catabolic process	Interproscan
GO:0007093 all species →	Biological Process	mitotic cell cycle checkpoint signaling	Interproscan
GO:0016567 all species →	Biological Process	protein ubiquitination	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	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

No KEGG orthology assignment for ENSDLIP00000017394.1.

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

Co-expression network

Genes whose expression across the transcriptome samples of Diadumene lineata 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.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Diadumene lineata, 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.	no expression matrix	–
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 →