Gene detail

Detailed information of aflo_s0062.g58.t1 in Acropora florida

Genomic Location: sc0000062_pilon:1569525...1573559
NR annotation: XP_029209608.1, E3 ubiquitin-protein ligase NRDP1-like [Acropora millepora]
Species Acropora florida · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

aflo_s0062.g58.t1

ATACGCATTCAACTGCGCAATTCACCAATCGAAAGTCACGCAAGCGTAACGTGACATTATTGTTTTGCAGTCCCAGAATGCAAATGTTGCTGAGTCGGCTTCTTTTGAACTGAGATAAATATGGCGACCATCGAAGATGTTTTCTCCGGAAATTTTCATTCCCGTCATCATCTATAACACAAAGCAGAAAAGTCATTGAGAGTGAATTTATATGAAAATTTACACTCGTAAACACGTAGGATCACTGCAGCTGTAGACATCAGTATCACGCATTCAAGGACTGCGAGAATGGGATATGACGTGTCAAGATTTATTAGTGCAGTAGACGAAGAACTCATTTGCACAATATGTGGTGGTGTCTTAGAGGATCCCCTCCAGGCTCCAGCCTGTGAGCATGCTTTCTGCGCAGCTTGTATTCACGAATGGTTGAATCACCAACAGACGTGTCCAGTAGATCGCCGAAATCTAACTCCTCATCAGCTGAAACAAGTGCCTAGGATTCTGAGAAACCTGTTGTCAAAGCTGACAATCCAGTGTGAAAATTCCATGTTTGGCTGCGCAGGTGTGGTGCGTCTGGACCAGTTACAGTCCCATTTATCGCAGTGTGAACACAACCCAAAAAGGCCAGTGAGTTGTGCGCAAGGATGTGGATTGGTGGTTCCATTTGATGAGATGCCACAACATAATTGTGTGCGTGAGTTAAACATCTTGATCCAAAATCAAAATTTCAAAATTGCTCAGTTGCAGGCCCAAATAGATGACCAGCGGCAACAGGCTAATGAACAAAAACGGGAGATCCAAGCTCTAAAGGACATGATCCGAGCTTTGAGCGTGGCCAACTTGCCACAAGTGCTGCCTCTGTTGCCAGGCAGCCTGCACCACCTTGAACACTATGATAATGAAATCCATCAATGGCTTAGCAGGTTACAGTCAGCGAGAGTGACCAGGTGGGGTGGTATGATATCAACACCTGATGCAGTGCTTCAAGCCATTATTCGTAGGTCTTTAGCCGACAGTGGTTGCCCTCCAACAATTTTAAATGAACTCATGGAAAATGCACATGAGCGCAAATGGCCTCCAGGGTTAAGTACCCTTGAAACACGACAACTGAATCGCCGTCGCTATGAACAGTATGTCTGCAAGAGAATTCCAGGCAAGCAAGCAGTGGTGATCATGGCTTGTGAGAATGAACATATGGGAGAATCCATGACACTAGACCCTGGGTTAGTAATGTTGTTTGCTCATGGAATTGAGTGAAATTATCAGTGCTGCAAATAGATTGAAGAAAGTAAATCTGCAATATTATTTTATTCATGTGCATTGTTATTTTAGCGTGATTTCATTTAAATGATAAAGTTGACAAGGAACCTCAGTACATCTCAAAGGGATTTCATTCAATGAATATAATTATACAGAAACTAAGAGACTCCAGACATAAAGATCAAGGCAAATAGATTGACTTCAAGCTCTAGATTTCTTCAGTTTTTATTTTCCTTTCCTTTCAAAAAAAACAAACATCAAACATCAGTGATGTCATTTAATGAATATAATACAGAAACTAAGAGACTTCAGACGTAAAGATCAATGCAAATAGTTTGACTTCAAGCTTCAGATTTCTTAAGTTCTTATTTTTCTTTCCTTCCAAAAAAAAAAAATCAAGGAAACTAGAATTTTTTGTTTTCATCACCAAGTATAGGAAAAATTTTTCTTGCCAATTGGCTTGATGCTCAGTCATACCTAGTGCCTTTGTACAAGAGAAAATTAGTCATTGGGTTCAAGGCAAGATTTTACATGAGAAGGGCCGCAGGCAGCCTAAGTTGTGATGAGTAACAAAAATTAATGCAGTTGAGGTTCTGGTTTTCACTAACTTAGTTACCACTTAGTAACTGTGGTGTCTCACATATAGTTCTTTTAGTTTCTCAATAATAGTAAACTATTGGAAGTGGCTATTCAAATGGCAGTGGCTGTATTACTTTCATCCACATGAAATTGGAGAGCCTGTGAGCCACATGAAATTGTGAGCCTGTGTGACTGACCTCCCCCATTCAAGCCAGTGTTTTTATCCAGACCACTGGACATCTTACTCTGTATGGAGAGCCACAGCCTAAATTATCGCAAAGTATGTCATTCCAATTTTGAGGCTAATGTTATTAATTGACTACGGGACCAAAACAAAGATTACTTTGTCATCTttgtaataataaaattaataataatct

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q5FWL3	E3 ubiquitin-protein ligase NRDP1 OS=Xenopus laevis OX=8355 GN=rnf41 PE=2 SV=1
Q9H4P4	E3 ubiquitin-protein ligase NRDP1 OS=Homo sapiens OX=9606 GN=RNF41 PE=1 SV=2
Q8BH75	E3 ubiquitin-protein ligase NRDP1 OS=Mus musculus OX=10090 GN=Rnf41 PE=1 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0001310 (this species only) · gene tree & orthology
Ubiquitin family	E3\|E3 activity RING\|RING · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 activity RING\|U-box · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF08941 all species →	USP8_interact	USP8 interacting	Domain	Interproscan
PF13923 all species →	zf-C3HC4_2	Zinc finger, C3HC4 type (RING finger)	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR015036 all species →	Domain	E3 ubiquitin-protein ligase NRDP1	Interproscan
IPR017907 all species →	Conserved_site	Zinc finger, RING-type, conserved site	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR037255 all species →	Homologous_superfamily	NRDP1, C-terminal	Interproscan
IPR003613 all species →	Domain	U-box domain	Interproscan
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR10131 all species →	TNF RECEPTOR ASSOCIATED FACTOR	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0016567 all species →	Biological Process	protein ubiquitination	Interproscan
GO:0061630 all species →	Molecular Function	ubiquitin protein ligase activity	Interproscan
GO:0004842 all species →	Molecular Function	ubiquitin-protein transferase 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
K11981	RNF41, NRDP1; E3 ubiquitin-protein ligase NRDP1	EC:2.3.2.27	Mitochondrial biogenesis	ko03029	deepkoala

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 Acropora florida 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 Acropora florida, 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 →