Gene detail

Detailed information of gene02113.t1 in Actinoscyphia liui

Genomic Location: chr1:33077247...33085832
NR annotation: XP_020901576.1, E3 ubiquitin-protein ligase AMFR [Exaiptasia diaphana]
Species Actinoscyphia liui · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

gene02113.t1

ATGACGTCATCGTTCACGATCGATTGCTCCATCCATGTTGATTTCAACGTCGAGCAAGCTCAACATGAAAAACAAGATTTCTACTCCTTCGTGACTAAAACTTCAACGATGACTCTAGTCTTTCTAGAACAGCTTCCTCTGCCGTCACTTAAAACGTACGTTACAGTCAGCTTTCTATTGTTTTTCTCCTCTCTTTTGTACGGTTTGAACAACGCTACAATATGGACGAAGGACCCGAAGCCCACGGACCTTCCAGACTCAAACGAATCTACGGAACCAGTAATGTCTTTGTACGAATTTATGACTGCGGATAATTTCTGCTTCTGGTCGAACTTGAACATGGCATACTGCTGCTTGTTTATTTTTGGGAAAGTTATACAGAGAGTTGTATTTGGGGACTTGAGAGAAGCAGAACTCCAGCAAATCCAAGACAAATTCTGGAACTTTGTATTCTACAAATTTATTTTTATTTTTGGTGTCCTCAATGTACAAAAAGTGGATGAGGTGATGTGGTGGACAGCGTGGTTTACATTGTTGGGCTTCTTCCATCTCTTTGCTCAGCTTTGTAAAAACAGATTTGAATATCTCTCCTTCTCTCCAACAACTACTGTCGCTACCCACAGCAAGATCATTGGTTTGCTTGTGGGCTTGATGATGTGTTGTAATGGGTTGTTCTTCCTGACTTTGTTCGTCGGCTGGCCTGATGGAGTACATACATTTACATTCATGCTGGCTGAGTGCATATTGTTACTCATCAAAATTGTGCATGTTGGGATAAGGTATGGAATTCATCTTTGGGACGTTGGTCATGTTGGTACCTGGGAAGGACGTACTACATGGTGTTATTACACTGACCTTCTTCTTGACCTGGGGATGTATGCTGTAGATCTTATCCACCATCTTCATATGCTGTTGTGGTCCAACATATTCCTGAGTATGGCCAGCCTTGTACTTTGCATGCAGCTCCGTCACCTTTTCTATGAAATTAAAAAGAGACTTGCAAGACACAGAAACTTTGTGAGGATTCTTCAATGTATGGAGAAAAAGTTCCCAGTGGCAACAATTGAAGAGCTGTCAGCCAACAATGACGACTGTGCCATCTGCTGGGATGTGATGTTAGTGGCACGGAAGCTTCCCTGTGGTCATCTCTTTCATGGCTCATGCCTGCGTTCATGGTTAGAGAACGACACATCTTGTCCAACATGCCGTCAGTCCTTAGCAGATGATCTGCAACCAGAATCTGCAGGACAAGATGAAGAACAACAACCAAGAGGAATGGCTGCATTCATGATGGGACGCGCAATCCGAAGGAACCACTTTTTCCACTTTGATGGCAGCCAAATTGCCAGTTGGTTTCCAAGCTTCTCTGTTGAAGTAGTGCACACCCATGCAAATGAACTGAATGACCAACAGCTTCCTGAAAGCAGACTGGAATTAATGGGACATCAAGTACAAGACTTATTTCCTCGTGTTCCTTTCAACATCATCATGGATGACTTAAGACAAACACACTCTGTTGAACTTACTACAGATAACTTTCTAGAAGGAAGAATTGCCGTCCCATCTGTTTGGACACCTCCTGAACAACAAGAACAAGCAGAACCAGAGCTCCTACAAAGAGCTCCTTCACCAGACACAAACAGACGACCAAGTGAACAAGATGACACAACAGAACAAACATATAATAATGAAGAAGAAAGTGCATCTAGTGAAGGCATTGAATCTATTGACCAAGAAAATCCACCACAATCTTCTACAATGTTGTCATCCATGGATGAAGAAAGGCCATCAATAAATTTAGGGCAGCATAATGCTGACAGTTCACAAACTTTACACAACTCACAAGAATCAACAGACTTCCATGTCTCTCCTGAGGAAAGGGAAATTTCACTTCGTAAAAGAAAGGAAGCATTTCTCCAGAATGCAAGAAGGCGATTCCTTGGGAAAGAGACCTCATCATCATCACAGTCCTCAGGAGCTGATTGAACATCAATTTTGCTTGAACAACAAGTTGTGTTTCTGAGGAAATGGAGGTTATTCCAAGTGTGGGATGCAGGGCAGATAAATAATACAGGTTCAGCTGCAATTGATTAGACTCTGTCGAGAGATCTTATAAAGCCTGAAGCATAAATATTCAGTCCAAAATATTCTTGTTTAAAGTGCTTAAGCGACTTATAATACATTATATACCAGGCACACATCTCATAAAGCTAAGCTTGTGTATGATGTACAAGTAGTACATGTGAAGTTATACATAAAATAGTCAACTCAATTTTACTATCAAATAGCATTGCATTGTTAGGGGTTGGCGAATGTTAAATCCAAGACTTATTCAGTCTGTGAGACACAGGTTATAAAAAACGAACCTGAGACTCTTTCTTAATTATATTTTCAATTTGGAGACCAAAACTACCACTTAACTGTTTCGTACAAGTTTCCAGACTGCAAGATCTTGAATTTCACTAAAAAACGAGATTCCAAAATGCACTGTACAGACGAGATTTTGAGATCCTTTAGGTAAATTTTGCGTGACTCTCTGATTTTCAGAGACCATTCACCACCCCTATTAGAGCAGATTTCGTAGGAGTGGGAACCCTACCGTGACTCTTAAATGGCTTCCGCTCGTGATTGGACGGTTTGTGATTTTGTGTATTGTGATTGGTTCAGAGCGGAAGCCATTTGAGTGTCACGGTACGGTAAGGTTCCCACTCGGACGAAATCTGCTCTATTTAAAGCTCACAAGGTCTTGTAGAATACATGTGCTTTGTGAAATGGCCAAAAATCAAGTTGAGAATTAAAATAATAACATTACCTTTTGTATGAGGTAAAAGTACAGTGGAATTTTAGAGAAAAAACTTCCAACTCGTACAAAAAACTATGTGTCACATACAGTGCTACCCAAATTGTACCCAAATGTACAATCATATGATTCAATTAAGTAAATTACCTTGAGGAATTAAAGTACATCTGGAGAATCCTTAAATCAATCTTTCAATGATGTTGTATGGCAGCATTTTCCTACCAGG

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
F1QB30	E3 ubiquitin-protein ligase AMFR OS=Danio rerio OX=7955 GN=amfra PE=1 SV=1
Q9R049	E3 ubiquitin-protein ligase AMFR OS=Mus musculus OX=10090 GN=Amfr PE=1 SV=2
Q9UKV5	E3 ubiquitin-protein ligase AMFR OS=Homo sapiens OX=9606 GN=AMFR PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006217 (this species only) · gene tree & orthology
Ubiquitin family	UBD\|Alpha-Helix\|CUE · all ubiquitin genes in this species
Ubiquitin family	E3\|E3 activity RING\|RING · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13639 all species →	zf-RING_2	Ring finger domain	Domain	Interproscan
PF02845 all species →	CUE	CUE domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR003892 all species →	Domain	Ubiquitin system component CUE	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR15067 all species →	E3 UBIQUITIN-PROTEIN LIGASE RNF8	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000151 all species →	Cellular Component	ubiquitin ligase complex	Interproscan
GO:0005783 all species →	Cellular Component	endoplasmic reticulum	Interproscan
GO:0005829 all species →	Cellular Component	cytosol	Interproscan
GO:0006511 all species →	Biological Process	ubiquitin-dependent protein catabolic process	Interproscan
GO:0016567 all species →	Biological Process	protein ubiquitination	Interproscan
GO:0030968 all species →	Biological Process	endoplasmic reticulum unfolded protein response	Interproscan
GO:0061630 all species →	Molecular Function	ubiquitin protein ligase activity	Interproscan
GO:0070936 all species →	Biological Process	protein K48-linked ubiquitination	Interproscan
GO:0043130 all species →	Molecular Function	ubiquitin 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

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K10636	AMFR, GP78; E3 ubiquitin-protein ligase AMFR	EC:2.3.2.36	Ubiquitin system	ko04121	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 Actinoscyphia liui 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 Actinoscyphia liui, 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 →