Gene detail

Detailed information of evm.model.HiC_scaffold_34.37 in Chrysaora quinquecirrha

Genomic Location: HiC_scaffold_34:414762...449804
NR annotation: XP_047138518.1, ubiquitin conjugation factor E4 A [Hydra vulgaris]
Species Chrysaora quinquecirrha · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

evm.model.HiC_scaffold_34.37

ATGGCAATAGAAAAAGATAACAGCTTACACCAAATGGAAGAAGAATTATCCAAGAATCCATTTGTAGCACTTTTTCCAAGCATTGAACATGCTAAAGATTACATTCAATCAACCAAAACAGATTCTGATTCTCCAAAAGATCATGGTTCTACTAAAAACACTAAACATGTTGAAAAAGCACATGAAAAGCCCAATACAGTTAAAGAAAGCAGCCTGGAAGAGGTGAAGAAATCTCCAGATGGGATATTGGTCAATGATTTTTACAAAGAATACAAAAAGCAGAGTGGCTGGAGAGGACATGGTTTACCTCTACCTGACTGTGTTTTGCTAAAAGGATTGCataaagaattaaaagaaaagaaatccaTGTTGATGCTAGATGCTGATAATCTGAACCAGGCTATAATGGAGAGACTTTCATTGACCCAAAAACATACAGTTGTATCATATGGACAGAAGACTTTGCTAGCAGATGTTGTATCATCAGCCGAAGAAACACATCTTATCAAATATCTTGCTCATTCACTGAGAAGACTACATGAACAAGAAAGTATATTCAACAGAAAACTCAGGGATTTATATCTTGTAGAGGAATTAGAATCTCTGAAGTCGACATGTGAATCGTTAATTACATCATATGCAGGATCCGTACTTTTGTCTCCCGATGTTTTTGCTACTACAGATCCACAGAAGCAACTTTTTGATTTGCTGATGAAGCCGGAAGAGTGCAAGTATTTGCCTGAATTTTTGGATGCGATTGTAAGACAATATAAAGATCAAAATGATTTGTCAGACATATTCCTGCCATTATTGGATATTTTAATGGGTGAAATAAAATCAACTACTTTGATGAGCCCAAGAATATTTATCATATTGGAGATCGTTTTGTATTTCTCAAAGAATTCAAGCCTCGCAATGATTCTCGTCTCAAGTGAACATTGGCTTCGTCCTGCACAAGCATCAGCTTCATCTACTGCTGGTTTGGACTTTGAAAGATTAACTCTTCTTGGTCCTTTGCTTGGAACAACTACATTGTCTTATGATAGAAACAAGCCTTCGCCCGACAATGGTGACTATGGCCAAGTCGTTAGCGTGTCTGACCCGAAATCTATGGTCAGCGGTCCCCTGGCGGTGTccaatagcacttgcttggcatTGCCGCTAATGGGTTCTGAAAGCCagGAATTTTTCATTGAACCTTCTAAACAGTCGCAAATGGAAATGGAAGTAATCATGAACAACTGTAGGAGACAACTCGATACAGTATCCTCAAAGATTTACATGATATTCAGAAATATTTTGGAAAACAAAGAATTACAACAAGACGTATTATATTGGATTGGTGCATGTCTGTATCATAACAGAAAAAGATCTCAGCTTTCTTTTGAGACTGGCTTCGCAAGCATGTTGACGCAGGCAAGAGATGGTTTCTTCCTTAATCTTGGCAATGTCCTGCTGAAACTTTGTGAGCCATTTCTTGATTTATCAGACAAATCGAAGAAATGTTTAAGAATAAACTCACTTTATTGTTTGGTTGATGCTGACATCAGTGACATAGCAAGACCCAATGCACCTGTACATTTGGTACAAAATCAAGAGGAACCAAAAATCGCAAACAGAACAGATGATATGAAAATGAAAGAGGTGCAAGGTGTAAAATTCAAATTTGTCACTGAATGTTTCTTCTTAACTCACAAATGTCTGAAAATTGGTTTTCTCAAAGCATCAAGCAGCTATCACAACTTAATGAAGAAATTACAAAAGCTGAGTGAAATTTATCAAGATGCCAGGGCTGGTGGATTTCATTCTGAAGATATGGAAAGAATAAAAATAGAATTTGAACAAAACATCCAGAGGCAGCTTTCTTTCAAGGCCCATTTGCTGAACCCGAGCCTGGCTGAGTTGATAATAAAATTCTGCTCTGTTACGTGTTATTGGTTAATACAGCAGTTGTTGGCTGATGAGGACTTTAATGATGGTCAACATCGAGAATTGGTTATTGAAAAGTTAGAAGACAAGGTGTATCCTGCCATGACAGTGATACCAGAATATATCGTTGAAAATGTTGCTGATTGTCTCATATTTTTTGAACATTTTGGAGATGACAACATAGAAAAATCTACTCATCTTTTGGAGAATGTCAtgattttcttttcattattcTTGGGGTCTTCAAAGTGTTTAAACAATCCACATTTGCGTGCAAAACTTGCTGAAGCACTTGCTGGTTTGTTGCCAAGGAAAAAGGATGAATTTGGTATTGCATCTACTAGCCATGGATACAAGATTTTTGAAGACTGTCCTATAATTGCAAAAATTCTTCCCGAAGCACTTCTGAAATTATTTGTCGATATTGAATATACTGGTCATTCGATGGAATTCGAACAAAAATTTGGTTATCGGCATCATATGTATGCTGTTTTGGAATATATCTGGGAGATACCAAGTTACAATAAAGTGTTCTGGGAACTGTTTGAAGAAGGCCGTAGATATTACTGTGCAAAATCTGAATTCTCAGCATTCCCAAGATTCATAAATCTTCTATTGAATGACAGTACATTTCTACTTGATGAAGCTATGCAGCATTTGTGCAAAATCCGTGaattagaaaaggaaaagaatgaAGGGCTTTGGGCGAAGTTGCCTCCACAAGCTCGTCAAGAGAAAGAAAGTAGTCTCTTTCAACTTGGAGAAATGACAAGGGGATATAACATTATGGCAAATGAGACCGTCCACGTTCTATGTTACATTACCAAAGATATCACAAGACCTTTTGCAAGTCCCTGTATGGTTGAACAGACGGCATCATTCTTGAATTATTTCCTCTTGCACCTTGTTGGACCAAAAAGCAAAGAGCTGAAGGTGAAAGATTTTGATAAGTTTCACTTCAAACCTAAAGAGCTTGTGAAGAACATTGCTCAAATTTTGGTGAATcttggaaatgaaaatgatttttgtCGTGCTATTGTCTCAGATGGTAGATCATATTCGCCAGAATTGTTTGTTCGCGCTCACGAGGTTTTGATCTACTTTTCTACTCGATACGAGGCTGTTGCTACTTGGTCCCATACGATCGTGTATTCGTCCATGCCCCATACGTCCTTGTATATTCATCTCATGTACCTCCGTGTCCCTTACGTCCGTGTATTTTTGTCTCATACTTCCATGTCCTTTACATCTGTGTATCTTGGAAATCATTGGATCCCCCCAGAGGAATTCATTGATCCTATATTGGGTACACTGATGTTTGAACCAGTAAGACTACCAAGCTCTAAGAAGATTCTTGATAAATCTACAATTGGAAGGCATCTTCTGAGCGATCCCAAAGACCCATTTAATCGAAGTCCATTAACACTTGATATGGTAGAACCAGTAGCAGATCTGAAGATAAGAATAGAAAAGTGGATGGACGAGCATGGTATGAAACGTCCTCAAAAATATACTTCAGAAGACTGTACTGGATAG

Transcript

evm.model.HiC_scaffold_34.37

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q6P7A2	Ubiquitin conjugation factor E4 A OS=Rattus norvegicus OX=10116 GN=Ube4a PE=2 SV=1
Q5R9G3	Ubiquitin conjugation factor E4 A OS=Pongo abelii OX=9601 GN=UBE4A PE=2 SV=2
A5PKG6	Ubiquitin conjugation factor E4 A OS=Bos taurus OX=9913 GN=UBE4A PE=2 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0003384 (this species only) · gene tree & orthology
Ubiquitin family	E3\|E3 activity RING\|U-box · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF10408 all species →	Ufd2P_core	Ubiquitin elongating factor core	Family	Interproscan
PF04564 all species →	U-box	U-box domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR019474 all species →	Domain	Ubiquitin conjugation factor E4, core	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR003613 all species →	Domain	U-box domain	Interproscan
IPR045132 all species →	Family	Ubiquitin conjugation factor E4	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13931 all species →	UBIQUITINATION FACTOR E4	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000151 all species →	Cellular Component	ubiquitin ligase complex	Interproscan
GO:0006511 all species →	Biological Process	ubiquitin-dependent protein catabolic process	Interproscan
GO:0016567 all species →	Biological Process	protein ubiquitination	Interproscan
GO:0034450 all species →	Molecular Function	ubiquitin-ubiquitin ligase activity	Interproscan
GO:0004842 all species →	Molecular Function	ubiquitin-protein transferase activity	Interproscan
GO:0000209 all species →	Biological Process	protein polyubiquitination	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0030433 all species →	Biological Process	obsolete ubiquitin-dependent ERAD pathway	Interproscan
GO:0036503 all species →	Biological Process	ERAD pathway	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
K10596	UBE4A; ubiquitin conjugation factor E4 A	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.

Co-expression network

Genes whose expression across the transcriptome samples of Chrysaora quinquecirrha 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 Chrysaora quinquecirrha, 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 →