Gene detail

Detailed information of ENSAVKP00000043587.1 in Catalaphyllia jardinei

Genomic Location: chr8:5215131...5224906
NR annotation: XP_020629491.1, ubiquitin fusion degradation protein 1 homolog [Orbicella faveolata]
Species Catalaphyllia jardinei · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

ENSAVKT00000047183

CAGCAATTCAAACTATTCGTACAGAAACTCAAAAGTcgataattttaattttttgtcaaTTCCACGCGTTTGTCTTTAAATATAATTACTTGTCAAGATGTTTGGTATGTTTGGTGCTATGCCAAGGACATTCAATACACAGTTTCGCTGCTATTCAGTTGTCATGTTCCCAGGAAACGAGCGAGAAGACGTGGAACGTGGTGGTAAAATTATAATGCCTCCTTCAGCCTTGGATCAATTAACAAGACTGCACATTGTGTATCCCATGTTGTTTAAACTCTCCAATTCAAGGTCAGGACGGAACACTCACTGTGGAGTACTAGAGTTTGTAGCTGATGAGGGCAAGATTTACCTGCCATACTGGATGATGCGCAATCTTCTGCTTGAGGAAGGAGGTCTGCTGCAAGTGGAAAGTGCTTCTTTACCAGTTGCATCTTATGCCAAGTTTCAACCACAATCTGTTGACTTTCTAGATATTACAAATCCAAAAGCGGTCCTAGAGAATGCACTTAGGTCATTTGCCTGTTTGACTAAGGGTGATATAATAGCAATCAAGTACAATGAAAGGaTCTATGAACTGTTAGTGTTGGAGACAAAACCTGGAAATGCAGTGTCCATTATTGAGTGTGATATGCAgGTCGAGTTTGCTCCTCCTGTTGGGTATGTTGAGCCAGAAAGACaagagagaagagaagagaagaaggAAGAAGAGCACACTGATGAAACTCATGTGGATCACGGTTTTCAGGCGTTCACTGGCTCAGGATTTCGCTTGGATGGCAAGAAAAAGAAGTCCAATGTTCCCTCCAACCCAGTCCCTATGGGACCTCCTGTTATCAAACGtggAATTCCTAATTATGACTTTGAGAAAGGAAAGATCACTTTCAAAAGGaacttaaacaaaacaaacaactcaCAGTTGAACAACAAATCAGAATCGACCAAGCCGGAATTTGAAGCTTTTAAAGGATCGGGAAAAACTCTACGacagaaaaggaaaaactaGCGACAAACAATATTTACTTAAAAACTACAGAGAAATATGGCGAAGAGCAATATTTATGGAGCGACATATATCCCGTATTAAGTACTGTGATATTTTCAAGAGAGAAAGATGGTCAGGTTACTTGGAAGCTAGTAGTCTCTGTCAAATTCGACTTTCAAGTGATAACCTTGGTCGCATGACACGACAGCGATGAGGGACAGGAGAATCGCATAGTTTTTTCCTTGTATACAGACTTCTCTAGTTGGGGAATCGCGCCATGGACGCAAATCTTAAGCTTTCCAATAAAAACCCGAATTCAATTTTTACGTTGTCGTTTAAAAACGAAAGAGAACACAAAGATTCCAGTTTGTATTATAATTAAATCAAAACGTATACAAGTCGTTTTCACGTTCTACTAGATGCAAGGTATTTTCATATTTAATTCATTTTTGATCCAAATAAAAATAACCACGACTTCAACATAGCAGATGAGACCAGATCGCAAGGGATTACCTCCGAGGTGACAAGTGTATGATCAGCACAATCAGCTATATAGGCATACATACATTCCGTGTAGAGGTCTTGCACGCATCGTATCCCAGTATGGTTCTCAGCGTATTGAGACGTATTACGAGAAATAGATCCTTGCTTCGAGTAATACAAATAAGCGTTCTCTACCTGGGCATTTCATGGGGTTGCAGTTAGCCTCAAAAAGTTCCCGCCCCTCTCCCATTACGCGATTGTTATTTGTGCTTACCAAATGGTGAGGGAGGCTTTTCAAAAATCCTTTCGCTTGCCCCCGCCCCTCTCCCACACCGAATTTGAGATCCTAGTACACAgctctaattaagaaatagaaaacatgttccgtgtttgtatcgagttatacaaacacgagtggaagtttgggagaacgagaaatgctgtaggaacacgagccgcaggcgagtgtttccacagctttttcgagttctcccaaactttcacgagtgtttgtataactcgatataaacacggagt

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q92890	Ubiquitin recognition factor in ER-associated degradation protein 1 OS=Homo sapiens OX=9606 GN=UFD1 PE=1 SV=3
Q9ES53	Ubiquitin recognition factor in ER-associated degradation protein 1 OS=Rattus norvegicus OX=10116 GN=Ufd1 PE=1 SV=1
P70362	Ubiquitin recognition factor in ER-associated degradation protein 1 OS=Mus musculus OX=10090 GN=Ufd1 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006188 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF03152 all species →	UFD1	Ubiquitin fusion degradation protein UFD1	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR042299 all species →	Homologous_superfamily	Ufd1-like, Nn domain	Interproscan
IPR004854 all species →	Family	Ubiquitin fusion degradation protein Ufd1-like	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR12555 all species →	UBIQUITIN FUSION DEGRADATON PROTEIN 1	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0006511 all species →	Biological Process	ubiquitin-dependent protein catabolic process	Interproscan
GO:0030433 all species →	Biological Process	obsolete ubiquitin-dependent ERAD pathway	Interproscan
GO:0031593 all species →	Molecular Function	polyubiquitin modification-dependent protein binding	Interproscan
GO:0034098 all species →	Cellular Component	VCP-NPL4-UFD1 AAA ATPase complex	Interproscan
GO:0071712 all species →	Biological Process	obsolete ER-associated misfolded protein catabolic process	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
K14016	UFD1; ubiquitin fusion degradation protein 1	-	Ribosome biogenesis	ko03009	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 Catalaphyllia jardinei 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 Catalaphyllia jardinei, 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 →