Gene detail

Detailed information of ENSOFVP00000007854.1 in Cyphastrea salae

Genomic Location: chr12:463947...489384
NR annotation: RMX44003.1, hypothetical protein pdam_00012973 [Pocillopora damicornis]
Species Cyphastrea salae · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

ENSOFVT00000008555

ATGCCAGTGGAAGGAACAAACCCTCTCATAAACGCCCGAGATAGGTTATTTCGCGCCctgtttttcaaaatggcgctCATGTATGCTCGTTCTTTTCCTCCGCCTGTTCGACTACTTTTGGAGATGGGAGTGCTCATGAAgGCAGTCACTTGTTTTGTGATTCTTGGCTACATACATAATGCTTTTTCAAGAACTCCTATAAACTGTTTGGATAATGTTAAAGACAAGTGGCCAAGAGATGGAGTACTGAGAGTTGTCATATCAAGGAGTACTCCAGCTGTTAGCAGATTATCAGAAAATGATACAACAAGAACTAACTTTACTAATTCCAACATTACTGAAAGTACCCATGTTAATATTAGTCACTTAGAAGTGGATGTTAAGTCAAATGATAATTCATCTTCTGTGGGGAATATGTACGAGCATTCATCGGATAGTGCACCACAAAAGAATCATCTTCCTGTAAGAGATACAGTGGTACCAAGTGCTTTTGAACTGTTAGCGCCAATCAAAGTTGAAGgtgaaaagaaagaagaatatGCTGTAGAATATGCCTTGGAGTATGGATTTCTAAGGTTGTCTTCAGAATCCAGGAAGAAGCTTGGTATTCCTGTCTTGCTTGTTGAACTTGACCCAGCTGTGGAAGAATGTTTTGGGGACAgtttgagtcgcttcttattgGATGAATTCCTTGGTTATGATGATGTATTAATGTCAAGTGTCAAGAGACTGGCAGAGTATGAGGACAACAAAGGTTATTTACGTAATGTTGTGACTGGAGACCACTTTCGGTTTGTCAGCATGTGGATGGCGCGCACATCATACTTGGTTGCTCTTGTCCTCATGTTCATATTTACAATTTCGATTTCAATGCTGTTGAGGTATTGTCATCATCAAATCTTTGTCTTCATAGGAATGGAAGCTATTATGTCTGAATTTTTTAATGACACCACAACAAGTTTTTACATTATCCTTATCGTCTGGACAGCAGATCAGTATGATGCTATTTGCTGTCATACACAACAGAGTAAAAAGTTTTGGCTCAGATTCTTCTACTTGTATCATTTTGCATTTTATGCATACCATTACCGTTTCAATGGGCAATACAGTGGACTTGCACTTGTTACTTCATGGCTTTTCATTcagCATTCCATGTTATTTTTCTTCCATCACTACGAGTTACCAGTGATCTTGAGTCACCAGGCTGATCCTGAAGAAGACCTGTTAGCAGATCCTATTGCTGCACTTACTGATGAAGTTAATGTGCCGGCAGCAGATGAACTTCCCAACCACCCTCCCCCTGGTAACTTCCCGCTACCCAGTGTTCCATTTAATGATGGTACGTCATCAGTATCTAGATATATAGAGAGTTACAGAAGAGGTCAAATTGATTCTTCCTTAACAAGAAGACGGTGGGCACAATCTAGTGATGCTGCAAGTGATGATTTGATGGAAGGACATAGTTTTCATCTTCCTGATGACATCAATACAGCAGATGAATTTGAGGGTTTTTCAAGGTACCATACATGGACACAGCAACACCAGGCACAAGACCTGACCCCAGCACAGAGTAGAGAAACTGGTGCCAGGACAGTGTTAGAGTGTCGTGTCTGTGAAGATGTGTTTACACTTCAAGGTGACAAAGTCCCAAGGTTGTTATTGTGTGGACACACAGTTTGTCACGACTGTCTGACACGCCTTCCTGTGCAAGGACGCCAACTGTACTGTCCATTTGATAGACAGTCTACAGAACTAGGTGACTCAGGAGTTTGGGGTCTTAAGAAGAACTTTGCATTGTTGGAATTACTTGAGAGACTTCAGGTGTTACCCGAACCATTGACAAAATGTGAGAATGAGAGTGGGGATGACACTGTACGatgtgatgaaaatgatgaacaTGTAGCCAATATTTATTGTACTGTCTGTAACACTAACTTGTGTAGTGATTGTGCAGAGAGCACACATTCAACCAAAACCCTTGAGAAACACAGAAGAATTCCTGTTTCTGAGAGACCAAAGGAGAAACCCAAGTGTGCACAACATTCAACGCATGTGATAGAGTTTACATGTTTAGAAGAAGAATGTCAAGATAATTCATTGATGTGCTTTGTGTGTCGTGATTATGGTAAACATCAAGGACATAAACACACTCTGCTGGAAAAGGAAGCAGAGAACATGCGCGAGTCAGTGACTAATGTTATACAACATGTCAGGACTTTCACTGATGAAGTTGATGGATTAGCTGGCAGGCTGTCCTCTGTTATTGAGGCAATTGAAGGTGGTATTTTAATGCAAGAAGAAGGGCAGGGTGTTCTGACTGCACAACACATTTCTGGTTCTGCCGAAGATGCTAGAAATAAAGTGCGAGCATATTTTGATGATCTGCGAGAGACAGTCAATAGGCAAGAAGAAGCTGGACTTGCTGTTGTCAACAATTATGTGCGAGAGAAACTACTGTCACTCAGACAACAGCAGGAAGACATGGCTGTTCTGATGTCACAAGTTACATCAGTGTGCATGGAATGTGAGAGGGCACTGAAGAGGAGTGATGCTGAGGTGATAGAAGCTAGAAACAGCATTCGCAGTCTCTTGGAAACAGTACAGGAGCAACAAGAACAGTTTACCAACATTGCCAGCCTGTGTGATACAGATGCTGCTATCCCTGTGGCCTTCACAAAAGACAACAGAGTACATATAGGGCCTAAAATGGAGATGAGAGTTGTTGCCTTGGGACTTGATGGGGCTGGAAAAACttcaattttatttaaaatgaaACAGGATGAGTTTGTCTCGCCTATTACAACCATTgGTTTTAATGTAGAGACTGTTGAACATCGCAGCCTTAAGTTTACTCTTTGGGATGTTGGAGGCCTGCAGAAACTCCGTCCTCTTTGGAGACATTATTATCTCAACACACAAGCTGTGATCTTTGTGATTGACAGCAACAATATTGAGCGCATCACAGAGGCTCATGAAGAGCTTGCAAAGTTAATGGCAGAGAAAAGACTGAAAGATGCTTTGTTGCTGATATATGCCAACAAACAGGACTTGCCAAGTGCTCTTAGTGTTGATGCCCTCACTGAACAGCTTGCCCTTCATAAGCTCTGCTGTGGCAGAAGCTGGAGTATATTTGCCTGCGATGCACACTCTGGTAAAGGCTTACATGAAGGTCTAGATTGGCTTGCAAGACAGCTCATGTCTGAATTTGCTCAGTGA

Transcript

ENSOFVT00000008555

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q8BGX0	E3 ubiquitin-protein ligase TRIM23 OS=Mus musculus OX=10090 GN=Trim23 PE=2 SV=1
P36406	E3 ubiquitin-protein ligase TRIM23 OS=Homo sapiens OX=9606 GN=TRIM23 PE=1 SV=1
P36407	E3 ubiquitin-protein ligase TRIM23 OS=Rattus norvegicus OX=10116 GN=Trim23 PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006461 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF13445 all species →	zf-RING_UBOX	RING-type zinc-finger	Domain	Interproscan
PF00025 all species →	Arf	ADP-ribosylation factor family	Domain	Interproscan
PF09746 all species →	Membralin	Tumour-associated protein	Family	Interproscan
PF00643 all species →	zf-B_box	B-box zinc finger	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR027370 all species →	Domain	Zinc finger, RING-type, eukaryotic	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR000315 all species →	Domain	B-box-type zinc finger	Interproscan
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR006689 all species →	Family	Small GTPase superfamily, ARF/SAR type	Interproscan
IPR005225 all species →	Domain	Small GTP-binding protein domain	Interproscan
IPR019144 all species →	Family	Membralin	Interproscan
IPR013087 all species →	Domain	Zinc finger C2H2-type	Interproscan
IPR003649 all species →	Domain	B-box, C-terminal	Interproscan
IPR027417 all species →	Homologous_superfamily	P-loop containing nucleoside triphosphate hydrolase	Interproscan
IPR017907 all species →	Conserved_site	Zinc finger, RING-type, conserved site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR21650 all species →	MEMBRALIN/KINETOCHORE PROTEIN NUF2	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0003924 all species →	Molecular Function	GTPase activity	Interproscan
GO:0005525 all species →	Molecular Function	GTP binding	Interproscan
GO:0005783 all species →	Cellular Component	endoplasmic reticulum	Interproscan
GO:0034976 all species →	Biological Process	response to endoplasmic reticulum stress	Interproscan
GO:1904294 all species →	Biological Process	positive regulation of 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

No KEGG orthology assignment for ENSOFVP00000007854.1.

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 Cyphastrea salae 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 Cyphastrea salae, 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 →