Gene detail

Detailed information of ENSVBPP00000018007.1 in Meandrina meandrites

Genomic Location: chr1:24328136...24352636
NR annotation: KAJ7355990.1, hypothetical protein OS493_027384 [Desmophyllum pertusum]
Species Meandrina meandrites · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

ENSVBPT00000018780

TCTCGGTGGCACCGACGGCTTATTAATCGCTATGGAGGAAGAAGTTGCAGTCTTCGAATTTGAGGGTGAACCCCAATTTGGTGGTCATGATTTTGAGTTTGTAGATGAGTTGTCTTCTGGCCAAACTTGCTCCGTTTGCCTTCTTGCCATGAGGAGCCCCGTGCAGACTGTGTGCGGTCATCGATTTTGCGAAAGCTGCTTGTTAGGAACATTCAGGGAAGGCCATGATCAAGTTTGTCCACAAGATAGGAATCCTATTCCTGAAGGAGGAGGGTTCTTTCGTGATGTGGCCTGGGAGAGGGAGATACTTTCTCTTCGTGTCAAATGTAAGAAGAGTACACGAGGATGTTGTTGGACTGGGCAACTGCGTCACTATGAGGAACATTACAACTTATGCAACTATGAGGATGTAACTTGTGATGACTGTACCGAAGAGATGCAGAGAAGACTCCTGCACAAACACACCACATCAGAATGTGCCAACAGGATCGTGCAATGTGAATACTGTAACAACGAGTTCCAATTCTGGCTCATACAGATTCACAAAGATAATGAATGCGTACGTTTTCCTGTTGATTGCCCTCAAGAATGTGGAGTGCAGGAGATACCCAGAGAGGAGGTGGAGTCTCATGTAAGGGACGATTGTATGATGACGATGGTAGTCTGTTCTTACGAAGGAGCTGGATGTACCTTTCATGACAAAAGGAGTAATTTGAAAGCCCATCTTGAATCCGCTAGTGAGGAGCACCTGAGCAAAACATGGTTTAAGCTCTTAAAGACAACACAGCGATTAAGTAAGTTGGAGGAAGTAGAAGTTCAAATTGGAGAATTGCAAGCCGATAAAGAATCCATGAAAAGGTTATTGGACAAAACAGGTGAAGAAATGTGCGATCTGAAGCTGTCGGAGAAAAAGCTGGAAGTGGAAAATATGGCATTGAAGAAAGAACTAGAAGATGTAAAACGTGCTGCTGCTAATGATCGGGAAGAGATCAGTTCGCTGAAACGACTTGTACTATCCATACAAACCAAGGTTGACGCTTTGGATGAAAAGCAACCAGAGAGTCGAACCAGTCAAAATGCAAAATGGTCGTTTCATGAAGTAGTGATCGAAGAACCGATGTGGAAAGACCGAGTAAACGATTCGAGTGAAAAGGAGAGGCCGCCAACGGTGTCTAATTTAAAAGCCGGAAAGAAGCCTGTCCGTGGATACAGcaGAAGAATGCTTACCCAGAAGCAGCCAATTCCAAAGAATCAATCCCCACAGAAGCCCTGCTTGGAAGCTGATTTCATGATTTTTGAAACTGACTAGATCCGGCGGACCAAGTTTAGCGCCAATCTTAATATTTGGTCAACCTTCAGTTATTGAACGTTTGGCAACAAAATGGTGTTGTAACAGTAAAAGCACATTTTTTCCCACCACTTCTATATGGGATGTGATTGACAACATATATAACTTCAGAAGTCCGTAAGCTAGAaatctacatctctggtaatgggctttgagatatgtctttcgcgagcaGGCTATTTTAGACCGGCTTTTCCGCGAACCAGTAGCGAGAAGCACTTGCCGTCCGGTTAGACCTGGTTAATTAGCTCCTTTGTCTTGACTGCCCTTTGAAGCATCGCTATCAACAAACACCTTCGGAATCGTGATGAAAAACTTTTGTAAAGGGCCCTCACAAACCAATTACGACCGCGACCGAAGGTCGAAATTTTGtttgcaacaatctcattgCAAGTAAACGCCATGATTGCACGTCCACGTTTGTTATAAAGATAGCCTACTCGCGACATAGCACGCTCCCAAATACTAGACGTAGACTTCgagcttatgaacttctgacAACTTTTGAAACCAGCTTTTATTTTCTGCCAAGTGTATAGTATAATATAATACGTTTTTAGCAATGACAGATCAGGGAAGTGTGTTCGCCCTGAATAGTATTAGTTAACAAAACAAATGGGTAGCATGTTGACTGTAATCAAGTCATCATCAGTTAAGCTTCAAATATTCCACACATGACTTACTGTTGGTGCAACTAAAGTAAACTTAAACATTTGCATGGCGTAAGAAAAAGAACTTAGTAGTATAGGTAACAAACTTGACGTGTTTGGCAACCAAATGCTTGTAGGCGCTGTTGGGCGAACATTCGTGGTCAAAGTGAGAGATGGCTGTAAAACTTTTTTGGCgttcaaacaaattaaactcatTGCAACATATGTTTGTAAACCAACCTCTTTTCTGAT

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q6IWL4	TNF receptor-associated factor 6 OS=Danio rerio OX=7955 GN=traf6 PE=1 SV=2
Q54FD5	TNF receptor-associated factor family protein DDB_G0290931 OS=Dictyostelium discoideum OX=44689 GN=DDB_G0290931 PE=3 SV=1

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0000066 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF02176 all species →	zf-TRAF	TRAF-type zinc finger	Family	Interproscan
PF21363 all species →	TRAF3_RING	TNF receptor-associated factor 2/3/5, RING domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR001841 all species →	Domain	Zinc finger, RING-type	Interproscan
IPR001293 all species →	Domain	Zinc finger, TRAF-type	Interproscan
IPR013083 all species →	Homologous_superfamily	Zinc finger, RING/FYVE/PHD-type	Interproscan
IPR049440 all species →	Domain	TNF receptor-associated factor 3/5, RING domain	Interproscan
IPR017907 all species →	Conserved_site	Zinc finger, RING-type, conserved site	Interproscan

PANTHER

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

Gene Ontology

GO term	Category	Description	Source
GO:0033209 all species →	Biological Process	tumor necrosis factor-mediated signaling pathway	Interproscan
GO:0070534 all species →	Biological Process	protein K63-linked ubiquitination	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion 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

No KEGG orthology assignment for ENSVBPP00000018007.1.

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 Meandrina meandrites 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 Meandrina meandrites, 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 →