Gene detail

Detailed information of BRAKERLUSP00000019827.1 in Blastomussa wellsi

Genomic Location: chr4:18470320...18475459
NR annotation: XP_020615350.1, tumor necrosis factor alpha-induced protein 3-like isoform X2 [Orbicella faveolata]
Species Blastomussa wellsi · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

BRAKERLUST00000019827

ATGGCTTCATTTCAGCCTCCGAGTCATCTTTTTGAGCGAAACATATCCTTGAACGATCTGGACTCCGCTTTGGACGTGAGAGAGCTCGTACGCAAAGATGTCGTGGTCCCAGAAGAGGTAACGAAACACCGCTATCTCGATTCTTCAACGAAGTATTCATTTGTGCTGCCATCGTTTCAAGGTTTCCCTATCGAGTTCCGCAAATTCGTGTACAGCTTTCTAGTGGACGGCCACATTCTCAGAGAGCTTGAGGTAGCGAGGAGGCTAAATTGGTGTCATTCCTCGTGTCGCATGATTACGGTGAATACTCTGGGCGATGGCAACTGCCTGATGCACGCAGCCTCAATTGGAATGTGGGCAGTGAACGATAGATATCAGATTCTTAGGAAAACTGTCTACGAAGCATTGGTGGAGGACGTGGAAGGATTTTACCATAGCCGTTGGAAATCCGAGGAAGAGCAGCAGATATTAAATCAAATTGGGGGATACAGACGAACAGAACAACAGTGGAATCACGAGTGGGAGGAAGTAATTAGACACATTTCTCAGAATGAATTCCCATTCGGACCAAATGGTGCACAGTTTGGAAGTCTGGAAGAAATCCATATATTTGTCCTTGCTAACATTCTGCGTCGTACCATCATAGTGCTGTCAGATGAGACTTTGAGAGGACCTTATGGCGATTCGTACTCTCCAATTAACTTTGGAGGTATTTATTTACCTCTGCTCTGGGACTCTGTTGACTGTGTAAAAAGTCCATTGGTAATAGGCTATGCAAATGGCCATTTTACTGCAGTTGTCAGTATCGAAGATGGTAAACTAGATCTGGGCACTGAAAACAGCCCAGGTTCAAGCAGCTCAGCTAATCCTATCCATGCAGTGCCATTAGTAAAATACGATGGGACACCATTACCAGTTCATTTCCTTTATGAGCAAGAGGCACCATTAGCAAGTGACCGTCTCCGGCAATACTTAGATTGTGCAAAGGTCCCCTTCTCCAGCAATCCAACAGAATCCAGGCAAACAGTTCTTGTTGCAAAATTGCATTTTTCAGACAACCCCCGCTGCATGAAAGACCTCATTGATGGTTACTTCATTAAGGCCAGGGAAGAACATCAGCGAGTGTCAAGACACAGTCAGCTTCATGCGCAGTCACAACCAGGTACCAAACTGCCAACTCTGCAGATTGTTCCATGTCAAACTCAGGGCTGTAGTTTCTTTGGATCTACTGAAACTGGCAATCGTTGCTCTAAATGCCTTAACGAGTATCTAAGGACCTTGGGATCTCCTTGTCAAATAGGTCAAAATGTTTCCATAAGGCAGATTCAGCAGCATATTGCAGTGGCAACAACACCACTAGGACCAAATGTCAGTGCACAGCAACAAATGGCCACAACACAAGCACCATCTAATACCAGCCGGGCATCTTCCATGACCCTCCCTGTGGCAAGTTCTGTTAAATGCCGCACTGGTGGATGCAAGTATGGAGCTATGCCTGACAGCGGTGGTCTTTGTGAGAGGTGCTTTGAAGCAGAGAGAAGTGCTGAAGAAATGGCTGCAAGCATGAGTTGCATGAATTTGGCATCAGCAAAGCATTGTTCCAATAGAGTGAATGGCTGCGAATTCTTTGGTTTACCTGAACATCATAACTTGTGTTCCAGATGCTACAGAACCTTCTGTCTTCGTATAGAAAACACTTTGGGGGTGCCATCTCCGACTGGATTGCCACCAAGTAGTCCAACACCGTCGACACCTCCAAACCGATGCCAGACTCCAGACTGTCCATCGCCAGGTGTCCCTGCATTGTATGGCATGTGTGTACAGTGCTACACTGGATGTATACATGCTTTCATAACCACTGAAGGGAGATCAGTTGGAGGTGTAACACAAGCCACACCACATCTGCCATCACCACCAATGGATGTCAGAAGAAAGAATCTGTTGCCTATGGGTGGCAGGAGGAAAGGTGTCTTGTGTGCTTCTCCTGGATGCTGCAATGAAGGAATCTTTCATTTGTCTGACCTGTGTGCAGAGTGCCATACAAGGAAATCTGGTCCATCACCATCACCGCAAATGAGAAACACTCCACCATCTGTAGCAGGTGTGATGAGTTTCCCAGTGGCTCCGCCTCCACCAACCTCCACGTCAGCATTAGCTGCTTCCACTCATCATCTGACATCAGCACTTGCAGGTGCCATTGGCTATTATTGTTCCAACCCATTTTGCAAGAACCCAGTAAGAAAGGATGGAAGAGGCTTATGTCAAAGGTGTGAAAGTCTGAGCGCCTTTCCTTCACATGCTAATCCTGCAGCTGGTTTGCAACAGCCATGCGCCCAACCAGTTGGTATGGCAACCACAACATCAAGCATGCCAGCAAGGCAGAACATGCAGGCTTACACCAGCTGTGCCGCTTTGCAAACTAATGCCACTCCTGGGGCCTCTTCATCTCGGGAGACAGGATTTCCCCATCAAGTTGCTGCACCACGTGCTGTAGCCAACACTGGTAAATGTGCCATGGGCTGTGATAAGCCAGCAGTGCAAGAAGGTGGTTTGTGTGATGTGTGCTATGCTGCAGCCTTTCAGCTGGAATTAAACAGACAAACAGTCTCCCAGCCAACCAGACAACAAGGAGCAGGGGCATCTGGCATTACAGGCAATCAGgTTGAACAAAGAAACATTGCTGAAACAAGCTCTGATAGAAATCAGCAACAGACAGAGGCAACAGCAGCTAAGAAAAAGTTAACACTACTGCCATGTACCTCAAAAGCATGTTTGGCATTTGGCACCCCAGAGCAAAATGGTCTATGTGACGATTGCTATCACAAGAAGGGCATCCGACAACAAGGTGTCTCATCAACTACTGCAGCTAATGAACAAGCAGCTTCAAGTATCAGTGCTCAAACTACTGCACAAGATCATCAGCCTGGCAACAGCTCCGCTCAGTCAGCATCTCATGGACTGCAGGGTCCAATACAAGTCTCCCAGCCTCAAAGTCCATTTAACGAATCAGGCATGGCACAGCAGAATTCAAATTCAGGAAATGGTGTCTTTGGTCAGAAATGTCGTGGTTACAACTGCACCCTGTTTGGAACGCCTGAGTCAAATGGCTACTGCTCTCGGTGCTTTTTGGAAAGCACAATGCCTGAGTCATACCCAAATTCAATTCCAGATTTTCCAGCTGATGTTTCATCGTCAACTGTTGCATCTCGCACAACCGATAAATTGTGCCTAGTTACTGGTTGTTCAAATTTTGCTGCACAAGAAAGGCATGGTCACTGCCTAGAATGCTTCACAAGATTTTACCCTGAAGTGATCCATCGTGAAAGACTTGTTAAAAGACAACGGTCAGAACTGGCTGCAAGTATTAATTAG

Transcript

BRAKERLUST00000019827

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q4R8W3	Tumor necrosis factor alpha-induced protein 3 OS=Macaca fascicularis OX=9541 GN=TNFAIP3 PE=2 SV=1
P21580	Tumor necrosis factor alpha-induced protein 3 OS=Homo sapiens OX=9606 GN=TNFAIP3 PE=1 SV=1
Q60769	Tumor necrosis factor alpha-induced protein 3 OS=Mus musculus OX=10090 GN=Tnfaip3 PE=1 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004502 (this species only) · gene tree & orthology
Ubiquitin family	DUB\|OTU\|OTU · all ubiquitin genes in this species
Ubiquitin family	UBD\|ZnF\|ZnF_A20 · all ubiquitin genes in this species

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF01754 all species →	zf-A20	A20-like zinc finger	Family	Interproscan
PF02338 all species →	OTU	OTU-like cysteine protease	Family	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR002653 all species →	Domain	Zinc finger, A20-type	Interproscan
IPR003323 all species →	Domain	OTU domain	Interproscan
IPR051346 all species →	Family	OTU Domain-Containing Deubiquitinase	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR13367 all species →	UBIQUITIN THIOESTERASE	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0008270 all species →	Molecular Function	zinc ion binding	Interproscan
GO:0004843 all species →	Molecular Function	cysteine-type deubiquitinase activity	Interproscan
GO:0005634 all species →	Cellular Component	nucleus	Interproscan
GO:0005737 all species →	Cellular Component	cytoplasm	Interproscan
GO:0007010 all species →	Biological Process	cytoskeleton organization	Interproscan
GO:0016477 all species →	Biological Process	cell migration	Interproscan
GO:0030177 all species →	Biological Process	positive regulation of Wnt signaling pathway	Interproscan
GO:0035523 all species →	Biological Process	protein K29-linked deubiquitination	Interproscan
GO:0070530 all species →	Molecular Function	K63-linked polyubiquitin modification-dependent protein binding	Interproscan
GO:0071947 all species →	Biological Process	protein deubiquitination involved in ubiquitin-dependent protein catabolic process	Interproscan
GO:1990168 all species →	Biological Process	protein K33-linked deubiquitination	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
K11859	TNFAIP3, A20, OTUD7C; tumor necrosis factor, alpha-induced protein 3	EC:3.4.19.12	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 Blastomussa wellsi 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 Blastomussa wellsi, 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 →