Detailed information of amic_s0158.g24.t1 in Acropora microphthalma

Genomic Location: sc0000158_pilon:379044...389455
NR annotation: XP_044174929.1, TNF receptor-associated factor 6-like [Acropora millepora]
Species Acropora microphthalma · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
B5DF45TNF receptor-associated factor 6 OS=Rattus norvegicus OX=10116 GN=Traf6 PE=2 SV=1
P70196TNF receptor-associated factor 6 OS=Mus musculus OX=10090 GN=Traf6 PE=1 SV=2
Q3ZCC3TNF receptor-associated factor 6 OS=Bos taurus OX=9913 GN=TRAF6 PE=2 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0000780 (this species only) · gene tree & orthology
Ubiquitin familyE3|E3 activity RING|RING · all ubiquitin genes in this species
Ubiquitin familyE3|E3 activity RING|U-box · all ubiquitin genes in this species

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF02176
all species →
zf-TRAFTRAF-type zinc fingerFamilyInterproscan
PF21355
all species →
TRAF-mep_MATHTRAF/meprin, MATH domainDomainInterproscan
PF13923
all species →
zf-C3HC4_2Zinc finger, C3HC4 type (RING finger)DomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR013083
all species →
Homologous_superfamilyZinc finger, RING/FYVE/PHD-typeInterproscan
IPR001841
all species →
DomainZinc finger, RING-typeInterproscan
IPR027139
all species →
DomainTNF receptor-associated factor 6, C3HC3D-type RING zinc fingerInterproscan
IPR017907
all species →
Conserved_siteZinc finger, RING-type, conserved siteInterproscan
IPR002083
all species →
DomainMATH/TRAF domainInterproscan
IPR001293
all species →
DomainZinc finger, TRAF-typeInterproscan
IPR049342
all species →
DomainTRAF1-6/MEP1A/B-like, MATH domainInterproscan
IPR008974
all species →
Homologous_superfamilyTRAF-likeInterproscan
IPR012227
all species →
FamilyTNF receptor-associated factor TRAF, metazoaInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR10131
all species →
TNF RECEPTOR ASSOCIATED FACTORInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0004842
all species →
Molecular Functionubiquitin-protein transferase activityInterproscan
GO:0005164
all species →
Molecular Functiontumor necrosis factor receptor bindingInterproscan
GO:0016567
all species →
Biological Processprotein ubiquitinationInterproscan
GO:0005515
all species →
Molecular Functionprotein bindingInterproscan
GO:0031663
all species →
Biological Processlipopolysaccharide-mediated signaling pathwayInterproscan
GO:0032813
all species →
Molecular Functiontumor necrosis factor receptor superfamily bindingInterproscan
GO:0033209
all species →
Biological Processtumor necrosis factor-mediated signaling pathwayInterproscan
GO:0045087
all species →
Biological Processinnate immune responseInterproscan
GO:0051092
all species →
Biological Processpositive regulation of NF-kappaB transcription factor activityInterproscan
GO:0061630
all species →
Molecular Functionubiquitin protein ligase activityInterproscan
GO:0070534
all species →
Biological Processprotein K63-linked ubiquitinationInterproscan
GO:0008270
all species →
Molecular Functionzinc ion bindingInterproscan
GO:0007165
all species →
Biological Processsignal transductionInterproscan
GO:0042981
all species →
Biological Processregulation of apoptotic processInterproscan

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
KOEnzymeEnzyme IDPathwayMap IDSource
K03175TRAF6; TNF receptor-associated factor 6EC:2.3.2.27
Ubiquitin systemko04121deepkoala

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 Acropora microphthalma 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 Acropora microphthalma, 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.

AnalysisWhat it doesStatus
Primer designDesign PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.template foundopen →
BLASTSearch 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 foundopen →
Expression heatmapDraw 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 / orthogroupLook 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 analysisStart a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.open →
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