Detailed information of amic_s0112.g34.t1 in Acropora microphthalma

Genomic Location: sc0000112_pilon:329606...332490
NR annotation: XP_015749040.1, PREDICTED: E3 ubiquitin-protein ligase TRIM71-like [Acropora digitifera]
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
E7FAM5E3 ubiquitin-protein ligase TRIM71 OS=Danio rerio OX=7955 GN=trim71 PE=1 SV=1
F6QEU4E3 ubiquitin-protein ligase TRIM71 OS=Xenopus tropicalis OX=8364 GN=trim71 PE=3 SV=1
Q1PRL4E3 ubiquitin-protein ligase TRIM71 OS=Gallus gallus OX=9031 GN=TRIM71 PE=2 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0000133 (this species only) · gene tree & orthology
Ubiquitin familyE3|E3 activity RING|RING · all ubiquitin genes in this species

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00643
all species →
zf-B_boxB-box zinc fingerDomainInterproscan
PF00630
all species →
FilaminFilamin/ABP280 repeatDomainInterproscan
PF13445
all species →
zf-RING_UBOXRING-type zinc-fingerDomainInterproscan
PF17170
all species →
DUF51286-bladed beta-propellerRepeatInterproscan
PF01436
all species →
NHLNHL repeatRepeatInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR013087
all species →
DomainZinc finger C2H2-typeInterproscan
IPR001841
all species →
DomainZinc finger, RING-typeInterproscan
IPR000315
all species →
DomainB-box-type zinc fingerInterproscan
IPR001258
all species →
RepeatNHL repeatInterproscan
IPR017868
all species →
RepeatFilamin/ABP280 repeat-likeInterproscan
IPR047153
all species →
FamilyTRIM45/56/19Interproscan
IPR027370
all species →
DomainZinc finger, RING-type, eukaryoticInterproscan
IPR013783
all species →
Homologous_superfamilyImmunoglobulin-like foldInterproscan
IPR017907
all species →
Conserved_siteZinc finger, RING-type, conserved siteInterproscan
IPR013083
all species →
Homologous_superfamilyZinc finger, RING/FYVE/PHD-typeInterproscan
IPR011042
all species →
Homologous_superfamilySix-bladed beta-propeller, TolB-likeInterproscan
IPR014756
all species →
Homologous_superfamilyImmunoglobulin E-setInterproscan
IPR003649
all species →
DomainB-box, C-terminalInterproscan
IPR001298
all species →
RepeatFilamin/ABP280 repeatInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR25462
all species →
BONUS, ISOFORM C-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0008270
all species →
Molecular Functionzinc ion bindingInterproscan
GO:0005515
all species →
Molecular Functionprotein bindingInterproscan

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 amic_s0112.g34.t1.

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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