Detailed information of amic_s0030.g45.t1 in Acropora microphthalma

Genomic Location: sc0000030_pilon:751659...756370
NR annotation: XP_015752309.1, PREDICTED: 26S protease regulatory subunit 6B [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
Q3T03026S proteasome regulatory subunit 6B OS=Bos taurus OX=9913 GN=PSMC4 PE=2 SV=1
P4368626S proteasome regulatory subunit 6B OS=Homo sapiens OX=9606 GN=PSMC4 PE=1 SV=2
Q4R7L326S proteasome regulatory subunit 6B OS=Macaca fascicularis OX=9541 GN=PSMC4 PE=2 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0000576 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF00004
all species →
AAAATPase family associated with various cellular activities (AAA)DomainInterproscan
PF17862
all species →
AAA_lid_3AAA+ lid domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR003960
all species →
Conserved_siteATPase, AAA-type, conserved siteInterproscan
IPR027417
all species →
Homologous_superfamilyP-loop containing nucleoside triphosphate hydrolaseInterproscan
IPR003593
all species →
DomainAAA+ ATPase domainInterproscan
IPR003959
all species →
DomainATPase, AAA-type, coreInterproscan
IPR050221
all species →
Family26S Proteasome Regulatory ATPaseInterproscan
IPR041569
all species →
DomainAAA ATPase, AAA+ lid domainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR23073
all species →
26S PROTEASOME REGULATORY SUBUNITInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005524
all species →
Molecular FunctionATP bindingInterproscan
GO:0016887
all species →
Molecular FunctionATP hydrolysis activityInterproscan
GO:0008540
all species →
Cellular Componentproteasome regulatory particle, base subcomplexInterproscan
GO:0036402
all species →
Molecular Functionproteasome-activating activityInterproscan
GO:0043161
all species →
Biological Processproteasome-mediated ubiquitin-dependent protein catabolic 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
K03063PSMC4, RPT3; 26S proteasome regulatory subunit T3-Proteasomeko03051deepkoala

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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