Detailed information of aacu_s0096.g41.t1 in Acropora acuminata

Genomic Location: sc0000096_pilon:1103638...1158924
NR annotation: XP_044171811.1, protein polybromo-1-like [Acropora millepora]
Species Acropora acuminata · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q90941Protein polybromo-1 OS=Gallus gallus OX=9031 GN=PBRM1 PE=1 SV=1
Q86U86Protein polybromo-1 OS=Homo sapiens OX=9606 GN=PBRM1 PE=1 SV=1
Q8BSQ9Protein polybromo-1 OS=Mus musculus OX=10090 GN=Pbrm1 PE=1 SV=4
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0002362 (this species only) · gene tree & orthology
Transcription factor familyHMG · all TF in this species

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF01426
all species →
BAHBAH domainDomainInterproscan
PF00505
all species →
HMG_boxHMG (high mobility group) boxDomainInterproscan
PF00439
all species →
BromodomainBromodomainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR001487
all species →
DomainBromodomainInterproscan
IPR036427
all species →
Homologous_superfamilyBromodomain-like superfamilyInterproscan
IPR037382
all species →
FamilyRemodelling complex subunit Rsc/polybromoInterproscan
IPR018359
all species →
Conserved_siteBromodomain, conserved siteInterproscan
IPR001025
all species →
DomainBromo adjacent homology (BAH) domainInterproscan
IPR009071
all species →
DomainHigh mobility group box domainInterproscan
IPR036910
all species →
Homologous_superfamilyHigh mobility group box domain superfamilyInterproscan
IPR043151
all species →
Homologous_superfamilyBromo adjacent homology (BAH) domain superfamilyInterproscan
IPR037968
all species →
DomainProtein polybromo-1, Bromodomain 5Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR16062
all species →
SWI/SNF-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005515
all species →
Molecular Functionprotein bindingInterproscan
GO:0003682
all species →
Molecular Functionchromatin bindingInterproscan
GO:0006338
all species →
Biological Processchromatin remodelingInterproscan
GO:0006368
all species →
Biological Processtranscription elongation by RNA polymerase IIInterproscan
GO:0016586
all species →
Cellular ComponentRSC-type complexInterproscan
GO:0043044
all species →
Biological Processchromatin remodelingInterproscan

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
K11757PBRM1, PB1; protein polybromo-1-Chromosome and associated proteinsko03036deepkoala

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 acuminata 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 acuminata, 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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