Detailed information of ANN24529-RA in Montipora grisea

Genomic Location: Scaffold_115__1_contigs__length_228693:141092...143272
NR annotation: WP_089372154.1, RNA polymerase factor sigma-54 [Dokdonia pacifica]
Species Montipora grisea · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
A0A0H2ZGR9RNA polymerase sigma-54 factor OS=Pseudomonas aeruginosa (strain UCBPP-PA14) OX=208963 GN=rpoN PE=3 SV=1
P49988RNA polymerase sigma-54 factor OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=rpoN PE=1 SV=2
Q9S0L2RNA polymerase sigma-54 factor OS=Shewanella violacea (strain JCM 10179 / CIP 106290 / LMG 19151 / DSS12) OX=637905 GN=rpoN PE=3 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0009864 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF04552
all species →		Sigma54_DBDSigma-54, DNA binding domainDomainInterproscan
PF04963
all species →		Sigma54_CBDSigma-54 factor, core binding domainDomainInterproscan
PF00072
all species →		Response_regResponse regulator receiver domainDomainInterproscan
PF00309
all species →		Sigma54_AIDSigma-54 factor, Activator interacting domain (AID) FamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR000394
all species →		FamilyRNA polymerase sigma factor 54Interproscan
IPR007634
all species →		DomainRNA polymerase sigma factor 54, DNA-bindingInterproscan
IPR011006
all species →		Homologous_superfamilyCheY-like superfamilyInterproscan
IPR007046
all species →		DomainRNA polymerase sigma factor 54, core-binding domainInterproscan
IPR038709
all species →		Homologous_superfamilyRNA polymerase sigma-54 factor, core-binding domain superfamilyInterproscan
IPR001789
all species →		DomainSignal transduction response regulator, receiver domainInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR32248
all species →		RNA POLYMERASE SIGMA-54 FACTORInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0001216
all species →		Molecular FunctionDNA-binding transcription activator activityInterproscan
GO:0016987
all species →		Molecular Functionsigma factor activityInterproscan
GO:0003677
all species →		Molecular FunctionDNA bindingInterproscan
GO:0006352
all species →		Biological ProcessDNA-templated transcription initiationInterproscan
GO:0000160
all species →		Biological Processphosphorelay signal transduction systemInterproscan

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 ANN24529-RA.

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 Montipora grisea 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 Montipora grisea, 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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