Detailed information of alor_g25823.t1 in Acropora loripes

Genomic Location: Acropora_loripes_35:2245287...2247304
NR annotation: XP_015754018.1, PREDICTED: DNA-directed RNA polymerase II subunit RPB11-a-like [Acropora digitifera]
Species Acropora loripes · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q32P79DNA-directed RNA polymerase II subunit RPB11 OS=Bos taurus OX=9913 GN=POLR2J PE=1 SV=1
P52435DNA-directed RNA polymerase II subunit RPB11-a OS=Homo sapiens OX=9606 GN=POLR2J PE=1 SV=1
O08740DNA-directed RNA polymerase II subunit RPB11 OS=Mus musculus OX=10090 GN=Polr2j PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0007674 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF13656
all species →		RNA_pol_L_2RNA polymerase Rpb3/Rpb11 dimerisation domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR009025
all species →		DomainDNA-directed RNA polymerase, RBP11-like dimerisation domainInterproscan
IPR036603
all species →		Homologous_superfamilyRNA polymerase, RBP11-like subunitInterproscan
IPR022905
all species →		FamilyDNA-directed RNA polymerase subunit Rpo11-likeInterproscan
IPR037685
all species →		FamilyRNA polymerase RBP11Interproscan
IPR008193
all species →		Conserved_siteDNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved siteInterproscan

 PANTHER
PANTHER termDescriptionSource
PTHR13946
all species →		DNA-DIRECTED RNA POLYMERASE I,II,IIIInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0006351
all species →		Biological ProcessDNA-templated transcriptionInterproscan
GO:0046983
all species →		Molecular Functionprotein dimerization activityInterproscan
GO:0001055
all species →		Molecular FunctionRNA polymerase II activityInterproscan
GO:0003899
all species →		Molecular FunctionDNA-directed 5'-3' RNA polymerase activityInterproscan
GO:0005665
all species →		Cellular ComponentRNA polymerase II, core complexInterproscan
GO:0006366
all species →		Biological Processtranscription by RNA polymerase IIInterproscan
GO:0003677
all species →		Molecular FunctionDNA 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
KOEnzymeEnzyme IDPathwayMap IDSource
K03008RPB11, POLR2J; DNA-directed RNA polymerase II subunit RPB11-DNA repair and recombination proteinsko03400deepkoala

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 loripes 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 loripes, 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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