Detailed information of aawi_s1489.g1.t1 in Acropora awi

Genomic Location: sc0001489_pilon:856...10231
NR annotation: XP_020624371.1, RNA polymerase-associated protein CTR9 homolog [Orbicella faveolata]
Species Acropora awi · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
Q4QR29RNA polymerase-associated protein CTR9 homolog OS=Xenopus laevis OX=8355 GN=ctr9 PE=2 SV=1
Q6DEU9RNA polymerase-associated protein CTR9 homolog OS=Xenopus tropicalis OX=8364 GN=ctr9 PE=2 SV=1
Q6PD62RNA polymerase-associated protein CTR9 homolog OS=Homo sapiens OX=9606 GN=CTR9 PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0003455 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF13181
all species →		TPR_8Tetratricopeptide repeatRepeatInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR011990
all species →		Homologous_superfamilyTetratricopeptide-like helical domain superfamilyInterproscan
IPR019734
all species →		RepeatTetratricopeptide repeatInterproscan
IPR031101
all species →		FamilyRNA polymerase-associated protein Ctr9Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR14027
all species →		RNA POLYMERASE-ASSOCIATED PROTEIN CTR9Interproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0005515
all species →		Molecular Functionprotein bindingInterproscan
GO:0000993
all species →		Molecular FunctionRNA polymerase II complex bindingInterproscan
GO:0006355
all species →		Biological Processregulation of DNA-templated transcriptionInterproscan
GO:0006368
all species →		Biological Processtranscription elongation by RNA polymerase IIInterproscan
GO:0016593
all species →		Cellular ComponentCdc73/Paf1 complexInterproscan

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 aawi_s1489.g1.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 awi 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 awi, 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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