Detailed information of XP_073227930.1 in Porites lutea

Genomic Location: chr12:2258679...2267395
NR annotation: no NCBI-NR hit recorded
Species Porites lutea · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0006678 (this species only) · gene tree & orthology

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF21262
all species →
RRP40_S1Exosome complex component RRP40, S1 domainDomainInterproscan
PF15985
all species →
KH_6KH domainDomainInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR012340
all species →
Homologous_superfamilyNucleic acid-binding, OB-foldInterproscan
IPR026699
all species →
FamilyExosome complex RNA-binding protein 1/RRP40/RRP4Interproscan
IPR036612
all species →
Homologous_superfamilyK Homology domain, type 1 superfamilyInterproscan
IPR037319
all species →
DomainRrp40, S1 domainInterproscan
IPR004088
all species →
DomainK Homology domain, type 1Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR21321
all species →
PNAS-3 RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0000176
all species →
Cellular Componentnuclear exosome (RNase complex)Interproscan
GO:0000177
all species →
Cellular Componentcytoplasmic exosome (RNase complex)Interproscan
GO:0000178
all species →
Cellular Componentexosome (RNase complex)Interproscan
GO:0000467
all species →
Biological Processexonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)Interproscan
GO:0003723
all species →
Molecular FunctionRNA bindingInterproscan
GO:0034427
all species →
Biological Processobsolete nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'Interproscan
GO:0034475
all species →
Biological ProcessU4 snRNA 3'-end processingInterproscan
GO:0043928
all species →
Biological Processobsolete exonucleolytic catabolism of deadenylated mRNAInterproscan
GO:0071034
all species →
Biological ProcessCUT catabolic processInterproscan
GO:0071035
all species →
Biological Processnuclear polyadenylation-dependent rRNA catabolic processInterproscan
GO:0071038
all species →
Biological ProcessTRAMP-dependent tRNA surveillance pathwayInterproscan
GO:0071051
all species →
Biological Processpoly(A)-dependent snoRNA 3'-end processingInterproscan

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
K03681RRP40, EXOSC3; exosome complex component RRP40-Messenger RNA biogenesisko03019deepkoala

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 Porites lutea 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 Porites lutea, 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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